Correction for founder effects in host-viral association studies via principal components

Viruses such as HIV and Hepatitis C (HCV) replicate rapidly and with high transcription error rates, which may facilitate their escape from immune detection through the encoding of mutations at key positions within human leukocyte antigen (HLA)-specific peptides, thus impeding T-cell recognition. Large-scale population-based host-viral association studies are conducted as hypothesis-generating analyses which aim to determine the positions within the viral sequence at which host HLA immune pressure may have led to these viral escape mutations. When transmission of the virus to the host is HLA-associated, however, standard tests of association can be confounded by the viral relatedness of contemporarily circulating viral sequences, as viral sequences descended from a common ancestor may share inherited patterns of polymorphisms, termed 'founder effects'. Recognizing the correspondence between this problem and the confounding of case-control genome-wide association studies by population stratification, we adapt methods taken from that field to the analysis of host-viral associations. In particular, we consider methods based on principal components analysis within a logistic regression framework motivated by alternative formulations in the Frisch-Waugh-Lovell Theorem. We demonstrate via simulation their utility in detecting true host-viral associations whilst minimizing confounding by associations generated by founder effects. The proposed methods incorporate relatively robust, standard statistical procedures which can be easily implemented using widely available software, and provide alternatives to the more complex computer intensive methods often implemented in this area

A methodology for systematic mapping in environmental sciences

Systematic mapping was developed in social sciences in response to a lack of empirical data when answering questions using systematic review methods, and a need for a method to describe the literature across a broad subject of interest. Systematic mapping does not attempt to answer a specific question as do systematic reviews, but instead collates, describes and catalogues available evidence (e.g. primary, secondary, theoretical, economic) relating to a topic or question of interest. The included studies can be used to identify evidence for policy-relevant questions, knowledge gaps (to help direct future primary research) and knowledge clusters (sub-sets of evidence that may be suitable for secondary research, for example systematic review). Evidence synthesis in environmental sciences faces similar challenges to those found in social sciences. Here we describe the translation of systematic mapping methodology from social sciences for use in environmental sciences. We provide the first process-based methodology for systematic maps, describing the stages involved: establishing the review team and engaging stakeholders; setting the scope and question; setting inclusion criteria for studies; scoping stage; protocol development and publication; searching for evidence; screening evidence; coding; production of a systematic map database; critical appraisal (optional); describing and visualising the findings; report production and supporting information. We discuss the similarities and differences in methodology between systematic review and systematic mapping and provide guidance for those choosing which type of synthesis is most suitable for their requirements. Furthermore, we discuss the merits and uses of systematic mapping and make recommendations for improving this evolving methodology in environmental sciences

Ingredient selection for plastic composite supports for L-(+)-lactic acid biofilm fermentation by Lactobacillus casei subsp. rhamnosus

Plastic composite supports containing 50% agricultural products (oat hulls, soybean hulls, yeast extract, soybean flour, dried bovine erythrocytes, bovine albumin, and/or mineral salts) and 50% (wt/wt) polypropylene were produced by high-temperature twin-screw extrusion. The research employed two half sets of a five-factorial fractional design (2(5 - 1)) to evaluate the effects of different agricultural components on the properties of the plastic composite supports and to select the best plastic composite support formulation for lactic acid fermentation. The biofilm population was affected by the contact angle and relative hydrophobicity of the supports (r = 0.79 to 0.82). Lactic acid was produced by the suspended cells (r = 0.96) and the biofilm on the plastic composite support discs (r = 0.85). Incorporation of yeast extract into plastic composite supports enhanced growth of free and attached cells in minimal medium (P \u3c 0.0001). The presence of soybean hulls, yeast extract, or mineral salts in plastic composite supports produced less hydrophobic supports (P \u3c 0.0001) and enhanced cell attachment (P \u3c 0.03). Under all conditions, suspended-cell and polypropylene disc controls gave negligible lactic acid production and cell density. Plastic composite supports containing soybean hulls, yeast extract, soybean flour, bovine albumin, and mineral salts gave the highest biofilm population (2.3 x 10(9) CFU/g of support), cell density (absorbance of 1.8 at 620 nm), and lactic acid concentration (7.6 g/liter) in minimal medium

Evidence for the effects of neonicotinoids used in arable crop production on non-target organisms and concentrations of residues in relevant matrices: a systematic map protocol

Background Neonicotinoid insecticides (NNIs) have been routinely used in arable crop protection since their development in the early 1990s. These insecticides have been subject to the same registration procedures as other groups of pesticides, thus meet the same environmental hazard standards as all crop protection products. However, during the last 10 years the debate regarding their possible detrimental impact on non-target organisms, particularly pollinators, has become increasingly contentious and widely debated. Against this background, legislators and politicians in some countries, have been faced with a need to make decisions on the future registration of some or all of this class of insecticides, based on published evidence that in some areas is incomplete or limited in extent. This has created much concern in agricultural communities that consider that the withdrawal of these insecticides is likely to have significant negative economic, socio-economic and environmental consequences. Methods The proposed systematic map aims to address the following primary question: What is the available evidence for the effects of neonicotinoids used in arable crop production on non-target organisms and concentrations of residues in relevant matrices? The primary question will be divided into two sub-questions to gather research literature for (1) the effect of NNIs on non-target organisms (2) the occurrence of concentrations of NNIs in matrices of relevance to non-target organisms (i.e. exposure routes). The systematic map will focus on NNIs used in arable crop production: imidacloprid, clothianidin, thiamethoxam, acetamiprid, thiacloprid and dinotefuran. Separate inclusion criteria have been developed for each sub-question. Traditional academic and grey literature will be searched for in English language and a searchable databases containing extracted meta-data from relevant included studies will be developed

Updating and amending systematic reviews and systematic maps in environmental management

Systematic reviews and systematic maps aim to provide an overview of the best available evidence to inform research, policy and practice. However, like any form of review, they will require updating periodically to ensure that the most recent evidence has been incorporated. Here we outline two types of review revisions as recognised in medicine: updates and amendments. Updates involve a search for new studies, expanding the evidence base through time. Any other change (e.g. in screening or synthesis) or correction to the original report is an amendment. Decisions as to whether/when it is appropriate to undertake an update or amendment must be made on a case-by-case basis, considering issues such as the reliability and scope of the existing review or map, likely volume of new evidence, resources available, and the likely value of including new information. Careful, consistent reporting is necessary to ensure transparency and repeatability, particularly where there are deviations from the original methods, and authors should highlight key advances relative to the original report. Updating environmental systematic reviews and maps will be an increasingly important activity as the numbers of both primary studies and synthetic reports in the literature continue to grow

The Flare-dominated Accretion Mode of a Radio-bright Candidate Transitional Millisecond Pulsar

© 2020. The American Astronomical Society. All rights reserved.. We report new simultaneous X-ray and radio continuum observations of 3FGL J0427.9-6704, a candidate member of the enigmatic class of transitional millisecond pulsars. These XMM-Newton and Australia Telescope Compact Array observations of this nearly edge-on, eclipsing low-mass X-ray binary were taken in the sub-luminous disk state at an X-ray luminosity of erg s-1. Unlike the few well-studied transitional millisecond pulsars, which spend most of their disk state in a characteristic high or low accretion mode with occasional flares, 3FGL J0427.9-6704 stayed in the flare mode for the entire X-ray observation of ∼20 hr, with the brightest flares reaching ∼2 × 1034 erg s-1. The source continuously exhibited flaring activity on timescales of ∼10-100 s in both the X-ray and optical/ultraviolet (UV). No measurable time delay between the X-ray and optical/UV flares is observed, but the optical/UV flares last longer, and the relative amplitudes of the X-ray and optical/UV flares show a large scatter. The X-ray spectrum can be well-fit with a partially absorbed power law (Γ ∼ 1.4-1.5), perhaps due to the edge-on viewing angle. Modestly variable radio continuum emission is present at all epochs, and is not eclipsed by the secondary, consistent with the presence of a steady radio outflow or jet. The simultaneous radio/X-ray luminosity ratio of 3FGL J0427.9-6704 is higher than any known transitional millisecond pulsars and comparable to that of stellar-mass black holes of the same X-ray luminosity, providing additional evidence that some neutron stars can be as radio-loud as black holes

Updating and amending systematic reviews and systematic maps in environmental management

Systematic reviews and systematic maps aim to provide an overview of the best available evidence to inform research, policy and practice. However, like any form of review, they will require updating periodically to ensure that the most recent evidence has been incorporated. Here we outline two types of review revisions as recognised in medicine: updates and amendments. Updates involve a search for new studies, expanding the evidence base through time. Any other change (e.g. in screening or synthesis) or correction to the original report is an amendment. Decisions as to whether/when it is appropriate to undertake an update or amendment must be made on a case-by-case basis, considering issues such as the reliability and scope of the existing review or map, likely volume of new evidence, resources available, and the likely value of including new information. Careful, consistent reporting is necessary to ensure transparency and repeatability, particularly where there are deviations from the original methods, and authors should highlight key advances relative to the original report. Updating environmental systematic reviews and maps will be an increasingly important activity as the numbers of both primary studies and synthetic reports in the literature continue to grow

Early stage morphology of quench condensed Ag, Pb and Pb/Ag hybrid films

Scanning Tunneling Microscopy (STM) has been used to study the morphology of Ag, Pb and Pb/Ag bilayer films fabricated by quench condensation of the elements onto cold (T=77K), inert and atomically flat Highly Oriented Pyrolytic Graphite (HOPG) substrates. All films are thinner than 10 nm and show a granular structure that is consistent with earlier studies of QC films. The average lateral diameter, $\bar {2r}$, of the Ag grains, however, depends on whether the Ag is deposited directly on HOPG ($\bar {2r}$ = 13 nm) or on a Pb film consisting of a single layer of Pb grains ($\bar {2r}$ = 26.8 nm). In addition, the critical thickness for electrical conduction ($d_{G}$) of Pb/Ag films on inert glass substrates is substantially larger than for pure Ag films. These results are evidence that the structure of the underlying substrate exerts an influence on the size of the grains in QC films. We propose a qualitative explanation for this previously unencountered phenomenon.Comment: 11 pages, 3 figures and one tabl

Nanosatellites for quantum science and technology

Bringing quantum science and technology to the space frontier offers exciting prospects for both fundamental physics and applications such as long-range secure communication and space-borne quantum probes for inertial sensing with enhanced accuracy and sensitivity. But despite important terrestrial pathfinding precursors on common microgravity platforms and promising proposals to exploit the significant advantages of space quantum missions, large-scale quantum testbeds in space are yet to be realized due to the high costs and leadtimes of traditional “Big Space” satellite development. But the “small space” revolution, spearheaded by the rise of nanosatellites such as CubeSats, is an opportunity to greatly accelerate the progress of quantum space missions by providing easy and affordable access to space and encouraging agile development. We review space quantum science and technology, CubeSats and their rapidly developing capabilities, and how they can be used to advance quantum satellite systems