Application of nox-restriction fragment length polymorphism for the differentiation of Brachyspira intestinal spirochetes isolated from pigs and poultry in Australia

Sixty-nine intestinal spirochetes isolated from pigs and poultry in eastern Australia were selected to evaluate the effectiveness of a species-specific PCR-based restriction fragment length polymorphism (RFLP) analysis of the Brachyspira nox gene. For comparative purposes, all isolates were subjected to species-specific PCRs for the pathogenic species Brachyspira hyodysenteriae and Brachyspira pilosicoli, and selected isolates were examined further by sequence analysis of the nox and 16S ribosomal RNA genes. Modifications to the original nox-RFLP method included direct inoculation of bacterial cells into the amplification mixture and purification of the PCR product, which further optimized the nox-RFLP for use in a veterinary diagnostic laboratory, producing sufficient product for both species identification and future comparisons. Although some novel profiles that prevented definitive identification were observed, the nox-RFLP method successfully classified 45 of 51 (88%) porcine and 15 of 18 (83%) avian isolates into 5 of the 6 recognized species of Brachyspira. This protocol represents a significant improvement over conventional methods currently used in veterinary diagnostic laboratories for rapid specific identification of Brachyspira spp. isolated from both pigs and poultry

Time-to-Event Modeling for Hospital Length of Stay Prediction for COVID-19 Patients

Providing timely patient care while maintaining optimal resource utilization is one of the central operational challenges hospitals have been facing throughout the pandemic. Hospital length of stay (LOS) is an important indicator of hospital efficiency, quality of patient care, and operational resilience. Numerous researchers have developed regression or classification models to predict LOS. However, conventional models suffer from the lack of capability to make use of typically censored clinical data. We propose to use time-to-event modeling techniques, also known as survival analysis, to predict the LOS for patients based on individualized information collected from multiple sources. The performance of six proposed survival models is evaluated and compared based on clinical data from COVID-19 patients

Some approaches to infrared spectroscopy for detection of buried objects

Detection of buried objects presents a formidable challenge which requires many different approaches. Infrared imaging has proven its versatility in a number of applications. Recent advances in technology have opened the door for spectroscopic imaging systems which can produce images of reflectivity or emissivity as a function of two spatial dimensions and wavelength. These imagers have been largely unexploited for detection of buried and surface-laid landmines. Several promising opportunities exist for this application in different parts of the infrared spectrum. Variations in soil moisture content, vegetation condition, and soil composition may well be related to the presence of shallow-buried objects. In addition, polarimetric signatures appear useful in detecting man-made objects on the surface and may even help in detecting buried objects. This paper will explore both the feasibility of using infrared spectral imagery in the 1-to-2.5 and 8-to-12 micrometer infrared bands to detect surface-laid and buried objects

Ανάπτυξη Web εφαρμογής για συσχέτιση γονιδίων

Frost, during reproductive developmental stages, especially post head emergence frost (PHEF), can result in catastrophic yield loss for wheat producers. Breeding for improved PHEF tolerance may allow greater yield to be achieved, by (i) reducing direct frost damage and (ii) facilitating earlier crop sowing to reduce the risk of late season drought and/or heat stress. This paper provides an economic feasibility analysis of breeding options for PHEF tolerant wheat varieties. It compares the economic benefit to growers with the cost of a wheat breeding program aimed at developing PHEF tolerant varieties. The APSIM wheat model, with a frost-impact and a phenology gene-based module, was employed to simulate direct and indirect yield benefits for various levels of improved frost tolerance. The economic model considers optimal profit, based on sowing date and nitrogen use, rather than achieving maximum yield. The total estimated fixed cost of breeding program was AUD 1293 million, including large scale seed production to meet seed demand, with AUD 1.2 million year(-1) to run breeding program after advanced development and large scale field experiments. The results reveal that PHEF tolerant varieties would lead to a significant increase in economic benefits through reduction in direct damage and an increase in yield through early sowing. The economic benefits to growers of up to AUD 4841 million could be realised from growing PHEF tolerant lines if useful genetic variation can be found. Sensitivity analyses indicated that the benefits are particularly sensitive to increases in fixed costs, seed replacement, discount rate, and to delays in variety release. However, the investment still remains viable for most tested scenarios. Based on comparative economic benefits, if breeders were able to develop PHEF tolerant varieties that could withstand cold temperatures -4 degrees C below the current damage threshold, there is very little further economic value of breeding total frost tolerant varieties

The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation

This document is the Accepted Manuscript version of a Published Work that appeared in final form in the Journal of the American Chemical Society, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://doi.org/10.1021/ja407644b.The ability to selectively activate function of particular proteins via pharmacological agents is a longstanding goal in chemical biology. Recently, we reported an approach for designing a de novo allosteric effector site directly into the catalytic domain of an enzyme. This approach is distinct from traditional chemical rescue of enzymes in that it relies on disruption and restoration of structure, rather than active site chemistry, as a means to achieve modulate function. However, rationally identifying analogous de novo binding sites in other enzymes represents a key challenge for extending this approach to introduce allosteric control into other enzymes. Here we show that mutation sites leading to protein inactivation via tryptophan-to-glycine substitution and allowing (partial) reactivation by the subsequent addition of indole are remarkably frequent. Through a suite of methods including a cell-based reporter assay, computational structure prediction and energetic analysis, fluorescence studies, enzymology, pulse proteolysis, x-ray crystallography and hydrogen-deuterium mass spectrometry we find that these switchable proteins are most commonly modulated indirectly, through control of protein stability. Addition of indole in these cases rescues activity not by reverting a discrete conformational change, as we had observed in the sole previously reported example, but rather rescues activity by restoring protein stability. This important finding will dramatically impact the design of future switches and sensors built by this approach, since evaluating stability differences associated with cavity-forming mutations is a far more tractable task than predicting allosteric conformational changes. By analogy to natural signaling systems, the insights from this study further raise the exciting prospect of modulating stability to design optimal recognition properties into future de novo switches and sensors built through chemical rescue of structure

Causal Maps and Indirect Influences Analysis in the Diagnosis of Second-Home Tourism Impacts

This paper proposes a method for diagnosing the impacts of second-home tourism and illustrates it for a Mediterranean Spanish destination. This method proposes the application of network analysis software to the analysis of causal maps in order to create a causal network model based on stakeholder-identified impacts. The main innovation is the analysis of indirect relations in causal maps for the identification of the most influential nodes in the model. The results show that the most influential nodes are of a political nature, which contradicts previous diagnoses identifying technical planning as the ultimate cause of problems.The project described in this paper was funded by the Spanish Ministry of Science and Education under the title Residential tourism: analysis of demand and proposals for restructuring consolidated destinations (SEJ/2005/04305)

“All those Elvis-meets-golf-player-looks”: A corpus-assisted analysis of creative compounds in fashion blogging.

This paper offers a comprehensive analysis of compounds as creative forms of self-expression in a leading fashion blog (Style.com), where users engage in conversations about fashion. The aim was to determine to what extent and how compounds are used by fashion bloggers, with particular attention to creativity, and how this usage may be influenced by the online communicative context. Compounds are notoriously difficult to investigate due to their marked structural variation and inconsistent orthographic representation. However, thanks to a corpus-assisted approach, it was possible to first systematically identify compounds in the blog, and then analyze them in context to detect forms, patterning, functions, and creative usage. Most compounds functioned as adjectives, in line with the descriptive and evaluative nature of fashion discourse. However, a high level of creativity was seen in compounds with uncommon structural components (e.g., verb + preposition as in go-to), novel combinations (e.g., skull-embellished), creative recycling of participial constituents (e.g., -inspired, -inducing), and especially phrasal structures that trigger striking mental images (e.g., stripper-cum-S&M freak). The study contributes to a better understanding of how bloggers use creative language to construct their identities as members of a distinctive and cohesive social community

Single Assay for Simultaneous Detection and Differential Identification of Human and Avian Influenza Virus Types, Subtypes, and Emergent Variants

For more than four decades the cause of most type A influenza virus infections of humans has been attributed to only two viral subtypes, A/H1N1 or A/H3N2. In contrast, avian and other vertebrate species are a reservoir of type A influenza virus genome diversity, hosting strains representing at least 120 of 144 combinations of 16 viral hemagglutinin and 9 viral neuraminidase subtypes. Viral genome segment reassortments and mutations emerging within this reservoir may spawn new influenza virus strains as imminent epidemic or pandemic threats to human health and poultry production. Traditional methods to detect and differentiate influenza virus subtypes are either time-consuming and labor-intensive (culture-based) or remarkably insensitive (antibody-based). Molecular diagnostic assays based upon reverse transcriptase-polymerase chain reaction (RT-PCR) have short assay cycle time, and high analytical sensitivity and specificity. However, none of these diagnostic tests determine viral gene nucleotide sequences to distinguish strains and variants of a detected pathogen from one specimen to the next. Decision-quality, strain- and variant-specific pathogen gene sequence information may be critical for public health, infection control, surveillance, epidemiology, or medical/veterinary treatment planning. The Resequencing Pathogen Microarray (RPM-Flu) is a robust, highly multiplexed and target gene sequencing-based alternative to both traditional culture- or biomarker-based diagnostic tests. RPM-Flu is a single, simultaneous differential diagnostic assay for all subtype combinations of type A influenza viruses and for 30 other viral and bacterial pathogens that may cause influenza-like illness. These other pathogen targets of RPM-Flu may co-infect and compound the morbidity and/or mortality of patients with influenza. The informative specificity of a single RPM-Flu test represents specimen-specific viral gene sequences as determinants of virus type, A/HN subtype, virulence, host-range, and resistance to antiviral agents

Economic assessment of wheat breeding options for potential improved levels of post head-emergence frost tolerance

Frost, during reproductive developmental stages, especially post head emergence frost (PHEF), can result in catastrophic yield loss for wheat producers. Breeding for improved PHEF tolerance may allow greater yield to be achieved, by (i) reducing direct frost damage and (ii) facilitating earlier crop sowing to reduce the risk of late-season drought and/or heat stress. This paper provides an economic feasibility analysis of breeding options for PHEF tolerant wheat varieties. It compares the economic benefit to growers with the cost of a wheat breeding program aimed at developing PHEF tolerant varieties. The APSIM wheat model, with a frost-impact and a phenology gene-based module, was employed to simulate direct and indirect yield benefits for various levels of improved frost tolerance. The economic model considers optimal profit, based on sowing date and nitrogen use, rather than achieving maximum yield. The total estimated fixed cost of breeding program was AUD 1293 million, including large scale seed production to meet seed demand, with AUD 1.2 million year−1 to run breeding program after advanced development and large scale field experiments. The results reveal that PHEF tolerant varieties would lead to a significant increase in economic benefits through reduction in direct damage and an increase in yield through early sowing. The economic benefits to growers of up to AUD 4841 million could be realised from growing PHEF tolerant lines if useful genetic variation can be found. Sensitivity analyses indicated that the benefits are particularly sensitive to increases in fixed costs, seed replacement, discount rate, and to delays in variety release. However, the investment still remains viable for most tested scenarios. Based on comparative economic benefits, if breeders were able to develop PHEF tolerant varieties that could withstand cold temperatures −4 °C below the current damage threshold, there is very little further economic value of breeding total frost tolerant varieties