Simulations of nonlinear harmonic generation by an internal wave beam incident on a pycnocline

Internal wave beams generated by oceanic tidal flows propagate upward and interact with the increasing stratification found at the pycnocline. The nonlinear generation of harmonic modes by internal wave beams incident on a pycnocline has recently been demonstrated by laboratory experiments and numerical simulations. In these previous studies, the harmonic modes were trapped within the pycnocline because their frequencies exceeded that of the stratified fluid below. Here, two-dimensional numerical simulations are used to explore the effect of incidence angle on harmonic generation at a thin pycnocline. At incidence angles less than 30 degrees (typical of oceanic beams), the lowest harmonic mode freely radiates in the form of an internal wave beam rather than being trapped within the pycnocline. The results indicate that nonlinear refraction is the primary mechanism for harmonic generation at incidence angles exceeding 30 degrees, but that interaction of the incident and reflected beams is more important at smaller incidence angles. The simulations are compared to weakly nonlinear theory based on refraction at the pycnocline. The results yield good agreement for trapped harmonics, but weakly nonlinear theory substantially underpredicts the amplitude of the radiated harmonics

Estimating percentages of fusarium-damaged kernels in hard wheat by near-infrared hyperspectral imaging

Fusarium head blight (FHB) is among the most common fungal diseases affecting wheat, resulting in decreased yield, low-density kernels, and production of the mycotoxin deoxynivalenol, a compound toxic to humans and livestock. Human visual analysis of representative wheat samples has been the traditional method for FHB assessment in both official inspection and plant breeding operations. While not requiring specialized equipment, visual analysis is dependent on a trained and consistent workforce, such that in the absence of these aspects, biases may arise among inspectors and evaluation dates. This research was intended to avoid such pitfalls by using longer wavelength radiation than the visible using hyperspectral imaging (HSI) on individual kernels. Linear discriminant analysis models to differentiate between sound and scab-damaged kernels were developed based on mean of reflectance values of the interior pixels of each kernel at four wavelengths (1100, 1197, 1308, and 1394 nm). Other input variables were examined, including kernel morphological properties and histogram features from the pixel responses of selected wavelengths of each kernel. The results indicate the strong potential of HSI in estimating fusarium damage. However, improvement in aligning this procedure to visual analysis is hampered by the inherent level of subjectivity in visual analysis

Near infrared hyperspectral imaging of blends of conventional and waxy hard wheats

Recent development of hard winter waxy (amylose-free) wheat adapted to the North American climate has prompted the quest to find a rapid method that will determine mixture levels of conventional wheat in lots of identity preserved waxy wheat. Previous work documented the use of conventional near infrared (NIR) reflectance spectroscopy to determine the mixture level of conventional wheat in waxy wheat, with an examined range, through binary sample mixture preparation, of 0–100% (weight conventional / weight total). The current study examines the ability of NIR hyperspectral imaging of intact kernels to determine mixture levels. Twenty-nine mixtures (0, 1, 2, 3, 4, 5, 10, 15, …, 95, 96, 97, 98, 99, 100%) were formed from known genotypes of waxy and conventional wheat. Two-class partial least squares discriminant analysis (PLSDA) and statistical pattern recognition classifier models were developed for identifying each kernel in the images as conventional or waxy. Along with these approaches, conventional PLS1 regression modelling was performed on means of kernel spectra within each mixture test sample. Results indicated close agreement between all three approaches, with standard errors of prediction for the better preprocess transformations (PLSDA models) or better classifiers (pattern recognition models) of approximately 9 percentage units. Although such error rates were slightly greater than ones previously published using non-imaging NIR analysis of bulk whole kernel wheat and wheat meal, the HSI technique offers an advantage of its potential use in sorting operations

Near infrared hyperspectral imaging of blends of conventional and waxy hard wheats

Recent development of hard winter waxy (amylose-free) wheat adapted to the North American climate has prompted the quest to find a rapid method that will determine mixture levels of conventional wheat in lots of identity preserved waxy wheat. Previous work documented the use of conventional near infrared (NIR) reflectance spectroscopy to determine the mixture level of conventional wheat in waxy wheat, with an examined range, through binary sample mixture preparation, of 0–100% (weight conventional / weight total). The current study examines the ability of NIR hyperspectral imaging of intact kernels to determine mixture levels. Twenty-nine mixtures (0, 1, 2, 3, 4, 5, 10, 15, …, 95, 96, 97, 98, 99, 100%) were formed from known genotypes of waxy and conventional wheat. Two-class partial least squares discriminant analysis (PLSDA) and statistical pattern recognition classifier models were developed for identifying each kernel in the images as conventional or waxy. Along with these approaches, conventional PLS1 regression modelling was performed on means of kernel spectra within each mixture test sample. Results indicated close agreement between all three approaches, with standard errors of prediction for the better preprocess transformations (PLSDA models) or better classifiers (pattern recognition models) of approximately 9 percentage units. Although such error rates were slightly greater than ones previously published using non-imaging NIR analysis of bulk whole kernel wheat and wheat meal, the HSI technique offers an advantage of its potential use in sorting operations

Measurement of Single Soybean Seed Attributes by Near-Infrared Technologies. A Comparative Study

Four near-infrared spectrophotometers, and their associated spectral collection methods, were tested and compared for measuring three soybean single-seed attributes: weight (g), protein (%), and oil (%). Using partial least-squares (PLS) and four preprocessing methods, the attribute that was significantly most easily predicted was seed weight (RPD > 3 on average) and protein the least. The performance of all instruments differed from each other. Performances for oil and protein predictions were correlated with the instrument sampling system, with the best predictions using spectra taken from more than one seed angle. This was facilitated by the seed spinning or tumbling during spectral collection as opposed to static sampling methods. From the preprocessing methods utilized, no single one gave the best overall performances but weight measurements were often more successful with raw spectra, whereas protein and oil predictions were often enhanced by SNV and SNV + detrending.Posted with permission from Journal of Agricultural and Food Chemistry 60 (2012): 8314–8322, doi:10.1021/jf3012807. Copyright 2012 American Chemical Society.</p

Veillonella rogosae sp. nov., an anaerobic, Gram-negative coccus isolated from dental plaque

Strains of a novel anaerobic, Gram-negative coccus were isolated from the supra-gingival plaque of children. Independent strains from each of six subjects were shown, at a phenotypic level and based on 16S rRNA gene sequencing, to be members of the genus Veillonella. Analysis revealed that the six strains shared 99.7 % similarity in their 16S rRNA gene sequences and 99.0 % similarity in their rpoB gene sequences. The six novel strains formed a distinct group and could be clearly separated from recognized species of the genus Veillonella of human or animal origin. The novel strains exhibited 98 and 91 % similarity to partial 16S rRNA and rpoB gene sequences of Veillonella parvula ATCC 10790T, the most closely related member of the genus. The six novel strains could be differentiated from recognized species of the genus Veillonella based on partial 16S rRNA and rpoB gene sequencing. The six novel strains are thus considered to represent a single novel species of the genus Veillonella, for which the name Veillonella rogosae sp. nov. is proposed. The type strain is CF100T (=CCUG 54233T=DSM 18960T)

COVID-19 publications: Database coverage, citations, readers, tweets, news, Facebook walls, Reddit posts

© 2020 The Authors. Published by MIT Press. This is an open access article available under a Creative Commons licence. The published version can be accessed at the following link on the publisher’s website: https://doi.org/10.1162/qss_a_00066The COVID-19 pandemic requires a fast response from researchers to help address biological, medical and public health issues to minimize its impact. In this rapidly evolving context, scholars, professionals and the public may need to quickly identify important new studies. In response, this paper assesses the coverage of scholarly databases and impact indicators during 21 March to 18 April 2020. The rapidly increasing volume of research, is particularly accessible through Dimensions, and less through Scopus, the Web of Science, and PubMed. Google Scholar’s results included many false matches. A few COVID-19 papers from the 21,395 in Dimensions were already highly cited, with substantial news and social media attention. For this topic, in contrast to previous studies, there seems to be a high degree of convergence between articles shared in the social web and citation counts, at least in the short term. In particular, articles that are extensively tweeted on the day first indexed are likely to be highly read and relatively highly cited three weeks later. Researchers needing wide scope literature searches (rather than health focused PubMed or medRxiv searches) should start with Dimensions (or Google Scholar) and can use tweet and Mendeley reader counts as indicators of likely importance

The Right Place at the Right Time: Creative Spaces in Libraries

Purpose This essay explores the recent trend in libraries: that of the establishment of spaces specifically set aside for creative work. The rise of these dedicated creative spaces is owed to a confluence of factors that happen to be finding their expression together in recent years. This essay examines the history of these spaces and explores the factors that gave rise to them and will fuel them moving forward. Design/Methodology/Approach A viewpoint piece, this essay combines historical research and historical/comparative analyses to examine the ways by which libraries have supported creative work in the past and how they may continue to do so into the 21st century. Findings The key threads brought together include a societal recognition of the value of creativity and related skills and attributes; the philosophies, values, and missions of libraries in both their longstanding forms and in recent evolutions; the rise of participatory culture as a result of inexpensive technologies; improved means to build community and share results of efforts; and library experience and historical practice in matters related to creativity. The chapter concludes with advice for those interested in the establishment of such spaces, grounding those reflections in the author’s experiences in developing a new creative space at Virginia Commonwealth University. Originality/value While a number of pieces have been written that discuss the practicalities of developing certain kinds of creative spaces, very little has been written that situates these spaces in larger social and library professional contexts; this essay begins to fill that gap

Evolution of light-harvesting complex proteins from Chl c-containing algae

<p>Abstract</p> <p>Background</p> <p>Light harvesting complex (LHC) proteins function in photosynthesis by binding chlorophyll (Chl) and carotenoid molecules that absorb light and transfer the energy to the reaction center Chl of the photosystem. Most research has focused on LHCs of plants and chlorophytes that bind Chl <it>a </it>and <it>b </it>and extensive work on these proteins has uncovered a diversity of biochemical functions, expression patterns and amino acid sequences. We focus here on a less-studied family of LHCs that typically bind Chl <it>a </it>and <it>c</it>, and that are widely distributed in Chl <it>c</it>-containing and other algae. Previous phylogenetic analyses of these proteins suggested that individual algal lineages possess proteins from one or two subfamilies, and that most subfamilies are characteristic of a particular algal lineage, but genome-scale datasets had revealed that some species have multiple different forms of the gene. Such observations also suggested that there might have been an important influence of endosymbiosis in the evolution of LHCs.</p> <p>Results</p> <p>We reconstruct a phylogeny of LHCs from Chl <it>c</it>-containing algae and related lineages using data from recent sequencing projects to give ~10-fold larger taxon sampling than previous studies. The phylogeny indicates that individual taxa possess proteins from multiple LHC subfamilies and that several LHC subfamilies are found in distantly related algal lineages. This phylogenetic pattern implies functional differentiation of the gene families, a hypothesis that is consistent with data on gene expression, carotenoid binding and physical associations with other LHCs. In all probability LHCs have undergone a complex history of evolution of function, gene transfer, and lineage-specific diversification.</p> <p>Conclusion</p> <p>The analysis provides a strikingly different picture of LHC diversity than previous analyses of LHC evolution. Individual algal lineages possess proteins from multiple LHC subfamilies. Evolutionary relationships showed support for the hypothesized origin of Chl <it>c </it>plastids. This work also allows recent experimental findings about molecular function to be understood in a broader phylogenetic context.</p

Near infrared spectroscopy and hyperspectral imaging for non-destructive quality assessment of cereal grains

Hyperspectral imaging (HSI) combines spectroscopy and imaging, providing information about the chemical properties of a material and their spatial distribution. It represents an advance of traditional Near-Infrared (NIR) spectroscopy. The present work reviews the most recent applications of NIR spectroscopy for cereal grain evaluation, then focused on the use of HSI in this field. The progress of research from ground material to whole grains and single kernels is detailed. The potential of NIR-based methods to predict protein content, sprout damage and α-amylase activity in wheat and barley is shown, in addition to assessment of quality parameters in other cereals such as rice, maize and oats, and the estimation of fungal infection. This analytical technique also offers the possibility to rapidly classify grains based on properties such as variety, geographical origin, kernel hardness, etc. Further applications of HSI are expected in the near future, for its potential for rapid single-kernel analysis