Evaluating hyperspectral imaging of wetland vegetation as a tool for detecting estuarine nutrient enrichment

Nutrient enrichment and eutrophication are major concerns in many estuarine and wetland ecosystems, and the need is urgent for fast, efficient, and synoptic ways to detect and monitor nutrients in wetlands and other coastal systems across multiple spatial and temporal scales. We integrated three approaches in a multi-disciplinary evaluation of the potential for using hyperspectral imaging as a tool to assess nutrient enrichment and vegetation responses in tidal wetlands. For hyperspectral imaging to be an effective tool, spectral signatures must vary in ways correlated with water nutrient content either directly, or indirectly via such proxies as vegetation responses to elevated nitrogen. Working in Elkhorn Slough, central California, where intensive farming practices generate considerable runoff of fertilizers and pesticides, we looked first for long- and short-term trends among temporally ephemeral point data for nutrients and other water quality characters collected monthly at 18 water sampling stations since 1988. Second, we assessed responses of the dominant wetland plant, Salicornia virginica (common pickleweed) to two fertilizer regimes in 0.25 m² experimental plots, and measured changes in tissue composition (C, H, N), biomass, and spectral responses at leaf and at canopy scales. Third, we used HyMap hyperspectral imagery (126 bands; 15–19 nm spectral resolution; 2.5 m spatial resolution) for a synoptic assessment of the entire wetland ecosystem of Elkhorn Slough. We mapped monospecific Salicornia patches (～ 56–500 m²) on the ground adjacent to the 18 regular water sampling sites, and then located these patches in the hyperspectral imagery to correlate long-term responses of larger patches to water nutrient regimes. These were used as standards for correlating plant canopy spectral responses with nitrogen variation described by the water sampling program. There were consistent positive relationships between nitrogen levels and plant responses in both the field experiment and the landscape analyses. Two spectral indices, the Photochemical Reflectance Index (PRI) and Derivative Chlorophyll Index (DCI), were correlated significantly with water nutrients. We conclude that hyperspectral imagery can be used to detect nutrient enrichment across three spatial and at least two temporal scales, and suggest that more quantitative information could be extracted with further research and a greater understanding of physiological and physical mechanisms linking water chemistry, plant properties and spectral imaging characteristics.     

Rotating magnetic field-driven flows in conductive inhomogeneous media: Part I—Numerical study

This paper presents a numerical study of the Lorentz force and fluid flow induced by a rotating magnetic field in a medium with a nonhomogeneous electric conductivity placed in a cylindrical vessel with insulated walls. The nonhomogeneity is modeled by the presence of a solid and a liquid phase of different electrical conductivity. The solid phase is located orthogonally to the axis of rotation, which corresponds to the case of unidirectional solidification. The simulations were performed for different locations of the solid front and different ratios of the electrical conductivity, σ _s /σ _l =0.2... 10. Here σ _s and σ _l are the electric conductivity of the solid and liquid phases, respectively. The results showed that the difference between electrical conductivity of solid and liquid phases has a noticeable effect on the mean-time Lorentz force and the velocity: namely, the presence of the solid phase (σ _s >σ _l ) leads to an increase of the Lorentz force and fluid flow in the cylinder.     

An adaptive non‐conforming finite‐element method for Reissner–Mindlin plates

Adaptive algorithms are important tools for efficient finite‐element mesh design. In this paper, an error controlled adaptive mesh‐refining algorithm is proposed for a non‐conforming low‐order finite‐element method for the Reissner–Mindlin plate model. The algorithm is controlled by a reliable and efficient residual‐based a posteriori error estimate, which is robust with respect to the plate's thickness. Numerical evidence for this and the efficiency of the new algorithm is provided in the sense that non‐optimal convergence rates are optimally improved in our numerical experiments. Copyright © 2003 John Wiley & Sons, Ltd.     

Effects of different cooking methods on the formation of food mutagens in meat

Hamburgers and chicken fillets were cooked in convection ovens, deep‐fried or contact fried and analysed for mutagenic activity using the Ames test. For the three different convection ovens, the cooking parameters studied included the presence of steam, air velocity, air temperature and holding time. For deep‐frying and contact frying, the cooking parameters included cooking temperature and cooking time. In cooked hamburgers, mutagenic activity was only detected in those that had been deep‐fried. In chicken fillets, mutagenic activity was detected in samples prepared with all cooking methods, being highest in the deep‐fried samples. Factorial analysis indicated that heat transfer was the most important factor affecting mutagenic activity. High temperature and high air velocity in the convection ovens enhanced mutagenic activity. The presence of steam reduced the mutagenic activity, except when high temperature was used in combination with high air velocity. In chicken fillets, high mutagenic activity correlated to high weight loss during cooking. Pan‐fried chicken fillets were analysed using high performance liquid chromatography (HPLC) and the mutagenic/carcinogenic heterocyclic amines 2‐amino‐3,8‐dimethylimidazo[4,5‐f ]‐quinoxaline (MeIQx), 2‐amino‐1‐methyl‐6‐phenylimidazo‐[4,5‐b]‐pyridine (PhIP) and the co‐mutagenic heterocyclic amine Norharman (9H‐pyrido[3,4‐b]‐indole) were identified. The HPLC fractions were tested for mutagenic activity and, apart from the mutagenic fractions corresponding to MeIQx and PhIP, several mutagenic fractions were detected that did not correspond to known heterocyclic amines.     

Physical map of the D6S149-D6S193 region on chromosome 6Q27 and its involvement in benign surface epithelial ovarian tumours

A detailed long range restriction map of the region defined by markers D6S149 and D6S193 on chromosome 6q27 has been constructed. This was achieved by YAC cloning and contig assembling of the same region. Seven YAC clones were found to span the almost 1000 Kb region flanked by the two markers which on the genetic map resulted to be 1.9 cM apart. With some of the characterized YAC clones we undertook a molecular cytogenetic analysis of 20 benign ovarian tumors. The rationale for this was the recent mapping to a region of chromosome 6q27, flanked by markers D6281 and D6S133, of a locus for the SV40-mediated immortalization of human cells (SEN6 gene). Noteworthy we found that the the D6S149-D6S193 region (comprised in the larger D6S281-D6S133 physical interval) was altered in all samples analysed adding support to the occurrence of a immortalization step in this type of tumors.     

Platyphylloside: Metabolism and digestibility reductionin vitro

The metabolism of platyphylloside [(5S)-5-hydroxy-1,7-bis-(4-hydroxyphenyl)-3-heptanone-5-O--d-glucopyranosidel]—known to reduce digestibility—was studiedin vitro in sheep rumen liquor. Platyphylloside is hydrolyzed to 5-hydroxy-3-platyphyllone [(5S)-5-hydroxy-1,7-bis-(4-hydroxyphenyl)-3-heptanone], which is reduced to centrolobol [1,7-bis-(4-hydroxyphenyl)-3-heptanol], via 3-platyphyllone [7-bis-(4-hydroxyphenyl)-3-heptanone]. The digestibility-reducing effect was shown to be correlated with the concentration of centrolobol.     

Learning effective color features for content based image retrieval in dermatology

We investigate the extraction of effective color features for a content-based image retrieval (CBIR) application in dermatology. Effectiveness is measured by the rate of correct retrieval of images from four color classes of skin lesions. We employ and compare two different methods to learn favorable feature representations for this special application: limited rank matrix learning vector quantization (LiRaM LVQ) and a Large Margin Nearest Neighbor (LMNN) approach. Both methods use labeled training data and provide a discriminant linear transformation of the original features, potentially to a lower dimensional space. The extracted color features are used to retrieve images from a database by a k-nearest neighbor search. We perform a comparison of retrieval rates achieved with extracted and original features for eight different standard color spaces. We achieved significant improvements in every examined color space. The increase of the mean correct retrieval rate lies between 10% and 27% in the range of k=1-25 retrieved images, and the correct retrieval rate lies between 84% and 64%. We present explicit combinations of RGB and CIE-Lab color features corresponding to healthy and lesion skin. LiRaM LVQ and the computationally more expensive LMNN give comparable results for large values of the method parameter κ of LMNN (κ≥25) while LiRaM LVQ outperforms LMNN for smaller values of κ. We conclude that feature extraction by LiRaM LVQ leads to considerable improvement in color-based retrieval of dermatologic images.     

Partial Reduction in BRCA1 Gene Dose Modulates DNA Replication Stress Level and Thereby Contributes to Sensitivity or Resistance

BRCA1 is a well-known breast cancer risk gene, involved in DNA damage repair via homologous recombination (HR) and replication fork protection. Therapy resistance was linked to loss and amplification of the BRCA1 gene causing inferior survival of breast cancer patients. Most studies have focused on the analysis of complete loss or mutations in functional domains of BRCA1. How mutations in non-functional domains contribute to resistance mechanisms remains elusive and was the focus of this study. Therefore, clones of the breast cancer cell line MCF7 with indels in BRCA1 exon 9 and 14 were generated using CRISPR/Cas9. Clones with successful introduced BRCA1 mutations were evaluated regarding their capacity to perform HR, how they handle DNA replication stress (RS), and the consequences on the sensitivity to MMC, PARP1 inhibition, and ionizing radiation. Unexpectedly, BRCA1 mutations resulted in both increased sensitivity and resistance to exogenous DNA damage, despite a reduction of HR capacity in all clones. Resistance was associated with improved DNA double-strand break repair and reduction in replication stress (RS). Lower RS was accompanied by increased activation and interaction of proteins essential for the S phase-specific DNA damage response consisting of HR proteins, FANCD2, and CHK1.