Depolarization metric spaces for biological tissues classification

Classification of tissues is an important problem in biomedicine. An efficient tissue classification protocol allows, for instance, the guided-recognition of structures through treated images or discriminating between healthy and unhealthy regions (e.g., early detection of cancer). In this framework, we study the potential of some polarimetric metrics, the so-called depolarization spaces, for the classification of biological tissues. The analysis is performed using 120 biological ex vivo samples of three different tissues types. Based on these data collection, we provide for the first time a comparison between these depolarization spaces, as well as with most commonly used depolarization metrics, in terms of biological samples discrimination. The results illustrate the way to determine the set of depolarization metrics which optimizes tissue classification efficiencies. In that sense, the results show the interest of the method which is general, and which can be applied to study multiple types of biological samples, including of course human tissues. The latter can be useful for instance, to improve and to boost applications related to optical biopsy.Agència de Gestió d'Ajuts Universitaris i de Recerca, Grant/Award Number: 2017-SGR-001500; Ministerio de Economía y Competitividad, Grant/Award Numbers: Fondos FEDER, RTI2018-097107-B-C3

Land cover classification using multi-temporal MERIS vegetation indices

The spectral, spatial, and temporal resolutions of Envisat's Medium Resolution Imaging Spectrometer (MERIS) data are attractive for regional- to global-scale land cover mapping. Moreover, two novel and operational vegetation indices derived from MERIS data have considerable potential as discriminating variables in land cover classification. Here, the potential of these two vegetation indices (the MERIS global vegetation index (MGVI), MERIS terrestrial chlorophyll index (MTCI)) was evaluated for mapping eleven broad land cover classes in Wisconsin. Data acquired in the high and low chlorophyll seasons were used to increase inter-class separability. The two vegetation indices provided a higher degree of inter-class separability than data acquired in many of the individual MERIS spectral wavebands. The most accurate landcover map (73.2%) was derived from a classification of vegetation index-derived data with a support vector machine (SVM), and was more accurate than the corresponding map derived from a classification using the data acquired in the original spectral wavebands

Serological Responses of Raccoons and Striped Skunks to Ontario Rabies Vaccine Bait in West Virginia during 2012–2016

Since the 1990s, oral rabies vaccination (ORV) has been used successfully to halt the westward spread of the raccoon rabies virus (RV) variant from the eastern continental USA. Elimination of raccoon RV from the eastern USA has proven challenging across targeted raccoon (Procyon lotor) and striped skunk (Mephitis mephitis) populations impacted by raccoon RV. Field trial evaluations of the Ontario Rabies Vaccine Bait (ONRAB) were initiated to expand ORV products available to meet the rabies management goal of raccoon RV elimination. This study describes the continuation of a 2011 trial inWest Virginia. Our objective was to evaluate raccoon and skunk response to ORV occurring in West Virginia for an additional two years (2012–2013) at 75 baits/km2 followed by three years (2014–2016) of evaluation at 300 baits/km2. We measured the change in rabies virus-neutralizing antibody (RVNA) seroprevalence in targeted wildlife populations by comparing levels pre- and post-ORV during each year of study. The increase in bait density from 75/km2 to 300/km2 corresponded to an increase in average post-ORV seroprevalence for raccoon and skunk populations. Raccoon population RVNA levels increased from 53% (300/565, 95% CI: 50–57%) to 82.0% (596/727, 95% CI: 79–85%) during this study, and skunk population RVNA levels increased from 11% (8/72, 95% CI: 6–20%) to 39% (51/130, 95% CI: 31–48%). The RVNA seroprevalence pre-ORV demonstrated an increasing trend across study years for both bait densities and species, indicating that multiple years of ORV may be necessary to achieve and maintain RVNA seroprevalence in target wildlife populations for the control and elimination of raccoon RV in the eastern USA

Tamoxifen for prevention of breast cancer: extended long-term follow-up of the IBIS-I breast cancer prevention trial

© Cuzick et al. Open Access article distributed under the terms of CC BY.http://dx.doi.org/10.1016/S1470-2045(14)71171-

Bayesian Classification and Regression Trees for Predicting Incidence of Cryptosporidiosis

Background Classification and regression tree (CART) models are tree-based exploratory data analysis methods which have been shown to be very useful in identifying and estimating complex hierarchical relationships in ecological and medical contexts. In this paper, a Bayesian CART model is described and applied to the problem of modelling the cryptosporidiosis infection in Queensland, Australia. Methodology/Principal Findings We compared the results of a Bayesian CART model with those obtained using a Bayesian spatial conditional autoregressive (CAR) model. Overall, the analyses indicated that the nature and magnitude of the effect estimates were similar for the two methods in this study, but the CART model more easily accommodated higher order interaction effects. Conclusions/Significance A Bayesian CART model for identification and estimation of the spatial distribution of disease risk is useful in monitoring and assessment of infectious diseases prevention and control

Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate

Hen egg-white lysozyme (HEWL) was the first enzyme to have its three-dimensional structure determined by X-ray diffraction techniques(1). A catalytic mechanism, featuring a long-lived oxo-carbenium-ion intermediate, was proposed on the basis of model-building studies(2). The `Phillips' mechanism is widely held as the paradigm for the catalytic mechanism of beta -glycosidases that cleave glycosidic linkages with net retention of configuration of the anomeric centre. Studies with other retaining beta -glycosidases, however, provide strong evidence pointing to a common mechanism for these enzymes that involves a covalent glycosyl-enzyme intermediate, as previously postulated(3). Here we show, in three different cases using electrospray ionization mass spectrometry, a catalytically competent covalent glycosyl-enzyme intermediate during the catalytic cycle of HEWL. We also show the three-dimensional structure of this intermediate as determined by Xray diffraction. We formulate a general catalytic mechanism for all retaining beta -glycosidases that includes substrate distortion, formation of a covalent intermediate, and the electrophilic migration of C1 along the reaction coordinate

Nuclear Isotopic Dilution of Highly-Enriched Uranium-235 and Uranium-233 by Dry Blending via the RM-2 Mill Technology

The United States Department of Energy has initiated numerous activities to identify strategies to disposition various excess fissile materials. Two such materials are the off-specification highly enriched uranium-235 oxide powder and the uranium-233 contained in unirradiated nuclear fuel both currently stored at the Idaho National Engineering and Environmental Laboratory. This report describes the development of a technology that could dilute these materials to levels categorized as low-enriched uranium, or further dilute the materials to a level categorized as waste. This dilution technology opens additional pathways for the disposition of these excess fissile materials as existing processing infrastructure continues to be retired

Composite structural motifs of binding sites for delineating biological functions of proteins

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs which represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures.Comment: 34 pages, 7 figure

Expression of Distal-less, dachshund, and optomotor blind in Neanthes arenaceodentata (Annelida, Nereididae) does not support homology of appendage-forming mechanisms across the Bilateria

The similarity in the genetic regulation of arthropod and vertebrate appendage formation has been interpreted as the product of a plesiomorphic gene network that was primitively involved in bilaterian appendage development and co-opted to build appendages (in modern phyla) that are not historically related as structures. Data from lophotrochozoans are needed to clarify the pervasiveness of plesiomorphic appendage forming mechanisms. We assayed the expression of three arthropod and vertebrate limb gene orthologs, Distal-less (Dll), dachshund (dac), and optomotor blind (omb), in direct-developing juveniles of the polychaete Neanthes arenaceodentata. Parapodial Dll expression marks premorphogenetic notopodia and neuropodia, becoming restricted to the bases of notopodial cirri and to ventral portions of neuropodia. In outgrowing cephalic appendages, Dll activity is primarily restricted to proximal domains. Dll expression is also prominent in the brain. dac expression occurs in the brain, nerve cord ganglia, a pair of pharyngeal ganglia, presumed interneurons linking a pair of segmental nerves, and in newly differentiating mesoderm. Domains of omb expression include the brain, nerve cord ganglia, one pair of anterior cirri, presumed precursors of dorsal musculature, and the same pharyngeal ganglia and presumed interneurons that express dac. Contrary to their roles in outgrowing arthropod and vertebrate appendages, Dll, dac, and omb lack comparable expression in Neanthes appendages, implying independent evolution of annelid appendage development. We infer that parapodia and arthropodia are not structurally or mechanistically homologous (but their primordia might be), that Dll’s ancestral bilaterian function was in sensory and central nervous system differentiation, and that locomotory appendages possibly evolved from sensory outgrowths