Issues in using whole slide imaging for diagnostic pathology: “routine” stains,immunohistochemistry and predictive markers

The traditional microscope, together with the “routine” hematoxylin and eosin (H & E) stain, remains the “gold standard” for diagnosis of cancer and other diseases; remarkably, it and the majority of associated biological stains are more than 150 years old. Immunohistochemistry has added to the repertoire of “stains” available. Because of the need for specific identification and even measurement of “biomarkers,” immunohistochemistry has increased the demand for consistency of performance and interpretation of staining results. Rapid advances in the capabilities of digital imaging hardware and software now offer a realistic route to improved reproducibility, accuracy and quantification by utilizing whole slide digital images for diagnosis, education and research. There also are potential efficiencies in work flow and the promise of powerful new analytical methods; however, there also are challenges with respect to validation of the quality and fidelity of digital images, including the standard H & E stain, so that diagnostic performance by pathologists is not compromised when they rely on whole slide images instead of traditional stained tissues on glass slides.     

Para-nitrophenyl Phosphate as a Substrate for Some Acid Phosphatases in Roots of Vicia faba

A cytochemical and biochemical study of acid phosphatases inroots of Vicia faba using p-nitrophenylphosphate(p-NPP) as substratehas shown the lack of specificity of the substrate which canbe acted upon by a K⁺-activated acyl phosphatase, nucleotidepyrophosphatase, glucox-6-phosphatase, 5' (3')-ribonucleotidephosphohydrolase, nucleotide phosph-transferase and those acidphosphatases demonstrable with ß-glycerophosphate.It is suggested that care should be taken in the interpretationof both biochemical and cytochemical studies employing sucha non-specific substrate as P-NPP. Vicia faba, broad bean, root, acid phosphatases     

Alliance and Conflict: The World System of the Iñupiaq Eskimos

Alliance and Conflict: The World System of the Iñupiaq Eskimos. Ernest S. Burch Jr. Lincoln: University of Nebraska Press, 2005.     

Effects of tree height on branch hydraulics, leaf structure and gas exchange in California redwoods

We examined changes in branch hydraulic, leaf structure and gas exchange properties in coast redwood ( Sequoia sempervirens ) and giant sequoia ( Sequoiadendron giganteum ) trees of different sizes. Leaf-specific hydraulic conductivity ( k _L) increased with height in S. sempervirens but not in S. giganteum , while xylem cavitation resistance increased with height in both species. Despite hydraulic adjustments, leaf mass per unit area (LMA) and leaf carbon isotope ratios ( δ ¹³C) increased, and maximum mass-based stomatal conductance ( g _mass) and photosynthesis ( A _mass) decreased with height in both species. As a result, both A _mass and g _mass were negatively correlated with branch hydraulic properties in S. sempervirens and uncorrelated in S. giganteum . In addition, A _mass and g _mass were negatively correlated with LMA in both species, which we attributed to the effects of decreasing leaf internal CO₂ conductance ( g _i). Species-level differences in wood density, LMA and area-based gas exchange capacity constrained other structural and physiological properties, with S. sempervirens exhibiting increased branch water transport efficiency and S. giganteum exhibiting increased leaf-level water-use efficiency with increasing height. Our results reveal different adaptive strategies for the two redwoods that help them compensate for constraints associated with growing taller, and reflect contrasting environmental conditions each species faces in its native habitat.     

The trouble with flippers: a report on the prevalence of digital anomalies in Cetacea

The forelimbs of cetaceans (whales, dolphins, and porpoises) are unique among mammals as the digits exhibit hyperphalangy, and the entire limb is encased in a soft tissue flipper that functions to generate lift. The typical morphology of cetacean digits has been well documented by detailed anatomical studies. This study however furthers our understanding of cetacean forelimb anatomy by conducting a taxonomically broad survey of cetacean digital anomalies. Forelimb radiographs from museum collections provided the basis upon which we calculated the prevalence and documented the morphology of cetacean digital abnormalities. Results indicated that 11% (n = 255) of toothed whales displayed some type of aberrant ossification: the majority of these cases displayed a fusion of elements within a single digital ray, whereas cases exhibiting branched digits were rare. A small sample of baleen whale radiographs (n = 6) contained the only documented case of baleen whale polydactyly in a specimen of the gray whale (Eschrichtius). Furthermore, some Balaenoptera specimens displayed ossified elements within the interdigital spaces that lacked attachment to the adjacent digits and carpus. In addition, we speculated on the role that several genes may have played in creating cetacean digital anomalies. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 722–735.     

Trophic level asynchrony in rates of phenological change for marine,freshwater and terrestrial environments

Recent changes in the seasonal timing (phenology) of familiar biological events have been one of the most conspicuous signs of climate change. However, the lack of a standardized approach to analysing change has hampered assessment of consistency in such changes among different taxa and trophic levels and across freshwater, terrestrial and marine environments. We present a standardized assessment of 25 532 rates of phenological change for 726 UK terrestrial, freshwater and marine taxa. The majority of spring and summer events have advanced, and more rapidly than previously documented. Such consistency is indicative of shared large scale drivers. Furthermore, average rates of change have accelerated in a way that is consistent with observed warming trends. Less coherent patterns in some groups of organisms point to the agency of more local scale processes and multiple drivers. For the first time we show a broad scale signal of differential phenological change among trophic levels; across environments advances in timing were slowest for secondary consumers, thus heightening the potential risk of temporal mismatch in key trophic interactions. If current patterns and rates of phenological change are indicative of future trends, future climate warming may exacerbate trophic mismatching, further disrupting the functioning, persistence and resilience of many ecosystems and having a major impact on ecosystem services.     

Gene structure,transcripts and calciotropic effects of the PTH family of peptides in <Emphasis Type="Italic">Xenopus</Emphasis> and chicken

Background  

Parathyroid hormone (PTH) and PTH-related peptide (PTHrP) belong to a family of endocrine factors that share a highly conserved N-terminal region (amino acids 1-34) and play key roles in calcium homeostasis, bone formation and skeletal development. Recently, PTH-like peptide (PTH-L) was identified in teleost fish raising questions about the evolution of these proteins. Although PTH and PTHrP have been intensively studied in mammals their function in other vertebrates is poorly documented. Amphibians and birds occupy unique phylogenetic positions, the former at the transition of aquatic to terrestrial life and the latter at the transition to homeothermy. Moreover, both organisms have characteristics indicative of a complex system in calcium regulation. This study investigated PTH family evolution in vertebrates with special emphasis on Xenopus and chicken.     

Morphological and molecular characterization of populations of plains bristlegrass (<i>Setaria macrostachya</i> Kunth) in Chihuahua,México

Plains bristlegrass (Setaria macrostachya Kunth) is a native grass with forage value. However, due to the lack of grazing management practices, populations and thus genetic diversity, have been reduced. Morphological and genetic variability were analyzed on 44 populations of plains bristlegrass in the State of Chihuahua. Plants were transplanted in a common area under natural conditions. Two years later, morphological characterization was evaluated measuring nine variables, and genetic variability using AFLP molecular markers. The principal components analysis (PC) showed that the three first principal components explained 73.74% of the variation. The variables with the greatest contribution to the variance in PC1 were plant height and inflorescence length; in CP2, tiller number and leaf width; and in PC3, tiller thickness. Application of four pairs of primers, presented 186 total bands, from which 87.10% showed polymorphism and 12.90% monomorphism. The combination of EcoRI-AGG MseI-CAG primers detected the highest percentage (93%) of polymorphism with 40 polymorphic bands. The cluster analysis and Dice coefficient indicated that populations clump into two groups. The wide genetic variability and morphological characteristics detected among populations represent the basis for the selection of populations that could be used with different purposes in the rehabilitation of ecosystems. In addition, this study will allow establishment of in situ conservation strategies.