Assessing ecological risk through automated drainage extraction and watershed delineation

Decision makers are frequently involved in projects requiring ecological risk definition, which are inherent to biological conservation process. It is important to recognize these risks in order to invest wisely in the management and protection of biological resources. In this matter, Geographic Information System tools and remote sensing data have been used frequently as important components in planning and management of conservation units, Rabus et al. (2003), Valeriano et al. (2009) and Valeriano et al. (2010) stressed the advantages of using data that were gathered during the Shuttle Radar Topographic Mission (SRTM) for biological and geomorphologic purposes. For Brazil's national territory, the SRTM data were refined (Valeriano, 2008) and offered as free access on the TOPODATA Project website (http://www.dsr.inpe.br/topodata) where geomorphometric information (including elevation data) at a resolution of 30 m are provided. The aim of this paper is to demonstrate an example of how TOPODATA products have been applied in order to determine the ecological risk of the border of a Conservation Unit, located in the State of São Paulo—Brazil, in the Brazilian Atlantic Forest, using automated drainage network and watershed extraction. A comparison between SRTM, TOPODATA, and ASTER DEM was carried out, showing an advantage of TOPODATA drainage network product. The vectors generated using this data are more similar to the official drainage network vectors than the drainage network extracted using ASTER-DEM or SRTM. The network product generated using ASTER-DEM produced many commission errors and the one generated using SRTM produced a poor network, with generalized vectors, less detailed than the others. The results showed that using the TOPODATA Project‘s Digital Elevation Model (DEM) can provide important data for ecological analysis and significant additional information for decision making, regarding drainage networks and watershed features. The produced map for border ecological risk showed to fit perfectly to the field work analyses, produced in other works. Furthermore, the extracted watershed polygons might furnish important information unrevealing best conservation unit boundaries, which means more efficient management and best biological conservation results.     

烟雾病5 例临床分析

目的:研究烟雾病(moyamoya disease,MMD)的临床及影像学特征。方法:回顾性分析5例烟雾病患者,分析其临床及影像学特点。结果:本组病例既往均无阳性病史,中、青年起病,男性居多,均以缺血性脑血管病起病,肢体瘫痪不重,经颅多普勒(TCD)及头颅核磁改变明显,数字减影血管造影(DSA)检查均存在血管闭塞及侧支开放,烟雾血管网形成,1例MRA证实烟雾血管网形成。结论:对于无既往史的中、青年脑卒中患者,要考虑MMD的可能,需完善TCD、头核磁检寻找证据,最后完善数字减影血管造影确诊。     

颅内静脉系统血栓形成6 例临床分析

目的:探讨颅内静脉系统血栓形成(CVT)的临床表现、影像学特征以及治疗方法对临床诊断的意义。方法:回顾性分析首都医科大学宣武医院收治的6例CVT患者的临床表现及影像学特征与治疗方法。结果:6例临床表现无特殊,4例经MRI+MRV确诊,3例DSA检查确诊,1例介入治疗,4例抗凝治疗,2例保守,无死亡患者。结论:静脉系统血栓形成临床症状缺乏特异性,临床遇到急性起病的头痛、呕吐,伴或不伴有局灶性神经功能缺损或癫痫发作、意识障碍的青中年人,应高度怀疑CVT。早期应用抗凝、溶栓等治疗方法,对改善预后具有较高的临床应用价值。     

Picoliter DNA sequencing chemistry on an electrowetting-based digital microfluidic platform

The results of investigations into performing DNA sequencing chemistry on a picoliter-scale electrowetting digital microfluidic platform are reported. Pyrosequencing utilizes pyrophosphate produced during nucleotide base addition to initiate a process ending with detection through a chemiluminescence reaction using firefly luciferase. The intensity of light produced during the reaction can be quantified to determine the number of bases added to the DNA strand. The logic-based control and discrete fluid droplets of a digital microfluidic device lend themselves well to the pyrosequencing process. Bead-bound DNA is magnetically held in a single location, and wash or reagent droplets added or split from it to circumvent product dilution. Here we discuss the dispensing, control, and magnetic manipulation of the paramagnetic beads used to hold target DNA. We also demonstrate and characterize the picoliter-scale reaction of luciferase with adenosine triphosphate to represent the detection steps of pyrosequencing and all necessary alterations for working on this scale.     

Evaluation of the hemoglobin-binding activity of Actinobacillus pleuropneumoniae using fluorescein-labeled pig hemoglobin and flow cytometry

In the present study, the hemoglobin (Hb)-binding activity of Actinobacillus pleuropneumoniae was examined using fluorescein-labeled pig Hb and flow cytometry. Comparison of the Hb-binding activity of A. pleuropneumoniae serotype 1 strain 4074 grown under iron-restricted conditions with cells grown under iron-sufficient conditions indicated that iron-restriction in A. pleuropneumoniae promotes the expression of Hb receptors, and that Hb-binding activity is, at least in part, iron-repressible. Hb-binding activity was also observed in representative strains of A. pleuropneumoniae belonging to serotypes 1 and 2. In addition, A. pleuropneumoniae serotype 1 LPS or capsule isogenic mutants were tested in flow cytometry in order to understand the influence of surface polysaccharides on Hb-binding activity. Experiments with an acapsulated mutant indicated that surface molecules with Hb-binding activity are more exposed at the cell surface in the absence of capsular polysaccharides. However, the Hb-binding activity of LPS mutants analyzed in this study was unchanged compared to the parent strain. The outer membrane proteins profile of A. pleuropneumoniae serotype 1 grown under iron-restricted or iron-sufficient conditions was also evaluated by polyacrylamide gel electrophoresis. Iron-regulated outer membrane proteins were observed under iron-restricted growth conditions which suggests that one or more of these outer membrane proteins may play a role in the Hb-binding activity detected by flow cytometry.     

Developing a denoising filter for electron microscopy and tomography data in the cloud

The low radiation conditions and the predominantly phase-object image formation of cryo-electron microscopy (cryo-EM) result in extremely high noise levels and low contrast in the recorded micrographs. The process of single particle or tomographic 3D reconstruction does not completely eliminate this noise and is even capable of introducing new sources of noise during alignment or when correcting for instrument parameters. The recently developed Digital Paths Supervised Variance (DPSV) denoising filter uses local variance information to control regional noise in a robust and adaptive manner. The performance of the DPSV filter was evaluated in this review qualitatively and quantitatively using simulated and experimental data from cryo-EM and tomography in two and three dimensions. We also assessed the benefit of filtering experimental reconstructions for visualization purposes and for enhancing the accuracy of feature detection. The DPSV filter eliminates high-frequency noise artifacts (density gaps), which would normally preclude the accurate segmentation of tomography reconstructions or the detection of alpha-helices in single-particle reconstructions. This collaborative software development project was carried out entirely by virtual interactions among the authors using publicly available development and file sharing tools.     

数字乳房X片中的伪彩色增强应用

利用数字图像处理中伪彩色理论,讨论了灰度一彩色变换函数,并用合适的线性变换函数对数字乳房X片进行处理。处理后的图像与原数字灰度图像相比较,可分辨性明显提高。可以利用这种变换,辅助医疗诊断,从而降低乳房癌的漏诊和误诊率。经验证,经过伪彩色增强后的数字乳房X片病灶区域的可分辨性明显优于原数字图像,有较高的临床价值。     

Landscape-scale patterns of shrub-species abundance in California chaparral – The role of topographically mediated resource gradients

We examine the degree to which landscape-scale spatial patterns of shrub-species abundance in California chaparral reflect topographically mediated environmental conditions, and evaluate whether these patterns correspond to known ecophysiological plant processes. Regression tree models are developed to predict spatial patterns in the abundance of 12 chaparral shrub and tree species in three watersheds of the Santa Ynez Mountains, California. The species response models are driven by five variables: average annual soil moisture, seasonal variability in soil moisture, average annual photosynthetically active radiation, maximum air temperature over the dry season (May–October), and substrate rockiness. The energy and moisture variables are derived by integrating high resolution (10 m) digital terrain data and daily climate observations with a process-based hydro-ecological model (RHESSys). Field-sampled data on species abundance are spatially integrated with the distributed environmental variables for developing and evaluating the species response models.The species considered are differentially distributed along topographically-mediated environmental gradients in ways that are consistent with known ecophysiological processes. Spatial patterns in shrub abundance are most strongly associated with annual soil moisture and solar radiation. Substrate rockiness is also closely associated with the establishment of certain species, such as Adenostoma fasciculatum and Arctostaphylos glauca. In general, species that depend on fire for seedling recruitment (e.g., Ceanothous megacarpus) occur at high abundance in xeric environments, whereas species that do not depend on fire (e.g., Heteromeles arbutifolia) occur at higher abundance in mesic environments. Model performance varies between species and is related to life history strategies for regeneration. The scale of our analysis may be less effective at capturing the processes that underlie the establishment of species that do not depend on fire for recruitment. Analysis of predication errors in relation to environmental conditions and the abundance of potentially competing species suggest factors not explicitly considered in the species response models.     

Endocytosis and Exocytosis Events Regulate Vesicle Traffic in Endothelial Cells

We used water-soluble styryl pyridinium dyes that fluoresce at the membrane-water interface to study vesicle traffic in endothelial cells. Cultured endothelial cells derived from bovine and human pulmonary microvessels were incubated in styryl probes, washed to remove dye from the plasmalemmal outer face, and observed by digital fluorescence microscopy. Vesicles that derived from plasmalemma by endocytosis were filled with the styryl dye. These vesicles were distributed throughout the cytosol as numerous particles of heterogeneous diameter and brightness. Vesicle formation was activated 2-fold following addition of extracellular albumin whereas a control protein, immunoglobulin G, had no effect. Dye uptake was abrogated by labeling at low temperatures and inhibitors of phosphoinositide-3-kinase (PI 3-kinase). Tyrosine kinase inhibitors (genistein and herbimycin A) prevented the albumin-induced vesicle formation. Cytochalasin B prevented vesicle redistribution indicating involvement of actin filaments in translocation of endosomes away from sites of vesicle formation. Styryl dye was lost from cells by exocytosis as evident by the disappearance of discrete fluorescent particles. N-ethylmaleimide and botulinum toxin types A and B caused cells to accumulate increased number of vesicles suggesting that exocytosis was regulated by NSF-dependent SNARE mechanism. The results suggest that phosphoinositide metabolism regulates endocytosis in endothelial cells and that extracellular albumin activates endocytosis by a mechanism involving tyrosine phosphorylation, whereas exocytosis is a distinct process regulated by the SNARE machinery. The results support the hypothesis that albumin regulates its internalization and release in vascular endothelial cells via activation of specific endocytic and exocytic pathways.     

Using digital image analysis to quantify the architectural parameters of roots grown in thin rhizotrons

Abstract

Roots grown in small chambers or rhizotrons combined with image analysis could be effective for screening traits of root morphology and architecture prior to field experimentation. The objective of this study was to evaluate and compare digital images of root systems with conventional root scans (RSCN) for several sorghum varieties grown in rhizotrons. Plants were grown in duplicate in slim (1.5‐cm thick) rhizotrons angled 15° to the vertical, filled with sandy topsoil and subsoil at field capacity (FC) or 50% available water content (AWC) in a split‐plot design in a glasshouse (16/24°C). Root growth visible on the glass surface was recorded weekly, and roots were washed out 42 and 90 days after sowing for digital imaging of the root systems on pin boards (PBI). The roots were then sub‐sampled to quantify the baseline root parameters from digital RSCN using WinRhizo® software with a flat‐bed scanner. Rhizotron images revealed little of the root system (1–2%) but PBI “recovered” up to 70% of the total root length (TRL) measured by RSCN. A high a priori image contrast, increased image resolution (9.1–12 megapixels) and optimized contrast threshold between roots and background were the key parameters in quantifying the roots from digital images. PBI revealed significant differences in rooting patterns, especially distribution of root length density (RLD) in the profile, which is useful for selecting varieties with improved resource capture. However, the root diameters estimated in the PBI were significantly larger than those measured by RSCN due to lack of contrast, root clustering and overlay.