Animating tree colonization and growth

In the early twentieth century the woodland at Heald Brow, north-west England, was largely a tree-less pasture, but changing land management practices lead to natural tree colonization and the development of a mixed deciduous woodland with ash (Fraxinus excelsior), oak (Quercus robur), yew (Taxus baccata) and small-leaved Lime (Tilia cordata) the main components. The research focused on T. cordata due to its rarity and conservation value, and aimed to investigate the timing of its appearance, rates of reproduction by layering and the effects of competition on its longer-term survival. A small, 0.32 ha area of woodland was mapped using standard field-based survey methods and increment cores were taken to provide minimum age estimates for living stems of all species present. The spatial and temporal data generated led to the development of a new micro-GIS animation method, using ArcGIS software, that visually highlighted secondary woodland establishment and development, and gave novel insights into the competitive interactions that governed the development. Results showed T. cordata colonization in the 1940s and layering developing in the 1960s. The later appearance and rapid establishment of T. baccata with its light-excluding canopy produced high competition scores and undoubtedly restricted further development of the main T. cordata canopy aided by F. excelsior at the periphery. This animation method and associated GIS analyses have potential application in both dendrochronological, wider ecological research and in conservation management.     

Automatic figure ranking and user interfacing for intelligent figure search

Background

Figures are important experimental results that are typically reported in full-text bioscience articles. Bioscience researchers need to access figures to validate research facts and to formulate or to test novel research hypotheses. On the other hand, the sheer volume of bioscience literature has made it difficult to access figures. Therefore, we are developing an intelligent figure search engine (http://figuresearch.askhermes.org). Existing research in figure search treats each figure equally, but we introduce a novel concept of “figure ranking”: figures appearing in a full-text biomedical article can be ranked by their contribution to the knowledge discovery.

Methodology/Findings

We empirically validated the hypothesis of figure ranking with over 100 bioscience researchers, and then developed unsupervised natural language processing (NLP) approaches to automatically rank figures. Evaluating on a collection of 202 full-text articles in which authors have ranked the figures based on importance, our best system achieved a weighted error rate of 0.2, which is significantly better than several other baseline systems we explored. We further explored a user interfacing application in which we built novel user interfaces (UIs) incorporating figure ranking, allowing bioscience researchers to efficiently access important figures. Our evaluation results show that 92% of the bioscience researchers prefer as the top two choices the user interfaces in which the most important figures are enlarged. With our automatic figure ranking NLP system, bioscience researchers preferred the UIs in which the most important figures were predicted by our NLP system than the UIs in which the most important figures were randomly assigned. In addition, our results show that there was no statistical difference in bioscience researchers'' preference in the UIs generated by automatic figure ranking and UIs by human ranking annotation.

Conclusion/Significance

The evaluation results conclude that automatic figure ranking and user interfacing as we reported in this study can be fully implemented in online publishing. The novel user interface integrated with the automatic figure ranking system provides a more efficient and robust way to access scientific information in the biomedical domain, which will further enhance our existing figure search engine to better facilitate accessing figures of interest for bioscientists.     

Correlation between apoptotic figure counting and the TUNEL technique

OBJECTIVE: To compare histologic detection of apoptotic (AP) figures and terminal transferase UTP nick end labeling (TUNEL) detection in colorectal carcinomas and lymphomas. STUDY DESIGN: We evaluated the percentage of AP cells by AP figure counting and by the TUNEL technique in formalin-paraffin material from 39 tumors--29 colorectal carcinomas and 10 non-Hodgkin's lymphomas. The Lucia G image analysis system (Laboratory Imaging, Prague, Czech Republic) was used for cellularity evaluation and AP counting. RESULTS: On average, 0.81 +/- 0.5% AP cells were detected by figure counting; 0.91 +/- 0.35% were identified by TUNEL. A statistically high correlation between these techniques was found using Pearson's correlation coefficient (r = .56, P < .001). TUNEL, although probably more sensitive, was difficult to standardize. CONCLUSION: AP figure counting seems to be the method of choice for routine work, particularly because of its cost effectiveness and reproducibility.     

Upstream of the SOS response: figure out the trigger

The bacterial SOS regulon encodes a response to DNA damage that not only functions to relieve the incurred damage but also enhances adaptation through mutagenesis and the lateral spread of virulence factors. Recent papers have demonstrated that certain stimuli can indirectly generate the SOS-inducing signal by activation of endogenous DNA damage mechanisms rather than by direct DNA damage. We suggest that these endogenous triggers have been recruited by bacteria to enable adaptation to various types of stresses.     

The three-dimensional aspect of the mammalian lung surfactant myelin figure.

Rodent and primate lung surfactant was studied at the ultrastructural level utilizing procedures that retained most of the carbohydrates and lipids in thin section. The three-dimensional aspect of tubular myelin surfactant was observed to be four, lipid bilayer membranes oriented at right angles so that in cross-section it was square. In longitudinal section it appeared as two parallel lipid bilayers. Inside the tubular myelin was a homogeneous matrix material that completely filled the tubule except for a small, central area. A single multilamellar body, after it expanded and rearranged lamellae to form tubular myelin surfactant, still retained its basic morphology so that it was possible to determine the number and orientation of bodies that comprised a given surfactant area. This enabled quantification of surfactant by serial sectioning. Each transformed multilamellar body was observed to contain from 2 to 13 groups of tubular myelin, oriented at angles within the transformed body. With three-dimensional understanding, many of the areas previously reported to be homogeneous were determined to actually be oblique cross or longitudinal sections through tubular myelin surfactant.Five distinct layers characterized tubular myelin surfactant: (1) Unexpanded layer—up to 63 recently secreted multilamellar bodies. (2) Formation layerp?aired lamellae expanding and rearranging to form tubules. (3) Mature layer—tubular myelin surfactant. (4) Air-surfactant interface layer—usually a single lipid bilayer which was the outermost layer of tubular myelin of from 1 to 12 transformed multilamellar bodies. (5) Degraded surfactant layer—lipid bilayer spheres were formed at the interface and degraded in the alveolar space.     

教学简笔画在药理学教学中的应用

教学简笔画是教师在教学中利用黑板,把文章的重点、难点和中心意义,以凝炼、概括的简图形式显示出来,使学生更直观、形象地理解文章内容的一种板书形式.作者认为以这种板书为媒介能有效建立教学中师生间的良性互动,从简图表达人体的细胞、组织、器官入手,讲授药物与机体之间的相互关系,直观清晰地表达药效学、药动学的有关概念,以此提高学习效率.     

Processing of figure and background motion in the visual system of the fly

The visual system of the fly is able to extract different types of global retinal motion patterns as may be induced on the eyes during different flight maneuvers and to use this information to control visual orientation. The mechanisms underlying these tasks were analyzed by a combination of quantitative behavioral experiments on tethered flying flies (Musca domestica) and model simulations using different conditions of oscillatory large-field motion and relative motion of different segments of the stimulus pattern. Only torque responses about the vertical axis of the animal were determined. The stimulus patterns consisted of random dot textures (Julesz patterns) which could be moved either horizontally or vertically. Horizontal rotatory large-field motion leads to compensatory optomotor turning responses, which under natural conditions would tend to stabilize the retinal image. The response amplitude depends on the oscillation frequency: It is much larger at low oscillation frequencies than at high ones. When an object and its background move relative to each other, the object may, in principle, be discriminated and then induce turning responses of the fly towards the object. However, whether the object is distinguished by the fly depends not only on the phase relationship between object and background motion but also on the oscillation frequency. At all phase relations tested, the object is detected only at high oscillation frequencies. For the patterns used here, the turning responses are only affected by motion along the horizontal axis of the eye. No influences caused by vertical motion could be detected. The experimental data can be explained best by assuming two parallel control systems with different temporal and spatial integration properties: TheLF-system which is most sensitive to coherent rotatory large-field motion and mediates compensatory optomotor responses mainly at low oscillation frequencies. In contrast, theSF-system is tuned to small-field and relative motion and thus specialized to discriminate a moving object from its background; it mediates turning responses towards objects mainly at high oscillation frequencies. The principal organization of the neural networks underlying these control systems could be derived from the characteristic features of the responses to the different stimulus conditions. The input to the model circuits responsible for the characteristic sensitivity of the SF-system to small-field and relative motion is provided by retinotopic arrays of local movement detectors. The movement detectors are integrated by a large-field element, the output cell of the network. The synapses between the detectors and the output cells have nonlinear transmission characteristics. Another type of large-field elements (pool cells) which respond to motion in front of both eyes and have characteristic direction selectivities are assumed to interact with the local movement detector channels by inhibitory synapses of the shunting type, before the movement detectors are integrated by the output cells. The properties of the LF-system can be accounted for by similar model circuits which, however, differ with respect to the transmission characteristic of the synapses between the movement detectors and the output cell; moreover, their pool cells are only monocular. This type of network, however, is not necessary to account for the functional properties of the LF-system. Instead, intrinsic properties of single neurons may be sufficient. Computer simulations of the postulated mechanisms of the SF-and LF-system reveal that these can account for the specific features of the behavioral responses under quite different conditions of coherent large-field motion and relative motion of different pattern segments.     

Body movements during the off-ice execution of back spins in figure skating

Using an optoelectronic motion capture system, we quantitatively assessed the arrangement of body segments and the displacement of the horizontal projection of the center of mass (CM) in seven skaters performing off-ice back spins on a rotating device (spinner). The position of the CM at the beginning of the spins was not a determining factor, but its rapid stabilization towards the center of the spinner, together with the achievement of a stable arrangement of trunk and limbs, was crucial to get the dynamic equilibrium, necessary for a lasting performance. At full spinning, however, there was an indicative variety of individual body postures. A final deceleration, associable with the loss of body equilibrium, was detected in the last spin of most of skaters.In conclusion, the current investigation demonstrated that the off-ice execution of back spin, a critical movement of ice skating, can be measured in laboratory, thus providing quantitative information to both the skaters and the coaches. The analysis is not invasive, and it may be proposed also for longitudinal evaluations of skating and postural training.