Autotag: A tool for creating structured document collections from printed materials

Today\u27s optical character recognition (OCR) devices ordinarily are not capable of delimiting or marking up specific structural information about the document such as the title, its authors, and titles of sections. Such information appears in the OCR device output, but would require a human to go through the output to locate the information. This type of information is highly useful for information retrieval (IR), allowing users much more flexibility in making queries of a retrieval system. This thesis will describe the design, implementation, and evaluation of a software system called Autotag. This system will automatically markup structural information in OCR-generated text. It will also establish a mapping between objects in page images and their corresponding ASCII representation. This mapping can then be used to design flexible image-based interfaces for information retrieval related applications

Seed‐to‐Seedling Transitions Exhibit Distance‐Dependent Mortality but No Strong Spacing Effects in a Neotropical Forest

Patterns of seed dispersal and seed mortality influence the spatial structure of plant communities and the local coexistence of competing species. Most seeds are dispersed in proximity to the parent tree, where mortality is also expected to be the highest, because of competition with siblings or the attraction of natural enemies. Whereas distance‐dependent mortality in the seed‐to‐seedling transition was often observed in tropical forests, few studies have attempted to estimate the shape of the survival‐distance curves, which determines whether the peak of seedling establishment occurs away from the parent tree (Janzen–Connell pattern) or if the peak attenuates but remains at the parent location (Hubbell pattern). In this study, we inferred the probability density of seed dispersal and two stages of seedling establishment (new recruits, and seedlings 20 cm or taller) with distance for 24 tree species present in the 50‐ha Forest Dynamics Plot of Barro Colorado Island, Panama. Using data from seed traps, seedling survey quadrats, and tree‐census records spanning the 1988–2014 period, we fit hierarchical Bayesian models including parameters for tree fecundity, the shape of the dispersal kernel, and overdispersion of seed or seedling counts. We combined predictions from multiple dispersal kernels to obtain more robust inferences. We find that Hubbell patterns are the most common and Janzen–Connell patterns are very rare among those species; that distance‐dependent mortality may be stronger in the seed stage, in the early recruit stage, or comparable in both; and that species with larger seeds experience less overall mortality and less distance‐dependent mortality. Finally, we describe how this modeling approach could be extended at a community scale to include less abundant species

Counting niches: Abundance- by- trait patterns reveal niche partitioning in a Neotropical forest

Tropical forests challenge us to understand biodiversity, as numerous seemingly similar species persist on only a handful of shared resources. Recent ecological theory posits that biodiversity is sustained by a combination of species differences reducing interspecific competition and species similarities increasing time to competitive exclusion. Together, these mechanisms counterintuitively predict that competing species should cluster by traits, in contrast with traditional expectations of trait overdispersion. Here, we show for the first time that trees in a tropical forest exhibit a clustering pattern. In a 50- ha plot on Barro Colorado Island in Panama, species abundances exhibit clusters in two traits connected to light capture strategy, suggesting that competition for light structures community composition. Notably, we find four clusters by maximum height, quantitatively supporting the classical grouping of Neotropical woody plants into shrubs, understory, midstory, and canopy layers.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/155460/1/ecy3019.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/155460/2/ecy3019-sup-0001-AppendixS1.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/155460/3/ecy3019_am.pd

Functional Traits of Tropical Trees and Lianas Explain Spatial Structure across Multiple Scales

Dispersal and density dependence are major determinants of spatial structure, population dynamics and coexistence for tropical forest plants. However, because these two processes can jointly influence spatial structure at similar scales, analysing spatial patterns to separate and quantify them is often difficult. Species functional traits can be useful indicators of dispersal and density dependence. However, few methods exist for linking functional traits to quantitative estimates of these processes that can be compared across multiple species. We analysed static spatial patterns of woody plant populations in the 50 ha Forest Dynamics Plot on Barro Colorado Island, Panama with methods that distinguished scale‐specific differences in species aggregation. We then tested how these differences related to seven functional traits: growth form, dispersal syndrome, tree canopy layer, adult stature, seed mass, wood density and shade tolerance. Next, we fit analytically tractable spatial moment models to the observed spatial structure of species characterized by similar trait values, which allowed us to estimate relationships of functional traits with the spatial scale of dispersal, and the spatial scale and intensity of negative density dependence. Our results confirm that lianas are more aggregated than trees, and exhibit increased aggregation within canopy gaps. For trees, increased seed mass, wood density and shade tolerance were associated with less intense negative density dependence, while higher canopy layers and increased stature were associated with decreased aggregation and better dispersal. Spatial structure for trees was also strongly determined by dispersal syndrome. Averaged across all spatial scales, zoochory was more effective than wind dispersal, which was more effective than explosive dispersal. However, at intermediate scales, zoochory was associated with more aggregation than wind dispersal, potentially because of differences in short‐distance dispersal and the intensity of negative density dependence. Synthesis. We develop new tools for identifying significant associations between functional traits and spatial structure, and for linking these associations to quantitative estimates of dispersal scale and the strength and scale of density dependence. Our results help clarify how these processes influence woody plant species on Barro Colorado, and demonstrate how these tools can be applied to other sites and systems

Tree Species Vary Widely in Their Tolerance for Liana Infestation: A Case Study of Differential Host Response to Generalist Parasites

Lianas are structural parasites of trees and reduce individual host tree growth, survival and fecundity. Thus, liana infestation is expected to affect tree population growth rates, with potentially different effects in different species depending on the frequency of liana infestation and the impact of liana infestation on population growth rates. Previous studies have documented the myriad negative effects of lianas on trees and variation in liana infestation among tree species; however, no study has quantified the impact of liana infestation on individual tree species population growth rates. Lianas are increasing in abundance in multiple Neotropical sites, which may have profound consequences for tree species composition if lianas differentially affect host tree species population growth. Here, we use long‐term data to evaluate the effects of liana infestation on the reproduction, growth, survival and ultimately population growth rates of dozens of tree species from Barro Colorado Island, Panama. We then test whether liana infestation affects tree species differentially with respect to two axes of life‐history variation: adult stature and position along the fast–slow axis, a measure of shade tolerance. Liana infestation decreased tree growth, survival and reproduction, with the strongest effects on survival in fast‐growing, light‐demanding species and on reproduction in large‐statured species. In combination, these effects reduced tree population growth rates such that liana‐infested populations declined by an average of 1.4% annually relative to conspecific liana‐free populations. The reduction in population growth rates was greatest among fast‐growing species and smaller in slow‐growing species. Synthesis. Our results demonstrate that liana infestation has strong negative effects on tree population growth rates, which vary systematically among tree species with tree life history. The finding that liana infestation is more harmful to fast‐growing tree species appears to be at odds with the general expectations in the literature. We propose that this is likely due to survivorship bias, as infestation greatly decreases survival in fast‐growing species such that the observable sample is biased towards those that survived and liana‐free. In combination with data on how tree species vary in liana infestation rates, these results provide a basis for predicting the impacts of changes in liana abundance on tree species composition

Activation of the beta interferon promoter by paramyxoviruses in the absence of virus protein synthesis

Conflicting reports exist regarding the requirement for virus replication in interferon (IFN) induction by paramyxoviruses. Our previous work has demonstrated that pathogen-associated molecular patterns capable of activating the IFN-induction cascade are not normally generated during virus replication, but are associated instead with the presence of defective interfering (DI) viruses. We demonstrate here that DIs of paramyxoviruses, including parainfluenza virus 5, mumps virus and Sendai virus, can activate the IFN-induction cascade and the IFN-β promoter in the absence of virus protein synthesis. As virus protein synthesis is an absolute requirement for paramyxovirus genome replication, our results indicate that these DI viruses do not require replication to activate the IFN-induction cascade

Vibrissal growth parameters of southern elephant seals Mirounga leonina : obtaining fine-scale, time-based stable isotope data

Stable isotopes provide a powerful, indirect approach to assess the trophic ecology of individuals on a spatial and temporally integrated basis (especially when combined with telemetry). However, using stable isotopes requires accurate, species-specific quantification of the period of biomolecule deposition in the sampled tissue. Sequentially sampled vibrissae (whiskers) provide a chronology of biogeochemical data, although knowledge of the vibrissal growth is required for temporal interpretations. We sampled vibrissae from southern elephant seals (Mirounga leonina, hereafter SES) at Marion Island, southern Indian Ocean to address the following aims: define the prevalence and timing of their vibrissal replacement; determine the vibrissal regrowth rate and temporal resolution of isotopic data captured along the length of sequentially sampled vibrissae; and explore assumptions regarding their vibrissal growth. Contrary to the previously described asynchronous vibrissal shedding pattern of SES, 71.1 % of individuals displayed vibrissal shedding during the annual pelage moult. Furthermore, vibrissa growth ceased once the asymptotic length was reached, and the vibrissae were retained before being replaced. Vibrissae with known growth histories were re-sampled at multiple, known intervals to control for unknown growth starting dates. Vibrissae followed a von Bertalanffy growth function [ ( )( ) ], as the growth rate decreased near the asymptotic length. The resolution of the isotopic data obtainable per 2 mm section ranged from 3.5 days at the vibrissal tip to > 40 days at the base. Using these defined growth rates and shedding patterns, researchers can prudently apply timestamps to stable isotope values along vibrissae.The South African Department of Science and Technology, through the National Research Foundation (NRF), within the South African National Antarctic Programme (SANAP).http://www.int-res.com/journals/meps/meps-home2017-11-30hb2016Mammal Research InstituteZoology and Entomolog

Tradeoffs in jet inlet design: a historical perspective

The design of the inlet(s) is one of the most demanding tasks of the development process of any gas turbine-powered aircraft. This is mainly due to the multi-objective and multidisciplinary nature of the exercise. The solution is generally a compromise between a number of conflicting goals and these conflicts are the subject of the present paper. We look into how these design tradeoffs have been reflected in the actual inlet designs over the years and how the emphasis has shifted from one driver to another. We also review some of the relevant developments of the jet age in aerodynamics and design and manufacturing technology and we examine how they have influenced and informed inlet design decision