Life-cycle assessment of redwood decking in the United States with a comparison to three other decking materials

Science.gov (United States)

R. Bergman; H. Sup-Han; E. Oneil; I. Eastin

2013-01-01

The goal of the study was to conduct a life-cycle inventory (LCI) of California redwood (Sequoia sempervirens) decking that would quantify the critical environmental impacts of decking from cradle to grave. Using that LCI data, a life-cycle assessment (LCA) was produced for redwood decking. The results were used to compare the environmental footprint...

Rangewide Genetic Variation in Coast Redwood Populations at a Chloroplast Microsatellite Locus

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Chris Brinegar

2012-01-01

Old growth and second growth populations of coast redwood (Sequoia sempervirens) were sampled at 10 locations throughout its range and analyzed at a highly variable chloroplast microsatellite locus. Very low FST values indicated that there was no significant genetic differentiation between adjacent old growth and second growth populations at each location. Genetic...

Management practices eelated to the Restoration of old dorest characteristics in coast redwood forests

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Gregory A. Guisti

2012-01-01

A standardized, interactive, interview process was used with practicing Registered Professional Foresters asking a suite of questions to ascertain their management approaches to coast redwood (Sequoia sempervirens [D. Don] Endl.) stands that could best be transferred to other projects and lands interested in recruiting older forest...

Sudden Oak Death in redwood forests: vegetation dynamics in the wake of tanoak decline

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Benjamin Ramage; Kevin O’Hara

2010-01-01

Numerous lines of inquiry have concluded that tanoak (Lithocarpus densiflorus) will continue to experience drastic population declines and may even disappear entirely from redwood (Sequoia sempervirens) forests as a result of the exotic disease sudden oak death (SOD) (Maloney and others 2005, McPherson and others 2005,...

Millennium-scale crossdating and inter-annual climate sensitivities of standing California redwoods.

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Carroll, Allyson L; Sillett, Stephen C; Kramer, Russell D

2014-01-01

Extremely decay-resistant wood and fire-resistant bark allow California's redwoods to accumulate millennia of annual growth rings that can be useful in biological research. Whereas tree rings of Sequoiadendron giganteum (SEGI) helped formalize the study of dendrochronology and the principle of crossdating, those of Sequoia sempervirens (SESE) have proven much more difficult to decipher, greatly limiting dendroclimatic and other investigations of this species. We overcame these problems by climbing standing trees and coring trunks at multiple heights in 14 old-growth forest locations across California. Overall, we sampled 1,466 series with 483,712 annual rings from 120 trees and were able to crossdate 83% of SESE compared to 99% of SEGI rings. Standard and residual tree-ring chronologies spanning up to 1,685 years for SESE and 1,538 years for SEGI were created for each location to evaluate crossdating and to examine correlations between annual growth and climate. We used monthly values of temperature, precipitation, and drought severity as well as summer cloudiness to quantify potential drivers of inter-annual growth variation over century-long time series at each location. SESE chronologies exhibited a latitudinal gradient of climate sensitivities, contrasting cooler northern rainforests and warmer, drier southern forests. Radial growth increased with decreasing summer cloudiness in northern rainforests and a central SESE location. The strongest dendroclimatic relationship occurred in our southernmost SESE location, where radial growth correlated negatively with dry summer conditions and exhibited responses to historic fires. SEGI chronologies showed negative correlations with June temperature and positive correlations with previous October precipitation. More work is needed to understand quantitative relationships between SEGI radial growth and moisture availability, particularly snowmelt. Tree-ring chronologies developed here for both redwood species have

Millennium-scale crossdating and inter-annual climate sensitivities of standing California redwoods.

Directory of Open Access Journals (Sweden)

Allyson L Carroll

Full Text Available Extremely decay-resistant wood and fire-resistant bark allow California's redwoods to accumulate millennia of annual growth rings that can be useful in biological research. Whereas tree rings of Sequoiadendron giganteum (SEGI helped formalize the study of dendrochronology and the principle of crossdating, those of Sequoia sempervirens (SESE have proven much more difficult to decipher, greatly limiting dendroclimatic and other investigations of this species. We overcame these problems by climbing standing trees and coring trunks at multiple heights in 14 old-growth forest locations across California. Overall, we sampled 1,466 series with 483,712 annual rings from 120 trees and were able to crossdate 83% of SESE compared to 99% of SEGI rings. Standard and residual tree-ring chronologies spanning up to 1,685 years for SESE and 1,538 years for SEGI were created for each location to evaluate crossdating and to examine correlations between annual growth and climate. We used monthly values of temperature, precipitation, and drought severity as well as summer cloudiness to quantify potential drivers of inter-annual growth variation over century-long time series at each location. SESE chronologies exhibited a latitudinal gradient of climate sensitivities, contrasting cooler northern rainforests and warmer, drier southern forests. Radial growth increased with decreasing summer cloudiness in northern rainforests and a central SESE location. The strongest dendroclimatic relationship occurred in our southernmost SESE location, where radial growth correlated negatively with dry summer conditions and exhibited responses to historic fires. SEGI chronologies showed negative correlations with June temperature and positive correlations with previous October precipitation. More work is needed to understand quantitative relationships between SEGI radial growth and moisture availability, particularly snowmelt. Tree-ring chronologies developed here for both redwood

Sudden Oak Death-Induced Tanoak Mortality in Coast Redwood Forests: Current and Predicted Impacts to Stand Structure

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Kevin L. O’Hara

2010-08-01

Full Text Available Tanoak (Notholithocarpus densiflorus syn. Lithocarpus densiflorus is one of the most widespread and abundant associates of coast redwood (Sequoia sempervirens, but little is known about the structural relationships between these two species. Knowledge of such relationships is essential for a thorough understanding of the impacts of sudden oak death (caused by the exotic pathogen Phytophthora ramorum, which is currently decimating tanoak populations throughout the redwood range. In this study, we utilized a stratified plot design and a stand reconstruction technique to assess structural impacts, at present and in the future, of this emerging disease. We found that residual trees in diseased plots were more aggregated than trees in unaffected plots, and we predicted that the loss of tanoak will lead to the following short-term changes: greater average diameter, height, height-to-live-crown, and crown length, as well as an increase in average nearest neighbor differences for diameter, height, and crown length. In addition, plots lacking tanoak (living or dead—as compared to plots with tanoak—exhibited greater average diameter and increased nearest neighbor differences with regard to diameter, height, and crown length. We also conducted a preliminary exploration of how sudden oak death-induced structural changes compare with typical old-growth characteristics, and how this disease may affect the structure of old-growth forests.

Physiology and growth of redwood and Douglas-fir planted after variable density retention outside redwood’s range

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Lucy Kerhoulas; Nicholas Kerhoulas; Wade Polda; John-Pascal Berrill

2017-01-01

Reforestation following timber harvests is an important topic throughout the coast redwood (Sequoia sempervirens (D. Don) Endl.) range. Furthermore, as drought-induced mortality spreads across many of California’s forests, it is important to understand how physiology and stand structure influence reforestation success. Finally, as climate...

Remote measurement of canopy water content in giant sequoias (Sequoiadendron giganteum) during drought

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Martin, Roberta E.; Asner, Gregory P.; Francis, Emily; Ambrose, Anthony; Baxter, Wendy; Das, Adrian J.; Vaughn, Nicolas R.; Paz-Kagan, Tarin; Dawson, Todd E.; Nydick, Koren R.; Stephenson, Nathan L.

2018-01-01

California experienced severe drought from 2012 to 2016, and there were visible changes in the forest canopy throughout the State. In 2014, unprecedented foliage dieback was recorded in giant sequoia (Sequoiadendron giganteum) trees in Sequoia National Park, in the southern California Sierra Nevada mountains. Although visible changes in sequoia canopies can be recorded, biochemical and physiological responses to drought stress in giant sequoia canopies are not well understood. Ground-based measurements provide insight into the mechanisms of drought responses in trees, but are often limited to few individuals, especially in trees of tall stature such as giant sequoia. Recent studies demonstrate that remotely measured forest canopy water content (CWC) is a general indicator of canopy response to drought, but the underpinning leaf- to canopy-level causes of observed variation in CWC remain poorly understood. We combined field and airborne remote sensing measurements taken in 2015 and 2016 to assess the biophysical responses of giant sequoias to drought. In 49 study trees, CWC was related to leaf water potential, but not to the other foliar traits, suggesting that changes in CWC were made at whole-canopy rather than leaf scales. We found a non-random, spatially varying pattern in mapped CWC, with lower CWC values at lower elevation and along the outer edges of the groves. This pattern was also observed in empirical measurements of foliage dieback from the ground, and in mapped CWC across multiple sequoia groves in this region, supporting the hypothesis that drought stress is expressed in canopy-level changes in giant sequoias. The fact that we can clearly detect a relationship between CWC and foliage dieback, even without taking into account prior variability or new leaf growth, strongly suggests that remotely sensed CWC, and changes in CWC, are a useful measure of water stress in giant sequoia, and valuable for assessing and managing these iconic forests in drought.

Plant Uptake of Atmospheric Carbonyl Sulfide in Coast Redwood Forests

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Campbell, J. E.; Whelan, M. E.; Berry, J. A.; Hilton, T. W.; Zumkehr, A.; Stinecipher, J.; Lu, Y.; Kornfeld, A.; Seibt, U.; Dawson, T. E.; Montzka, S. A.; Baker, I. T.; Kulkarni, S.; Wang, Y.; Herndon, S. C.; Zahniser, M. S.; Commane, R.; Loik, M. E.

2017-12-01

The future resilience of coast redwoods (Sequoia sempervirens) is now of critical concern due to the detection of a 33% decline in California coastal fog over the 20th century. However, ecosystem-scale measurements of photosynthesis and stomatal conductance are challenging in coast redwood forests, making it difficult to anticipate the impacts of future changes in fog. To address this methodological problem, we explore coastal variations in atmospheric carbonyl sulfide (COS or OCS), which could potentially be used as a tracer of these ecosystem processes. We conducted atmospheric flask campaigns in coast redwood sites, sampling at surface heights and in the canopy ( 70 m), at the University of California Landels-Hill Big Creek Reserve and Big Basin State Park. We simulated COS atmosphere-biosphere exchange with a high-resolution 3-D model to interpret these data. Flask measurements indicated a persistent daytime drawdown between the coast and the downwind forest (45 ± 6 ppt COS) that is consistent with the expected relationship between COS plant uptake, stomatal conductance, and gross primary production. Other sources and sinks of COS that could introduce noise to the COS tracer technique (soils, anthropogenic activity, nocturnal plant uptake, and surface hydrolysis on leaves) are likely to be small relative to daytime COS plant uptake. These results suggest that COS measurements may be useful for making ecosystem-scale estimates of carbon, water, and energy exchange in coast redwood forests.

Structure and Composition of Old-Growth and Unmanaged Second-Growth Riparian Forests at Redwood National Park, USA

Directory of Open Access Journals (Sweden)

Christopher R. Keyes

2014-02-01

Full Text Available Restoration of second-growth riparian stands has become an important issue for managers of redwood (Sequoia sempervirens [D. Don] Endl. forest reserves. Identifying differences between old-growth and second-growth forest vegetation is a necessary step in evaluating restoration needs and targets. The objective of this study was to characterize and contrast vegetation structure and composition in old-growth and unmanaged second-growth riparian forests in adjacent, geomorphologically similar watersheds at Redwood National Park. In the old-growth, redwood was the dominant overstory species in terms of stem density, basal area, and importance values. Second-growth was dominated by red alder (Alnus rubra Bong., Douglas-fir (Pseudotsuga menziesii [Mirbel] Franco, and redwood. Understory species were similar in both forests, with several key differences: Oxalis oregana Nutt. and Trillium ovatum Pursh had greater importance values in the old-growth, and Vaccinium parvifolium Sm., Dryopteris spp. and sedges Carex spp. had greater importance values in the second-growth. Notable differences in structure and composition suggest that restoration practices such as thinning could expedite the acquisition of old-growth characteristics in second-growth riparian forests.

'Pygmy' old-growth redwood characteristics on an edaphic ecotone in Mendocino County, California

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Will Russell; Suzie. Woolhouse

2012-01-01

The 'pygmy forest' is a specialized community that is adapted to highly acidic, hydrophobic, nutrient deprived soils, and exists in pockets within the coast redwood forest in Mendocino County. While coast redwood is known as an exceptionally tall tree, stunted trees exhibit unusual growth-forms on pygmy soils. We used a stratified random sampling procedure to...

Coping with gravity: the foliar water relations of giant sequoia.

Science.gov (United States)

Williams, Cameron B; Reese Næsborg, Rikke; Dawson, Todd E

2017-10-01

In tall trees, the mechanisms by which foliage maintains sufficient turgor pressure and water content against height-related constraints remain poorly understood. Pressure-volume curves generated from leafy shoots collected crown-wide from 12 large Sequoiadendron giganteum (Lindley) J. Buchholz (giant sequoia) trees provided mechanistic insights into how the components of water potential vary with height in tree and over time. The turgor loss point (TLP) decreased with height at a rate indistinguishable from the gravitational potential gradient and was controlled by changes in tissue osmotica. For all measured shoots, total relative water content at the TLP remained above 75%. This high value has been suggested to help leaves avoid precipitous declines in leaf-level physiological function, and in giant sequoia was controlled by both tissue elasticity and the balance of water between apoplasm and symplasm. Hydraulic capacitance decreased only slightly with height, but importantly this parameter was nearly double in value to that reported for other tree species. Total water storage capacity also decreased with height, but this trend essentially disappeared when considering only water available within the typical range of water potentials experienced by giant sequoia. From summer to fall measurement periods we did not observe osmotic adjustment that would depress the TLP. Instead we observed a proportional shift of water into less mobile apoplastic compartments leading to a reduction in hydraulic capacitance. This collection of foliar traits allows giant sequoia to routinely, but safely, operate close to its TLP, and suggests that gravity plays a major role in the water relations of Earth's largest tree species. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Coast redwood science symposium—2016: Past successes and future direction

Science.gov (United States)

Richard B. Standiford; Yana Valachovic

2017-01-01

There is no more iconic tree or more closely watched forest ecosystem than coast redwood. With its limited range and high value, the coast redwood forest is a microcosm of many of the emerging science and management issues facing today’s forested landscapes. As new information is collected and new management approaches and treatments tried, it is critical that policies...

Air pollution effects on giant sequoia ecosystems.

Science.gov (United States)

P.R. Miller; Nancy Grulke; K.W. Stolte

1994-01-01

Giant sequoia [Sequoiadendron giganteum (Lindl.) Buchholz] groves are found entirely within the Sierra Nevada mixed-conifer type. Several of its companion tree species, mainly ponderosa pine (Pinus ponderosa Dougl. ex Laws.) and Jeffrey pine (P. jeffreyi Grev. & Balf.), show foliar injury after...

Reference conditions for old-growth redwood restoration on alluvial flats

Science.gov (United States)

Christa M. Dagley; John-Pascal. Berrill

2012-01-01

We quantified structural attributes in three alluvial flat old-growth coast redwood stands. Tree size parameters and occurrences of distinctive features (e.g., burls, goose pens) were similar between stands. Occurrence of distinctive features was greater among larger trees. Tree sizefrequency distributions conformed to a reverse-J diameter distribution. The range of...

Black bear damage to northwestern conifers in California: a review

Science.gov (United States)

Kenneth O. Fulgham; Dennis Hosack

2017-01-01

A total of 789 black bear damaged trees were investigate over a multi-year period on 14 different study sites chosen on lands of four participating timber companies. The sites ranged from 30 to 50 years of age. Four different conifer species were found to have black bear damage: coastal redwood (Sequoia sempervirens (D. Don) Endl.), Douglas-fir (...

Leaf to landscape responses of giant sequoia to hotter drought: An introduction and synthesis for the special section

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Nydick, Koren R.; Stephenson, Nathan L.; Ambrose, Anthony R.; Asner, Gregory P.; Baxter, Wendy L.; Das, Adrian J.; Dawson, Todd E.; Martin, Roberta E.; Paz-Kagan, Tarin

2018-01-01

Hotter droughts are becoming more common as climate change progresses, and they may already have caused instances of forest dieback on all forested continents. Learning from hotter droughts, including where on the landscape forests are more or less vulnerable to these events, is critical to help resource managers proactively prepare for the future. As part of our Leaf to Landscape Project, we measured the response of giant sequoia, the world’s largest tree species, to the extreme 2012–2016 hotter drought in California. The project integrated leaf-level physiology measurements, crown-level foliage dieback surveys, and remotely sensed canopy water content (CWC) to shed light on mechanisms and spatial patterns in drought response. Here we summarize initial findings, present a conceptual model of drought response, and discuss management implications; details are presented in the other four articles of the special section on Giant Sequoias and Drought. Giant sequoias exhibited both leaf- and canopy-level responses that were effective in protecting whole-tree hydraulic integrity for the vast majority of individual sequoias. Very few giant sequoias died during the drought compared to other mixed conifer tree species; however, the magnitude of sequoia drought response varied across the landscape. This variability was partially explained by local site characteristics, including variables related to site water balance. We found that low CWC is an indicator of recent foliage dieback, which occurs when stress levels are high enough that leaf-level adjustments alone are insufficient for giant sequoias to maintain hydraulic integrity. CWC or change in CWC may be useful indicators of drought stress that reveal patterns of vulnerability to future hotter droughts. Future work will measure recovery from the drought and strengthen our ability to interpret CWC maps. Our ultimate goal is to produce giant sequoia vulnerability maps to help target management actions, such as

76 FR 75558 - Environmental Impact Statement for Restoration of the Mariposa Grove of Giant Sequoias, Yosemite...

Science.gov (United States)

2011-12-02

... tree. Fire plays an important role in giant sequoia ecology, creating canopy openings and releasing soil nutrients needed for seedling establishment. Fire scars on the trees indicate that fires occurred... and sites within the Grove include the parking areas, gift shop, ticket booth, tram staging area...

Patterns and correlates of giant sequoia foliage dieback during California’s 2012–2016 hotter drought

Science.gov (United States)

Stephenson, Nathan L.; Das, Adrian J.; Ampersee, Nicholas J.; Cahill, Kathleen G.; Caprio, Anthony C.; Sanders, John E.; Williams, A. Park

2018-01-01

Hotter droughts – droughts in which unusually high temperatures exacerbate the effects of low precipitation – are expected to increase in frequency and severity in coming decades, challenging scientists and managers to identify which parts of forested landscapes may be most vulnerable. In 2014, in the middle of California’s historically unprecedented 2012–2016 hotter drought, we noticed apparently drought-induced foliage dieback in giant sequoias (Sequoiadendron giganteum Lindl. [Buchholz]) in Sequoia and Kings Canyon national parks, California. Characteristics of the dieback were consistent with a controlled process of drought-induced senescence: younger (distal) shoots remained green while older (proximal) shoots were preferentially shed. As part of an ongoing interdisciplinary effort to understand and map sequoia vulnerability to hotter droughts, we reviewed historical records for evidence of previous foliage dieback events, surveyed dieback along trail corridors in eight sequoia groves, and analyzed tree-ring data from a high- and a low-foliage-dieback area. In sharp contrast to the greatly elevated mortality of other coniferous species found at low and middle elevations, we estimate that <1% of sequoias died during the drought. Foliage dieback was notably elevated in 2014 – the most severe single drought year in our 122-year record – but much lower in subsequent years. We found no historical records of similar foliage dieback during previous droughts. Dieback in 2014 was highly variable both within and among groves, ranging from virtually no dieback in some areas to nearly 50% in others. Dieback was highest (1) at low elevations, probably due to higher temperatures, reduced snowpack, and earlier snowmelt; (2) in areas of low adult sequoia densities, which likely reflect intrinsically more stressful sites; and (3) on steep slopes, probably reflecting reduced water availability. Average sequoia ring widths were narrower at the high-dieback than the

Changes in gas exchange characteristics during the life span of giant sequoia: Implications for response to current and future concentrations of atmospheric ozone

Energy Technology Data Exchange (ETDEWEB)

Grulke, N.E.; Miller, P.R. (USDA Forest Service, Riverside, CA (United States))

Native stands of giant sequoia are being exposed to relatively high concentrations of atmospheric ozone produced in urban and agricultural areas upwind. The expected change in environmental conditions over the next 100 y is likely to be unprecendented in the life span (ca 2,500 y) of giant sequoia. Changes in the physiological responses of three age classes of giant sequoia (current year, 12 y and 25 y) to different concentrations of ozone were determined, and age-related differences in sensitivity to pollutants were assessed by examining physiological changes (gas exchange, water use efficiency) across the life span of giant sequoia. The CO[sub 2] exchange rate (CER) was greater in current year (12.1 [mu]mol CO[sub 2]/m[sup 2]s) and 2 year old seedlings (4.8 [mu]mol CO[sub 2]/m[sup 2]s) than in all older trees (average of 3.0 [mu]mol CO[sub 2]/m[sup 2]s). Dark respiration was highest for current year seedlings and was increased twofold in symptotic individuals exposed to elevated ozone concentrations. Stomatal conductance was greater in current-year and 2 year old seedlings (335 and 200 mmol H[sub 2]O/m[sup 2]s), respectively, than in all older trees (50 mmol H[sub 2]O/m[sup 2]s), indicating that the ozone concentration in substomatol cavities is higher in young seedlings than in older trees. Significant changes in water use efficiency occurred in trees between ages 5 and 20 years. It is concluded that giant sequoia seedlings are sensitive to atmospheric ozone until they are ca 5 y old. Low conductance, high water use efficiency, and compact mesophyll all contribute to a natural ozone tolerance, or defense, or both, in foliage of older trees. 11 refs., 1 fig., 1 tab.

A natural resource condition assessment for Sequoia and Kings Canyon National Parks: Appendix 11a: giant sequoias

Science.gov (United States)

York, Robert A.; Stephenson, Nathan L.; Meyer, Marc; Hanna, Steve; Tadashi, Moody; Caprio, Anthony C.; Battles, John J.

2013-01-01

For natural resource managers in the southern Sierra Nevada, giant sequoia requires very little introduction. It receives great attention as an icon of western forests and as a common namesake with the areas where it occurs. While it is a single component of a very complex system, its attention in this assessment and in general is well deserved. Giant sequoia is one of the few "destination species" that attracts a wide swath of the public by nature of it simply being present. It draws people, who otherwise may not travel, to a natural environment. The result is an expansion of the public’s sense of natural resource stewardship. Because park managers could not achieve their mission without public support, this fostering role of giant sequoia is critical for park natural resources and is important for natural resources in general. Despite its social relevance and physical size, we re-emphasize here that the giant sequoia resource is a relatively small component of the ecosystems of the southern Sierra Nevada. As is the case with all of the resources assessed in the NRCA, we focus on giant sequoia with the understanding that other resources will be considered simultaneously when evaluating management decisions that impact giant sequoia. While we attempt to explicitly address the interaction of giant sequoia with other resources and stressors, we also realize that ultimately managers will integrate much more information than is presented here when making decisions that influence giant sequoia. The autecology and management issues surrounding giant sequoia have been thoroughly reviewed elsewhere (Harvey et al. 1980, Aune 1994, Stephenson 1996). Stephenson (1996), in particular, should be reviewed when considering any management decisions that potentially impact giant sequoia. For those who may not be familiar with giant sequoia ecology, a summary of basic information is provided in a table below. In some parts of this assessment, we reproduce text from Stephenson�

Characterizing large strain crush response of redwood

International Nuclear Information System (INIS)

Cramer, S.M.; Hermanson, J.C.

1996-12-01

Containers for the transportation of hazardous and radioactive materials incorporate redwood in impact limiters. Redwood is an excellent energy absorber, but only the most rudimentary information exists on its crush properties. The objectives of the study were to fill the information gap by collecting triaxial load-deformation data for redwood; to use these data to characterize redwood crush, assess current wood failure theories, provide developments toward a complete stress-strain theory for redwood; and to review the literature on strain-rate effects on redwood crush performance. The load-deformation responses of redwood at temperature conditions corresponding to ambient (70 degrees F), 150 degrees F, and -20 degrees F conditions were measured in approximately 100 confined compression tests for crush levels leading to material densification. Data analysis provided a more complete description of redwood crush performance and a basis for assessing proposed general orthotropic stress-strain relationships for redwood. A review of existing literature indicated that strain-rate effects cause at most a 20 percent increase in crush stress parallel to grain

Managing redwood ecosystems using Sudden Oak Death as a silvicultural tool

Science.gov (United States)

Frederick D. Euphrat

2015-01-01

In response to the wave of sudden oak death (SOD), caused by Phytophthora ramorum, sweeping the redwood forest ecosystems of California's North Coast, the role of foresters and other ecosystem managers is being tested. On Bear Flat Tree Farm, near Healdsburg, California, Forest, Soil & Water, Inc. (FSW) has conducted a multi-year,...

Five years of monitoring infection and mortality in redwood tanoak forests

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Richard C. Cobb; Shannon C. Lynch; Ross K. Meentemeyer; David M. Rizzo

2008-01-01

Rates of disease incidence and tree mortality in redwood-tanoak forests were determined by repeated sampling across a system of 120 plots at five long-term research sites from 2001 through 2006. Plots were located within the known geographic area of Phytophthora ramorum in California, ranging from Monterey to Sonoma counties. All overstory species...

Tractor-logging costs and production in old-growth redwood forests

Science.gov (United States)

Kenneth N. Boe

1963-01-01

A cost accounting analysis of full-scale logging operations in old-growth redwood during 2 years revealed that it cost $12.24 per M bd. ft. (gross Scribner log scale) to get logs on trucks. Road development costs averaged another $5.19 per M bd. ft. Felling-bucking production was calculated by average tree d.b.h. Both skidding and loading outputs per hour were...

The influence of prefire tree growth and crown condition on postfire mortality of sugar pine following prescribed fire in Sequoia National Park

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Nesmith, Jonathan C. B.; Das, Adrian J.; O'Hara, Kevin L.; van Mantgem, Phillip J.

2015-01-01

Tree mortality is a vital component of forest management in the context of prescribed fires; however, few studies have examined the effect of prefire tree health on postfire mortality. This is especially relevant for sugar pine (Pinus lambertiana Douglas), a species experiencing population declines due to a suite of anthropogenic factors. Using data from an old-growth mixed-conifer forest in Sequoia National Park, we evaluated the effects of fire, tree size, prefire radial growth, and crown condition on postfire mortality. Models based only on tree size and measures of fire damage were compared with models that included tree size, fire damage, and prefire tree health (e.g., measures of prefire tree radial growth or crown condition). Immediately following the fire, the inclusion of different metrics of prefire tree health produced variable improvements over the models that included only tree size and measures of fire damage, as models that included measures of crown condition performed better than fire-only models, but models that included measures of prefire radial growth did not perform better. However, 5 years following the fire, sugar pine mortality was best predicted by models that included measures of both fire damage and prefire tree health, specifically, diameter at breast height (DBH, 1.37 m), crown scorch, 30-year mean growth, and the number of sharp declines in growth over a 30-year period. This suggests that factors that influence prefire tree health (e.g., drought, competition, pathogens, etc.) may partially determine postfire mortality, especially when accounting for delayed mortality following fire.

Landscape-scale variation in canopy water content of giant sequoias during drought

Science.gov (United States)

Paz-Kagan, Tarin; Vaughn, Nicolas R.; Martin, Roberta E.; Brodrick, Philip G.; Stephenson, Nathan L.; Das, Adrian; Nydick, Koren R.; Asner, Gregory P.

2018-01-01

Recent drought (2012–2016) caused unprecedented foliage dieback in giant sequoias (Sequoiadendron giganteum), a species endemic to the western slope of the southern Sierra Nevada in central California. As part of an effort to understand and map sequoia response to droughts, we studied the patterns of remotely sensed canopy water content (CWC), both within and among sequoia groves in two successive years during the drought period (2015 and 2016). Our aims were: (1) to quantify giant sequoia responses to severe drought stress at a landscape scale using CWC as an indicator of crown foliage status, and (2) to estimate the effect of environmental correlates that mediate CWC change within and among giant sequoia groves. We utilized airborne high fidelity imaging spectroscopy (HiFIS) and light detection and ranging (LiDAR) data from the Carnegie Airborne Observatory to assess giant sequoia foliage status during 2015 and 2016 of the 2012–2016 droughts. A series of statistical models were generated to classify giant sequoias and to map their location in Sequoia and Kings Canyon National Parks (SEKI) and vicinity. We explored the environmental correlates and the spatial patterns of CWC change at the landscape scale. The mapped CWC was highly variable throughout the landscape during the two observation years, and proved to be most closely related to geological substrates, topography, and site-specific water balance. While there was an overall net gain in sequoia CWC between 2015 and 2016, certain locations (lower elevations, steeper slopes, areas more distant from surface water sources, and areas with greater climate water deficit) showed CWC losses. In addition, we found greater CWC loss in shorter sequoias and those growing in areas with lower sequoia stem densities. Our results suggest that CWC change indicates sequoia response to droughts across landscapes. Long-term monitoring of giant sequoia CWC will likely be useful for modeling and predicting their population

The New Economies of the Redwood Region in the 21st Century

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William Stewart

2007-01-01

The redwood region of California has experienced a number of major land use changes over the past one hundred and fifty years. A review of recent economic trends in the redwood region suggests the emergence of three new themes. First, it appears that the transition from an old growth to a young growth redwood industry is essentially complete. Lower revenues and...

Roles of Fog and Topography in Redwood Forest Hydrology

Science.gov (United States)

Francis, E. J.; Asner, G. P.

2017-12-01

Spatial variability of water in forests is a function of both climatic gradients that control water inputs and topo-edaphic variation that determines the flows of water belowground, as well as interactions of climate with topography. Coastal redwood forests are hydrologically unique because they are influenced by coastal low clouds, or fog, that is advected onto land by a strong coastal-to-inland temperature difference. Where fog intersects the land surface, annual water inputs from summer fog drip can be greater than that of winter rainfall. In this study, we take advantage of mapped spatial gradients in forest canopy water storage, topography, and fog cover in California to better understand the roles and interactions of fog and topography in the hydrology of redwood forests. We test a conceptual model of redwood forest hydrology with measurements of canopy water content derived from high-resolution airborne imaging spectroscopy, topographic variables derived from high-resolution LiDAR data, and fog cover maps derived from NASA MODIS data. Landscape-level results provide insight into hydrological processes within redwood forests, and cross-site analyses shed light on their generality.

Rare Plants of the Redwood Forest and Forest Management Effects

Science.gov (United States)

Teresa Sholars; Clare Golec

2007-01-01

Coast redwood forests are predominantly a timber managed habitat type, subjected to repeated disturbances and short rotation periods. What does this repeated disturbance mean for rare plants associated with the redwood forests? Rare plant persistence through forest management activities is influenced by many factors. Persistence of rare plants in a managed landscape is...

Magnetic record associated with tree ring density: Possible climate proxy

Czech Academy of Sciences Publication Activity Database

Kletetschka, Günther; Pruner, Petr; Venhodová, Daniela; Kadlec, Jaroslav

2007-01-01

Roč. 8, - (2007), s. 1-11 ISSN 1467-4866 Institutional research plan: CEZ:AV0Z3013912 Keywords : palaeo-climatic indicator * sequoia tree * magnetic properties Subject RIV: DB - Geology ; Mineralogy Impact factor: 1.842, year: 2007

Does water chemistry limit the distribution of New Zealand mud snails in Redwood National Park?

Science.gov (United States)

Vazquez, Ryan; Ward, Darren M.; Sepulveda, Adam

2016-01-01

New Zealand mud snails (NZMS) are exotic mollusks present in many waterways of the western United States. In 2009, NZMS were detected in Redwood Creek in Redwood National Park, CA. Although NZMS are noted for their ability to rapidly increase in abundance and colonize new areas, after more than 5 years in Redwood Creek, their distribution remains limited to a ca. 300 m reach. Recent literature suggests that low specific conductivity and environmental calcium can limit NZMS distribution. We conducted laboratory experiments, exposing NZMS collected from Redwood Creek to both natural waters and artificial treatment solutions, to determine if low conductivity and calcium concentration limit the distribution of NZMS in Redwood National Park. For natural water exposures, we held NZMS in water from their source location (conductivity 135 μS/cm, calcium 13 mg/L) or water from four other locations in the Redwood Creek watershed encompassing a range of conductivity (77–158 μS/cm) and calcium concentration (4 months) in the lowest conductivity waters from Redwood Creek and all but the lowest-conductivity treatment solutions, regardless of calcium concentration. However, reproductive output was very low in all natural waters and all low-calcium treatment solutions. Our results suggest that water chemistry may inhibit the spread of NZMS in Redwood National Park by reducing their reproductive output.

Aspen Characteristics - Sequoia National Forest [ds377

Data.gov (United States)

California Natural Resource Agency — The database represents point locations and associated stand assessment data collected within aspen stands in the Cannell Meadows Ranger District, Sequoia National...

Aspen Delineation - Sequoia National Forest [ds378

Data.gov (United States)

California Natural Resource Agency — The database represents delineations of aspen stands associated with stand assessment data (SEQUOIA_NF_PTS) collected in aspen stands in the Cannell Meadows Ranger...

Growth of 11 introduced tree species on selected forest sites in Hawaii

Science.gov (United States)

Michael G Buck; Roger H. Imoto

1982-01-01

Growth and volume data for trees on 25 plots reprsenting 11 introduced species in Hawaii were recorded during a 21-year period. Tree were measured at about 5-year intervals to determine overall growth and stand development. The sites selected were considered better-than-average in terms of elevation, amount of precipitation, and soil quality. Except for redwood, stands...

Northern California redwood forests provide important seasonal habitat for migrant bats

Science.gov (United States)

Theodore J. Weller; Craig A. Stricker

2012-01-01

Bats are known to roost in redwood forests year-round, but their activities outside the summer season are poorly understood. To improve understanding of the use of redwoods by resident and migrant bats, we conducted 74 mist net surveys between February 2008 and October 2010. Captures were dominated by Yuma myotis (M. yumanensis) in the summer and...

A Multiple Logistic Regression Model for Predicting the Development of Phytophthora ramorum symptoms in Tanoak (Lithocarpus densiflorus)

Science.gov (United States)

Mark Spencer; Kevin O' Hara

2007-01-01

Phytophthora ramorum attacks tanoak (Lithocarpus densiflorus) in California and Oregon. We present a stand-level study examining the presence of disease symptoms in individual stems. Working with data from four plots in redwood (Sequoia sempervirens)/tanoak forests in Marin County, and three plots in Mendocino...

Visual Impacts of Prescribed Burning on Mixed Conifer and Giant Sequoia Forests

Science.gov (United States)

Lin Cotton; Joe R. McBride

1987-01-01

Prescribed burning programs have evolved with little concern for the visual impact of burning and the potential prescribed burning can have in managing the forest scene. Recent criticisms by the public of the prescribed burning program at Sequoia National Park resulted in an outside review of the National Park fire management programs in Sequoia, Kings Canyon, and...

Biological and Management Implications of Fire-Pathogen Interactions in the Giant Sequoia Ecosystem

Science.gov (United States)

Douglas D. Piirto; John R. Parmeter; Fields W. Cobb; Kevin L. Piper; Amy C. Workinger; William J. Otrosina

1998-01-01

An overriding management goal for national parks is the maintenance or, where necessary, the restoration of natural ecological processes. In Sequoia-Kings Canyon and Yosemite National Parks, there is concern about the effects of fire suppression on the giant sequoia-mixed conifer forest ecosystem. The National Park Service is currently using prescribed fire management...

78 FR 66380 - Final Environmental Impact Statement for the Restoration of the Mariposa Grove of Giant Sequoias...

Science.gov (United States)

2013-11-05

... sequoia habitat, wetlands, and soundscapes within the Mariposa Grove, this alternative would relocate... for restoration of wetlands, soundscapes, and giant sequoia habitat within the Mariposa Grove by...

Fog and soil weathering as sources of nutrients in a California redwood forest

Science.gov (United States)

Holly A. Ewing; Kathleen C. Weathers; Amanda M. Lindsey; Pamela H. Templer; Todd E. Dawson; Damon C. Bradbury; Mary K. Firestone; Vanessa K.S. Boukili

2012-01-01

Fog water deposition is thought to influence the ecological function of many coastal ecosystems, including coast redwood forests. We examined cation and anion inputs from fog and rain, as well as the fate of these inputs, within a Sonoma County, California, coast redwood forest to elucidate the availability of these ions and some of the biotic and abiotic processes...

Proteomic profiling of proteins associated with the rejuvenation of Sequoia sempervirens (D. Don Endl

Directory of Open Access Journals (Sweden)

Chen Yu-Ting

2010-12-01

Full Text Available Abstract Background Restoration of rooting competence is important for rejuvenation in Sequoia sempervirens (D. Don Endl and is achieved by repeatedly grafting Sequoia shoots after 16 and 30 years of cultivation in vitro. Results Mass spectrometry-based proteomic analysis revealed three proteins that differentially accumulated in different rejuvenation stages, including oxygen-evolving enhancer protein 2 (OEE2, glycine-rich RNA-binding protein (RNP, and a thaumatin-like protein. OEE2 was found to be phosphorylated and a phosphopeptide (YEDNFDGNSNVSVMVpTPpTDK was identified. Specifically, the protein levels of OEE2 increased as a result of grafting and displayed a higher abundance in plants during the juvenile and rejuvenated stages. Additionally, SsOEE2 displayed the highest expression levels in Sequoia shoots during the juvenile stage and less expression during the adult stage. The expression levels also steadily increased during grafting. Conclusion Our results indicate a positive correlation between the gene and protein expression patterns of SsOEE2 and the rejuvenation process, suggesting that this gene is involved in the rejuvenation of Sequoia sempervirens.

Ansel Adams's Eucalyptus Tree, Fort Ross: Nature, Photography, and the Search for California

OpenAIRE

Adam Arenson

2005-01-01

This article considers the image of California evoked in the unusual Ansel Adams photograph Eucalyptus Tree, Fort Ross, California (1969), a Polaroid Land image of the garrison fence and an aged eucalyptus tree. Considering the participation of Russian occupation, Australian cross-pollination, Carleton Watkins's early photographs of redwoods, automotive and tourist images in the creation of this distinctive California place, the article argues that to understand Ansel Adams's work, we must no...

78 FR 16294 - Draft Environmental Impact Statement for Restoration of the Mariposa Grove of Giant Sequoias...

Science.gov (United States)

2013-03-14

... Environmental Impact Statement for Restoration of the Mariposa Grove of Giant Sequoias, Yosemite National Park, Madera, and Mariposa Counties, CA AGENCY: National Park Service, Interior. ACTION: Notice of availability... the Mariposa Grove of giant sequoias in Yosemite National Park. This Draft EIS presents three...

Annosus Root disease of Western Conifers (FIDL)

Science.gov (United States)

Craig L. Schmitt; John R. Parmeter; John T. Kliejunas

2000-01-01

Annosus root disease is found on all western conifer species but is of most concern on true firs, hemlocks, and pines. Incense cedar, coast redwood and sequoia are sometimes infected in California. Western juniper is infected throughout its range. Annosus is common and causes extensive decay in old-growth western and mountain hemlock stands. Many mixed conifer stands...

Impacts of fire management on aboveground tree carbon stocks in Yosemite and Sequoia & Kings Canyon National Parks

Science.gov (United States)

Matchett, John R.; Lutz, James A.; Tarnay, Leland W.; Smith, Douglas G.; Becker, Kendall M.L.; Brooks, Matthew L.

2015-01-01

Forest biomass on Sierra Nevada landscapes constitutes one of the largest carbon stocks in California, and its stability is tightly linked to the factors driving fire regimes. Research suggests that fire suppression, logging, climate change, and present management practices in Sierra Nevada forests have altered historic patterns of landscape carbon storage, and over a century of fire suppression and the resulting accumulation in surface fuels have been implicated in contributing to recent increases in high severity, stand-replacing fires. For over 30 years, fire management at Yosemite (YOSE) and Sequoia & Kings Canyon (SEKI) national parks has led the nation in restoring fire to park landscapes; however, the impacts on the stability and magnitude of carbon stocks have not been thoroughly examined.

Isozyme markers associated with O3 tolerance indicate shift in genetic structure of ponderosa and Jeffrey pine in Sequoia National Park, California

International Nuclear Information System (INIS)

Staszak, J.; Grulke, N.E.; Marrett, M.J.; Prus-Glowacki, W.

2007-01-01

Effects of canopy ozone (O 3 ) exposure and signatures of genetic structure using isozyme markers associated with O 3 tolerance were analyzed in ∼20-, ∼80-, and >200-yr-old ponderosa (Pinus ponderosa Dougl. ex Laws.) and Jeffrey pine (Pinus jeffreyi Grev. and Balf.) in Sequoia National Park, California. For both species, the number of alleles and genotypes per loci was higher in parental trees relative to saplings. In ponderosa pine, the heterozygosity value increased, and the fixation index indicated reduction of homozygosity with increasing tree age class. The opposite tendencies were observed for Jeffrey pine. Utilizing canopy attributes known to be responsive to O 3 exposure, ponderosa pine was more symptomatic than Jeffrey pine, and saplings were more symptomatic than old growth trees. We suggest that these trends are related to differing sensitivity of the two species to O 3 exposure, and to higher O 3 exposures and drought stress that younger trees may have experienced during germination and establishment. - Genetic variation in isozyme markers associated with ozone tolerance differed between parental trees and their progeny in two closely related species of yellow pine

Foliar uptake of fog in the coast redwood ecosystem: a novel drought-alleviation strategy shared by most redwood forest plants

Science.gov (United States)

Emily Limm; Kevin Simonin; Tod. Dawson

2012-01-01

Fog inundates the coast redwood forests of northern California frequently during the summer months (May to September) when rainfall is largely absent (Azevedo and Morgan 1974, Byers 1953, Oberlander 1956). This maritime fog modifies otherwise warm and dry summer climate by increasing humidity, decreasing the air temperature, reducing solar radiation, and...

Isozyme markers associated with O{sub 3} tolerance indicate shift in genetic structure of ponderosa and Jeffrey pine in Sequoia National Park, California

Energy Technology Data Exchange (ETDEWEB)

Staszak, J. [A Mickiewicz University, Genetics Department, ul. Umultowska 89, 61-614 Poznan (Poland); Grulke, N.E. [USDA Forest Service, 4955 Canyon Crest Drive, Riverside, CA 92507 (United States)], E-mail: ngrulke@fs.fed.us; Marrett, M.J. [5184 Tower Road, Riverside, CA 92506 (United States); Prus-Glowacki, W. [A Mickiewicz University, Genetics Department, ul. Umultowska 89, 61-614 Poznan (Poland)

2007-10-15

Effects of canopy ozone (O{sub 3}) exposure and signatures of genetic structure using isozyme markers associated with O{sub 3} tolerance were analyzed in {approx}20-, {approx}80-, and >200-yr-old ponderosa (Pinus ponderosa Dougl. ex Laws.) and Jeffrey pine (Pinus jeffreyi Grev. and Balf.) in Sequoia National Park, California. For both species, the number of alleles and genotypes per loci was higher in parental trees relative to saplings. In ponderosa pine, the heterozygosity value increased, and the fixation index indicated reduction of homozygosity with increasing tree age class. The opposite tendencies were observed for Jeffrey pine. Utilizing canopy attributes known to be responsive to O{sub 3} exposure, ponderosa pine was more symptomatic than Jeffrey pine, and saplings were more symptomatic than old growth trees. We suggest that these trends are related to differing sensitivity of the two species to O{sub 3} exposure, and to higher O{sub 3} exposures and drought stress that younger trees may have experienced during germination and establishment. - Genetic variation in isozyme markers associated with ozone tolerance differed between parental trees and their progeny in two closely related species of yellow pine.

Modeling mountain pine beetle habitat suitability within Sequoia National Park

Science.gov (United States)

Nguyen, Andrew

Understanding significant changes in climate and their effects on timber resources can help forest managers make better decisions regarding the preservation of natural resources and land management. These changes may to alter natural ecosystems dependent on historical and current climate conditions. Increasing mountain pine beetle (MBP) outbreaks within the southern Sierra Nevada are the result of these alterations. This study better understands MPB behavior within Sequoia National Park (SNP) and model its current and future habitat distribution. Variables contributing to MPB spread are vegetation stress, soil moisture, temperature, precipitation, disturbance, and presence of Ponderosa (Pinus ponderosa) and Lodgepole (Pinus contorta) pine trees. These variables were obtained using various modeled, insitu, and remotely sensed sources. The generalized additive model (GAM) was used to calculate the statistical significance of each variable contributing to MPB spread and also created maps identifying habitat suitability. Results indicate vegetation stress and forest disturbance to be variables most indicative of MPB spread. Additionally, the model was able to detect habitat suitability of MPB with a 45% accuracy concluding that a geospatial driven modeling approach can be used to delineate potential MPB spread within SNP.

Life-Cycle Inventory Analysis of Manufacturing Redwood Decking

Science.gov (United States)

Richard D. Bergman; Han-Sup Han; Elaine Oneil; Ivan L. Eastin

2012-01-01

Green building has become increasingly important. Therefore, consumers and builders often take into account the environmental attributes of a building material. This study determined the environmental attributes associated with manufacturing 38-mm × 138-mm (nominal 2 × 6) redwood decking in northern California using the life-cycle inventory method. Primary data...

Export of fine particulate organic carbon from redwood-dominated catchments

Science.gov (United States)

Madej, Mary Ann

2015-01-01

Recently, researchers have recognized the significant role of small mountainous river systems in the transport of carbon from terrestrial environments to the ocean, and the scale of such studies have ranged from channel bed units to continents. In temperate zones, these mountain river systems commonly drain catchments that are largely forested. However, the magnitude of carbon export from rivers draining old-growth redwood forests has not been evaluated to date. Old-growth redwood stands support some of the largest quantities of biomass in the world, up to 350 000 Mg of stem biomass km-2 and soil organic carbon can reach 46 800 Mg km-2. In north coastal California, suspended sediment samples were collected at three gaging stations for two to four years on streams draining old-growth redwood forests. Carbon content, determined through loss-on-ignition tests, was strongly correlated with turbidity, and continuous turbidity records from the gaging stations were used to estimate annual carbon exports of 1 · 6 to 4 · 2 Mg km-2 yr-1. These values, representing 13 to 33% of the suspended sediment load, are some of the highest percentages reported in the global literature. The fraction of organic carbon as part of the suspended sediment load decreased with discharge, but reached an asymptote of 5 to 10% at flows 10 to 20 times the mean annual flows. Although larger rivers in this region exhibit high sediment yields (up to 3600 Mg km-2 yr-1), mainly attributed to high rates of uplift, mass movement, and timber harvest, the small pristine streams in this study have sediment yields of only 8 to 100 Mg km-2 yr-1. Because the current extent of old-growth redwood stands is less than 5% of its pre-European-settlement distribution, the present organic carbon signature in suspended sediment loads in this region is likely different from that in the early 20th century. Published 2015. This article is a U.S. Government work and is in the public

Management of Giant Sequoia on Mountain Home Demonstration State Forest

Science.gov (United States)

Norman J. Benson

1986-01-01

Established in 1946, the Mountain Home Demonstration State Forest, Tulare County, California, is managed by the California Department of Forestry. It is a multiple-use forest with recreation as its primary focus, although timber management has always played an important role. Giant sequoia (Sequoiadendron giganteum [Lindl. ] Buchholz) occurs in...

Mortality and community changes drive sudden oak death impacts on litterfall and soil nitrogen cycling.

Science.gov (United States)

Cobb, Richard C; Eviner, Valerie T; Rizzo, David M

2013-10-01

Few studies have quantified pathogen impacts to ecosystem processes, despite the fact that pathogens cause or contribute to regional-scale tree mortality. We measured litterfall mass, litterfall chemistry, and soil nitrogen (N) cycling associated with multiple hosts along a gradient of mortality caused by Phytophthora ramorum, the cause of sudden oak death. In redwood forests, the epidemiological and ecological characteristics of the major overstory species determine disease patterns and the magnitude and nature of ecosystem change. Bay laurel (Umbellularia californica) has high litterfall N (0.992%), greater soil extractable NO3 -N, and transmits infection without suffering mortality. Tanoak (Notholithocarpus densiflorus) has moderate litterfall N (0.723%) and transmits infection while suffering extensive mortality that leads to higher extractable soil NO3 -N. Redwood (Sequoia sempervirens) has relatively low litterfall N (0.519%), does not suffer mortality or transmit the pathogen, but dominates forest biomass. The strongest impact of pathogen-caused mortality was the potential shift in species composition, which will alter litterfall chemistry, patterns and dynamics of litterfall mass, and increase soil NO3 -N availability. Patterns of P. ramorum spread and consequent mortality are closely associated with bay laurel abundances, suggesting this species will drive both disease emergence and subsequent ecosystem function. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Communicating the role of science in managing giant sequoia groves

Science.gov (United States)

Douglas D. Pilrto; Robert R. Rogers; Mary Chislock Bethke

1997-01-01

Management of giant sequoia groves has been and continues to be a hotly debated issue. The debate has reached Congress, with all parties seeking resolution as to what constitutes an ecologically and publicly acceptable management approach. Determining the correct management approach and communicating that approach to the general public is the crux of the problem....

High-resolution 3D simulations of NIF ignition targets performed on Sequoia with HYDRA

Science.gov (United States)

Marinak, M. M.; Clark, D. S.; Jones, O. S.; Kerbel, G. D.; Sepke, S.; Patel, M. V.; Koning, J. M.; Schroeder, C. R.

2015-11-01

Developments in the multiphysics ICF code HYDRA enable it to perform large-scale simulations on the Sequoia machine at LLNL. With an aggregate computing power of 20 Petaflops, Sequoia offers an unprecedented capability to resolve the physical processes in NIF ignition targets for a more complete, consistent treatment of the sources of asymmetry. We describe modifications to HYDRA that enable it to scale to over one million processes on Sequoia. These include new options for replicating parts of the mesh over a subset of the processes, to avoid strong scaling limits. We consider results from a 3D full ignition capsule-only simulation performed using over one billion zones run on 262,000 processors which resolves surface perturbations through modes l = 200. We also report progress towards a high-resolution 3D integrated hohlraum simulation performed using 262,000 processors which resolves surface perturbations on the ignition capsule through modes l = 70. These aim for the most complete calculations yet of the interactions and overall impact of the various sources of asymmetry for NIF ignition targets. This work was performed under the auspices of the Lawrence Livermore National Security, LLC, (LLNS) under Contract No. DE-AC52-07NA27344.

A natural resource condition assessment for Sequoia and Kings Canyon National Parks: Appendix 14: plants of conservation concern

Science.gov (United States)

Huber, Ann; Das, Adrian; Wenk, Rebecca; Haultain, Sylvia

2013-01-01

Database (CNDDB 2010a). There are an additional 66 taxa not formally listed by CNDDB that are recognized as having special status because their distribution is restricted to the Sierra Nevada. Special status plants are distributed throughout the two parks and inhabit a wide range of environments along the length of the elevation gradient that characterizes these parks. Ideally, we would assess the condition (status and trends) of each of the taxa on the SEKI special status plant list, documenting current population sizes, demographic rates and demographic trends. We would also hope to quantify the effects of individual stressors on each species based on existing monitoring and research. However, no data are available for most of the species on the special status plant list. For those few species (12 herbaceous species and two tree species) for which we possess some change over time information, the data are not adequate to make a competent assessment. Note that we have not explored the tree demographic information in any detail, as is covered in the NRCA Intact Forest/Five Needle Pines and Sequoia chapters. In general, we are unable to present an ‗integrity‘ metric for special status species in the parks, since the data to quantify the condition of each species in such a manner is not available. In contrast, the park does possess substantial data describing biodiversity in the parks. Therefore, our analysis focuses on describing the distribution and rarity of special status plants within the parks, with a particular focus on assessing the spatial distribution of species richness. We hope that such information will prove useful to park managers in determining which areas in the parks merit the most attention (for example in developing monitoring protocols). We also assess potential vulnerability of special status species to the stressors chosen by the NRCA working group, using both park data and available literature. As a first step, we spent considerable effort

The penalty of a long, hot summer. Photosynthetic acclimation to high CO2 and continuous light in "living fossil" conifers.

Science.gov (United States)

Osborne, Colin P; Beerling, David J

2003-10-01

Deciduous forests covered the ice-free polar regions 280 to 40 million years ago under warm "greenhouse" climates and high atmospheric pCO2. Their deciduous habit is frequently interpreted as an adaptation for minimizing carbon losses during winter, but experiments with "living fossils" in a simulated warm polar environment refute this explanation. Measured carbon losses through leaf abscission of deciduous trees are significantly greater than losses through winter respiration in evergreens, yet annual rates of primary productivity are similar in all species. Here, we investigate mechanisms underlying this apparent paradox by measuring the seasonal patterns of leaf photosynthesis (A) under pCO2 enrichment in the same trees. During spring, A increased significantly in coastal redwood (Sequoia sempervirens), dawn redwood (Metasequoia glyptostroboides), and swamp cypress (Taxodium distichum) at an elevated pCO2 of 80 Pa compared with controls at 40 Pa. However, strong acclimation in Rubisco carboxylation capacity (Vc,max) completely offset the CO2 response of A in all species by the end of 6 weeks of continuous illumination in the simulated polar summer. Further measurements demonstrated the temporary nature of acclimation, with increases in Vc,max during autumn restoring the CO2 sensitivity of A. Contrary to expectations, the acclimation of Vc,max was not always accompanied by accumulation of leaf carbohydrates, but was associated with a decline in leaf nitrogen in summer, suggesting an alteration of the balance in plant sources and sinks for carbon and nitrogen. Preliminary calculations using A indicated that winter carbon losses through deciduous leaf abscission and respiration were recovered by 10 to 25 d of canopy carbon fixation during summer, thereby explaining the productivity paradox.

The Penalty of a Long, Hot Summer. Photosynthetic Acclimation to High CO2 and Continuous Light in “Living Fossil” Conifers1

Science.gov (United States)

Osborne, Colin P.; Beerling, David J.

2003-01-01

Deciduous forests covered the ice-free polar regions 280 to 40 million years ago under warm “greenhouse” climates and high atmospheric pCO2. Their deciduous habit is frequently interpreted as an adaptation for minimizing carbon losses during winter, but experiments with “living fossils” in a simulated warm polar environment refute this explanation. Measured carbon losses through leaf abscission of deciduous trees are significantly greater than losses through winter respiration in evergreens, yet annual rates of primary productivity are similar in all species. Here, we investigate mechanisms underlying this apparent paradox by measuring the seasonal patterns of leaf photosynthesis (A) under pCO2 enrichment in the same trees. During spring, A increased significantly in coastal redwood (Sequoia sempervirens), dawn redwood (Metasequoia glyptostroboides), and swamp cypress (Taxodium distichum) at an elevated pCO2 of 80 Pa compared with controls at 40 Pa. However, strong acclimation in Rubisco carboxylation capacity (Vc,max) completely offset the CO2 response of A in all species by the end of 6 weeks of continuous illumination in the simulated polar summer. Further measurements demonstrated the temporary nature of acclimation, with increases in Vc,max during autumn restoring the CO2 sensitivity of A. Contrary to expectations, the acclimation of Vc,max was not always accompanied by accumulation of leaf carbohydrates, but was associated with a decline in leaf nitrogen in summer, suggesting an alteration of the balance in plant sources and sinks for carbon and nitrogen. Preliminary calculations using A indicated that winter carbon losses through deciduous leaf abscission and respiration were recovered by 10 to 25 d of canopy carbon fixation during summer, thereby explaining the productivity paradox. PMID:12972654

The effects of raking on sugar pine mortality following prescribed fire in Sequoia and Kings Canyon National Parks, California, USA

Science.gov (United States)

Nesmith, Jonathan C. B.; O'Hara, Kevin L.; van Mantgem, Phillip J.; de Valpine, Perry

2010-01-01

Prescribed fire is an important tool for fuel reduction, the control of competing vegetation, and forest restoration. The accumulated fuels associated with historical fire exclusion can cause undesirably high tree mortality rates following prescribed fires and wildfires. This is especially true for sugar pine (Pinus lambertiana Douglas), which is already negatively affected by the introduced pathogen white pine blister rust (Cronartium ribicola J.C. Fisch. ex Rabenh). We tested the efficacy of raking away fuels around the base of sugar pine to reduce mortality following prescribed fire in Sequoia and Kings Canyon national parks, California, USA. This study was conducted in three prescribed fires and included 457 trees, half of which had the fuels around their bases raked away to mineral soil to 0.5 m away from the stem. Fire effects were assessed and tree mortality was recorded for three years after prescribed fires. Overall, raking had no detectable effect on mortality: raked trees averaged 30% mortality compared to 36% for unraked trees. There was a significant effect, however, between the interaction of raking and average pre-treatment forest floor fuel depth: the predicted probability of survival of a 50 cm dbh tree was 0.94 vs. 0.96 when average pre-treatment fuel depth was 0 cm for a raked and unraked tree, respectively. When average pre-treatment forest floor fuel depth was 30 cm, the predicted probability of survival for a raked 50 cm dbh tree was 0.60 compared to only 0.07 for an unraked tree. Raking did not affect mortality when fire intensity, measured as percent crown volume scorched, was very low (0% scorch) or very high (>80% scorch), but the raking treatment significantly increased the proportion of trees that survived by 9.6% for trees that burned under moderate fire intensity (1% to 80% scorch). Raking significantly reduced the likelihood of bole charring and bark beetle activity three years post fire. Fuel depth and anticipated fire intensity need

Using Scientific Information to Develop Management Strategies for Commercial Redwood Timberlands

Science.gov (United States)

Jeffrey C. Barrett

2007-01-01

In 1999, PALCO (Pacific Lumber Company), a private landowner, and the state and federal governments agreed to implement a unique Habitat Conservation Plan (HCP) on 89,000 hectares of commercial redwood and Douglas-fir timberlands in Humboldt County, California. The aquatics portion of the PALCO HCP contains a set of "interim" conservation strategies developed...

Summary of watershed conditions in the vicinity of Redwood National Park, California

Science.gov (United States)

Janda, Richard J.

1977-01-01

The Redwood Creek Unit of Redwood National Park is located in the downstream end of an exceptionally rapidly eroding drainage basin. Spatial distribution and types of erosional landforms, observed in the field and on time-sequential aerial photographs, measured sediment loads, and the lithologic heterogeneity of streambed materials indicated (1) that sediment discharges reflect a complex suite of natural and man-induced mass movement and fluvial erosion processes operating on a geologically heterogeneous, naturally unstable terrain, and (2) that although infrequent exceptionally intense storms control the timing and general magnitude of major erosion events, the loci, types, and amounts of erosion occurring during those events are substantially influence by land use. Erosional impacts of past timber harvest in the Redwood Creek basin reflect primarily the cumulative impact of many small erosion problems caused not so much by removal. Recently modified riparian and aquatic environments reflect stream channel adjustments to recently increased water and sediment discharges, and are classified by the National Park Service as damaged resources because the modifications reflect, in part, unnatural causes. Newly strengthened State regulations and cooperative review procedures result in proposed timber harvest plans being tailored to specific site conditions, as well as smaller, more dispersed harvest units and more sophisticated attempts at minimizing ground-surface disruption than those used in most previous timber harvesting in this basin. However, application of improved timber harvest technology alone will not assure protection of park resources. Much remaining intact residual commercial old-growth timber is on hillslopes that are steeper, wetter, more susceptible to landsliding, and more nearly adjacent to major stream channels than most of the previously harvested hillslopes in the lower Redwood Creek basin. Moreover, natural debris barriers along streams flowing

Subdivide or silviculture: choices facing family forest owners in the redwood region

Science.gov (United States)

William Stewart; Shasta Ferranto; Gary Nakamura; Christy Getz; Lynn Huntsinger; Maggi. Kelly

2012-01-01

Families or family businesses own nearly all of the private redwood forestland in California. Family forest owners have practiced both subdivision and silviculture for decades but the dominant theme for most family owners is environmental stewardship. Parcel size is more important than expressed values as a predictor of resource management activities. All landowners...

Edge effects and the effective size of old-growth coast redwood preserves

Science.gov (United States)

William H. Russell; Joe R. McBride; Ky Carnell

2000-01-01

Data were collected to determine the depth of influence of conditions created by clear-cut timber harvest on adjacent old-growth stands of coast redwood. Fourteen variables related to stand structure and composition, wildlife habitat, and physical environment exhibited significant correlation to distance from the timber harvest boundary. Results were applied to the...

Crush performance of redwood for developing design procedures for impact limiters

International Nuclear Information System (INIS)

Cramer, S.M.; Hermanson, J.C.; McMurtry, W.M.

1995-01-01

Containers for the transportation of hazardous and radioactive materials incorporate redwood in impact limiters. Redwood is an excellent energy absorber, but only the most simplistic information exists on its crush properties. Tbe stress-strain interrelationship for any wood species subject to three-dimensional stresses is largely unknown for any all stress condition and wood behavior at both high strains and high strain-rates is known only in general terms. Both stress-strain and crush failure theories have been developed based only on uniaxial load tests. The anisotropy of wood adds an additional complexity to measuring wood response and developing suitable theories to describe it. A long history of wood utilization in the building industry has led to design procedures and property information related to simple uniaxial loadings that do not inflict damage to the wood. This lack of knowledge may be surprising for a material that has a long history of engineered use, but the result is difficulty in utilizing wood in more sophisticated designs such as impact limiters. This study provides a step toward filling the information gap on wood material response for high performance applications such as impact limiters

The History of Redwood Records: Cultural and Economic Perspectives on a Feminist Subculture.

Science.gov (United States)

Lont, Cynthia M.

Using interviews and subcultural artifacts, such as inner sleeves of albums, this paper reports on the career of Holly Near and the history of Redwood Records, a label providing music to the lesbian-feminist subculture. First, the paper discusses the political and artistic avenues that were available to Near, the reasons she chose political music,…

Participation of gibberellin in the control of apical dominance in soybean and redwood

Energy Technology Data Exchange (ETDEWEB)

Ruddat, M.; Pharis, R.P.

1966-01-01

Loss of apical dominance in soybeans and redwood was increased when the plants were treated with the growth retardant AMO-1618. Simultaneous application of gibberellin reduced the number of elongating buds and promoted growth of the first or second uppermost auxillary bud, thus restoring apical dominance. It is concluded that gibberellin participates in the expression of apical dominance. 30 references, 2 tables.

A method of detecting carbonyl compounds in tree leaves in China.

Science.gov (United States)

Huang, Juan; Feng, Yanli; Fu, Jiamo; Sheng, Guoying

2010-06-01

Carbonyl compounds have been paid more and more attention because some carbonyl species have been proven to be carcinogenic or a risk for human health. Plant leaves are both an important emission source and an important sink of carbonyl compounds. But the research on carbonyl compounds from plant leaves is very scarce. In order to make an approach to the emission mechanism of plant leaves, a new method was established to extract carbonyl compounds from fresh plant leaves. The procedure combining derivatization with ultrasonication was developed for the fast extraction of carbonyl compounds from tree leaves. Fresh leaves (Metasequoia glyptostroboides), were selected and extracted by this method. Seven carbonyl compounds, including formaldehyde, acetaldehyde, acetone, acrolein, p-tolualdehyde, m/o-tolualdehyde, and hexaldehyde were determined and quantified. The most common carbonyl species of the four tree leaves were formaldehyde, acrolein, and m/o-tolualdehyde. They accounted for 67.3% in cedar, 50.8% in sweet olive, 45.8% in dawn redwood, and 44.6% in camphor tree, respectively. Camphor tree had the highest leaf level of m/o-tolualdehyde with 15.0 +/- 3.4 microg g(-1)(fresh leaf weight), which indicated that camphor tree may be a bioindicator of the level of tolualdehyde or xylene in the atmosphere. By analyzing carbonyl compounds from different tree leaves, it is not only helpful for further studying the relationship between sink and emission of carbonyls from plants, but also helpful for exploring optimum plant population in urban greening.

Implementation of a thinning and burning study in tanoak-redwood stands in Santa Cruz and Mendocino counties

Science.gov (United States)

Kevin L. O?Hara; Kristen M. Waring

2008-01-01

Three silvicultural treatment study sites are being established to examine the effects of thinning and prescribed burning on infection and spread of Phytophthora ramorum. Study sites are located in Mendocino and Santa Cruz counties, California. Stands are even-aged redwood/tanoak mixtures.

Family forest owners in the redwood region: management priorities and opportunities in a carbon market

Science.gov (United States)

Erin Clover Kelly; Joanna Di Tommaso; Arielle Weisgrau

2017-01-01

California’s cap-and-trade carbon market has included forest offset projects, available to all private landowners across the United States. The redwood region has been at the forefront of the market, creating the earliest forest carbon projects. From carbon registries, we compiled a database of all forest carbon projects in the market, in order to determine...

Watershed restoration, jobs-in-the woods, and community assistance: Redwood National Park and the Northwest Forest Plan.

Science.gov (United States)

Christopher E. DeForest

1999-01-01

There are many parallels between the 1978 legislation to expand Redwood National Park and the Northwest Forest Plan, which together with the Northwest Economic Adjustment Initiative formed the 1993 Pacific Northwest Initiative. In both situations, the Federal Government sought to promote retraining for displaced workers, to undertake watershed assessment and...

Monte Carlo simulation of the resolution volume for the SEQUOIA spectrometer

Directory of Open Access Journals (Sweden)

Granroth G.E.

2015-01-01

Full Text Available Monte Carlo ray tracing simulations, of direct geometry spectrometers, have been particularly useful in instrument design and characterization. However, these tools can also be useful for experiment planning and analysis. To this end, the McStas Monte Carlo ray tracing model of SEQUOIA, the fine resolution fermi chopper spectrometer at the Spallation Neutron Source (SNS of Oak Ridge National Laboratory (ORNL, has been modified to include the time of flight resolution sample and detector components. With these components, the resolution ellipsoid can be calculated for any detector pixel and energy bin of the instrument. The simulation is split in two pieces. First, the incident beamline up to the sample is simulated for 1 × 1011 neutron packets (4 days on 30 cores. This provides a virtual source for the backend that includes the resolution sample and monitor components. Next, a series of detector and energy pixels are computed in parallel. It takes on the order of 30 s to calculate a single resolution ellipsoid on a single core. Python scripts have been written to transform the ellipsoid into the space of an oriented single crystal, and to characterize the ellipsoid in various ways. Though this tool is under development as a planning tool, we have successfully used it to provide the resolution function for convolution with theoretical models. Specifically, theoretical calculations of the spin waves in YFeO3 were compared to measurements taken on SEQUOIA. Though the overall features of the spectra can be explained while neglecting resolution effects, the variation in intensity of the modes is well described once the resolution is included. As this was a single sharp mode, the simulated half intensity value of the resolution ellipsoid was used to provide the resolution width. A description of the simulation, its use, and paths forward for this technique will be discussed.

Upland log volumes and conifer establishment patterns in two northern, upland old-growth redwood forests, a brief synopsis

Science.gov (United States)

Daniel J. Porter; John O. Sawyer

2007-01-01

We characterized the volume, weight and top surface area of naturally fallen logs in an old-growth redwood forest, and quantified conifer recruit densities on these logs and on the surrounding forest floor. We report significantly greater conifer recruit densities on log substrates as compared to the forest floor. Log substrate availability was calculated on a per...

Demography of the California spotted owl in the Sierra National Forest and Sequoia/Kings Canyon National Parks

Science.gov (United States)

George N. Steger; Thomas E. Munton; Kenneth D. Johnson; Gary P. Eberlein

2002-01-01

Nine years (1990–1998) of demographic data on California spotted owls (Strix occidentalis occidentalis) in two study areas on the western slopes of the Sierra Nevada—one in the Sierra National Forest (SNF), the other in Sequoia/Kings Canyon National Parks (SNP)—are summarized. Numbers of territorial owls fluctuated from 85 to 50 in SNF and 80 to 58...

Determination of total Betta-activity and heavy metals in biomonitor species (phytomonitors) from the area of ITR-Sofia

International Nuclear Information System (INIS)

Dimitrov, S.; Yovchev, M.; Geleva, E.

2010-01-01

For the purposes of environmental assessment of the area around the Research reactor in Sofia, species from monitored control points, selected in a certain way (habitat, population, air and hydrogeological parameters) are examined. Samples from following phytomonitored species: Betula pendula (silver birch) popullus canadensis (Canadian populus), Quercus sp. (Oak), Dactilus glomerata (Cock's-foot), Abies alba (Silver Fir) and Sequoia sempervirens (Coast Redwood) were analyzed. The total beta activity was determined by radiometric analysis and heavy metals content was measured using X-ray fluorescence analysis. The results are discussed in terms of radiation monitoring program of INRNE (gamma-background, aerosols, surface and groundwater, soil, plants) and obtained values are compared with reference points in the country

Effect of Preservative Treatment on Fungal Colonization of Teak, Redwood, and Western Red Cedar

DEFF Research Database (Denmark)

Cabrera Orozco, Yohanna; Freitag, F.; Morrell, Jeffrey J.

Fungal flora present in preservative treated samples or non-treated samples from sapwood and heartwood of teak, western red cedar, redwood, and southern yellow pine was assessed after 6 to 18 months of exposure near Hilo, Hawaii. The objectives were to compare fungal composition and diversity...... between treated and non-treated samples, and to examine the use of molecular techniques for assessing fungal community structure in a ground-proximity-test located in Hilo, Hawaii. Fungi were recovered in culture after 6, 12, or 18 months, yielding 178 unique DNA sequences that represented 85 taxa...

The effect of low- and high-power microwave irradiation on in vitro grown Sequoia plants and their recovery after cryostorage.

Science.gov (United States)

Halmagyi, A; Surducan, E; Surducan, V

2017-09-01

Two distinct microwave power levels and techniques have been studied in two cases: low-power microwave (LPM) irradiation on in vitro Sequoia plants and high-power microwave (HPM) exposure on recovery rates of cryostored (-196°C) Sequoia shoot apices. Experimental variants for LPM exposure included: (a) in vitro plants grown in regular conditions (at 24 ± 1°C during a 16-h light photoperiod with a light intensity of 39.06 μEm -2 s -1 photosynthetically active radiation), (b) in vitro plants grown in the anechoic chamber with controlled environment without microwave irradiation, and (c) in vitro plants grown in the anechoic chamber with LPM irradiation for various times (5, 15, 30, 40 days). In comparison to control plants, significant differences in shoot multiplication and growth parameters (length of shoots and roots) were observed after 40 days of LPM exposure. An opposite effect was achieved regarding the content of total soluble proteins, which decreased with increasing exposure time to LPM. HPM irradiation was tested as a novel rewarming method following storage in liquid nitrogen. To our knowledge, this is the first report using this type of rewarming method. Although, shoot tips subjected to HPM exposure showed 28% recovery following cryostorage compared to 44% for shoot tips rewarmed in liquid medium at 22 ± 1 °C, we consider that the method represent a basis and can be further improved. The results lead to the overall conclusion that LPM had a stimulating effect on growth and multiplication of in vitro Sequoia plants, while the HPM used for rewarming of cryopreserved apices was not effective to achieve high rates of regrowth after liquid nitrogen exposure.

Soil carbon storage following road removal and timber harvesting in redwood forests

Science.gov (United States)

Seney, Joseph; Madej, Mary Ann

2015-01-01

Soil carbon storage plays a key role in the global carbon cycle and is important for sustaining forest productivity. Removal of unpaved forest roads has the potential for increasing carbon storage in soils on forested terrain as treated sites revegetate and soil properties improve on the previously compacted road surfaces. We compared soil organic carbon (SOC) content at several depths on treated roads to SOC in adjacent second-growth forests and old-growth redwood forests in California, determined whether SOC in the upper 50 cm of soil varies with the type of road treatment, and assessed the relative importance of site-scale and landscape-scale variables in predicting SOC accumulation in treated road prisms and second-growth redwood forests. Soils were sampled at 5, 20, and 50 cm depths on roads treated by two methods (decommissioning and full recontouring), and in adjacent second-growth and old-growth forests in north coastal California. Road treatments spanned a period of 32 years, and covered a range of geomorphic and vegetative conditions. SOC decreased with depth at all sites. Treated roads on convex sites exhibited higher SOC than on concave sites, and north aspect sites had higher SOC than south aspect sites. SOC at 5, 20, and 50 cm depths did not differ significantly between decommissioned roads (treated 18–32 years previous) and fully recontoured roads (treated 2–12 years previous). Nevertheless, stepwise multiple regression models project higher SOC developing on fully recontoured roads in the next few decades. The best predictors for SOC on treated roads and in second-growth forest incorporated aspect, vegetation type, soil depth, lithology, distance from the ocean, years since road treatment (for the road model) and years since harvest (for the forest model). The road model explained 48% of the variation in SOC in the upper 50 cm of mineral soils and the forest model, 54%

Instituto SEQUOIA : Um serviço privado,  multidisciplinar e de cuidado aos idosos SEQUOIA Institute: A multidisciplinary private service for the care of senior citizens L’Institut SEQUOIA : Un service privé multidisciplinaire pour les soins des personnes du troisième âge Instituto SEQUOIA : Un servicio privado y multidisciplinario de atención a las personas de la tercera edad

Directory of Open Access Journals (Sweden)

Anelise Fonseca

2011-10-01

Full Text Available Population aging is a reality all over the world, requiring a change in the way care is perceived and resources are divided for different age groups. In Brazil, current indicators and projections place the country among those with the highest number of elderly people. By contrast, there is a shortage of action plans and inter- and multi-disciplinary teams, as well as public policies and professionals, focusing on the elderly, in part as a consequence of an accelerated aging process in developing countries. Within this context, the SEQUOIA Institute (IS was created to attend to this process by monitoring the overall health of patients. The institute's routine work includes clinical actions, team meetings, socialization projects and lectures. The IS features a 10% yearly growth in medical assistance, a 20% rise in psychological treatments, and a 50% increase in lecture attendance.Le vieillissement de la population est un phénomène mondial qui exige de revoir la façon dont sont perçus les soins et dont sont divisées les ressources en fonction des différentes tranches d’âge. Les indicateurs et les projections actuels montrent que le Brésil est le pays qui compte la plus grande proportion de personnes âgées. Et pourtant, les plans d’action, les équipes inter- et pluridisciplinaires, mais aussi les politiques publiques et les professionnels spécialistes des questions liées aux personnes âgées sont en nombre insuffisant, notamment en raison d’un processus de vieillissement accéléré dans les pays en développement. C’est dans ce contexte qu’a été créé l’Institut SEQUOIA (IS, dont la mission consiste à gérer ce processus en effectuant un suivi de la santé générale des patients. Les principales tâches de l’institut incluent études cliniques, réunions d’équipes, projets impliquant des débats et conférences. L’IS affiche une croissance annuelle de 10 % dans le secteur de l’assistance médicale, de 20

An approach to study the effect of harvest and wildfire on watershed hydrology and sediment yield in a coast redwood forest

Science.gov (United States)

Christopher G. Surfleet; Arne Skaugset; Brian Dietterick

2012-01-01

The Little Creek watershed, within California State Polytechnic University’s Swanton Pacific Ranch, is the location of a paired and nested watershed study to investigate the watershed effects of coast redwood forest management. Streamflow, suspended sediment, and stream turbidity have been collected during storms at two locations on the North Fork Little Creek and at...

Laboratory evaluation of the Sequoia Scientific LISST-ABS acoustic backscatter sediment sensor

Science.gov (United States)

Snazelle, Teri T.

2017-12-18

Sequoia Scientific’s LISST-ABS is an acoustic backscatter sensor designed to measure suspended-sediment concentration at a point source. Three LISST-ABS were evaluated at the U.S. Geological Survey (USGS) Hydrologic Instrumentation Facility (HIF). Serial numbers 6010, 6039, and 6058 were assessed for accuracy in solutions with varying particle-size distributions and for the effect of temperature on sensor accuracy. Certified sediment samples composed of different ranges of particle size were purchased from Powder Technology Inc. These sediment samples were 30–80-micron (µm) Arizona Test Dust; less than 22-µm ISO 12103-1, A1 Ultrafine Test Dust; and 149-µm MIL-STD 810E Silica Dust. The sensor was able to accurately measure suspended-sediment concentration when calibrated with sediment of the same particle-size distribution as the measured. Overall testing demonstrated that sensors calibrated with finer sized sediments overdetect sediment concentrations with coarser sized sediments, and sensors calibrated with coarser sized sediments do not detect increases in sediment concentrations from small and fine sediments. These test results are not unexpected for an acoustic-backscatter device and stress the need for using accurate site-specific particle-size distributions during sensor calibration. When calibrated for ultrafine dust with a less than 22-µm particle size (silt) and with the Arizona Test Dust with a 30–80-µm range, the data from sensor 6039 were biased high when fractions of the coarser (149-µm) Silica Dust were added. Data from sensor 6058 showed similar results with an elevated response to coarser material when calibrated with a finer particle-size distribution and a lack of detection when subjected to finer particle-size sediment. Sensor 6010 was also tested for the effect of dissimilar particle size during the calibration and showed little effect. Subsequent testing revealed problems with this sensor, including an inadequate temperature

Structural inspection and wind analysis of redwood cooling towers at the Portsmouth Gaseous Diffusion Plant

International Nuclear Information System (INIS)

Chung, T.; Solack, T.; Hortel, J.

1991-01-01

As part of the plant upgrade program, structural analyses and field inspections were performed on four redwood cooling towers at the DOE Portsmouth gaseous diffusion plant located in Piketon, Ohio. The cooling towers are categorized as important hazard facilities. The loadings are derived from UCRL-15910 according to the pertinent hazard category. In addition to the seismic and wind loadings, the wood cooling towers are constantly subject to adverse environmental effects such as elevated temperature, chemical attack, icing and snow load, and motor vibrations. A thorough structural evaluation for all load combinations was performed for each of the cooling towers based on the structural code requirements of the Cooling Tower Institute and National Forest Products Association. Most stress criteria are unique for the redwood material. This evaluation was performed using finite element techniques on the global structural integrity and supplemented by hand calculations on the individual connection joints. Overloaded wood structural members and joints are identified by the analysis. The rectangular tower structure sits on a concrete basin that span across 60 ft by 200 ft. A major part of the cooling towers upgrading program involved field inspections of the individual cells of each tower. The primary purpose of these inspections was to identify any existing structural damage or deficiencies such as failed members, degraded wood, and deficiencies resulting from poor construction practice. Inspection of 40 cells identified some generic deficiencies that mostly are consistent with the analytical finding. Based on the analysis, some effective but inexpensive upgrading techniques were developed and recommended to bring the cooling towers into compliance with current DOE requirements

SEQUOIA Institute: A multidisciplinary private service for the care of senior citizens L’Institut SEQUOIA : Un service privé multidisciplinaire pour les soins des personnes du troisième âge Instituto SEQUOIA : Un servicio privado y multidisciplinario de atención a las personas de la tercera edad

Directory of Open Access Journals (Sweden)

Anelise Fonseca

2011-10-01

Full Text Available Population aging is a reality all over the world, requiring a change in the way care is perceived and resources are divided for different age groups. In Brazil, current indicators and projections place the country among those with the highest number of elderly people. By contrast, there is a shortage of action plans and inter- and multi-disciplinary teams, as well as public policies and professionals, focusing on the elderly, in part as a consequence of an accelerated aging process in developing countries. Within this context, the SEQUOIA Institute (IS was created to attend to this process by monitoring the overall health of patients. The institute's routine work includes clinical actions, team meetings, socialization projects and lectures. The IS features a 10% yearly growth in medical assistance, a 20% rise in psychological treatments, and a 50% increase in lecture attendance.Le vieillissement de la population est un phénomène mondial qui exige de revoir la façon dont sont perçus les soins et dont sont divisées les ressources en fonction des différentes tranches d’âge. Les indicateurs et les projections actuels montrent que le Brésil est le pays qui compte la plus grande proportion de personnes âgées. Et pourtant, les plans d’action, les équipes inter- et pluridisciplinaires, mais aussi les politiques publiques et les professionnels spécialistes des questions liées aux personnes âgées sont en nombre insuffisant, notamment en raison d’un processus de vieillissement accéléré dans les pays en développement. C’est dans ce contexte qu’a été créé l’Institut SEQUOIA (IS, dont la mission consiste à gérer ce processus en effectuant un suivi de la santé générale des patients. Les principales tâches de l’institut incluent études cliniques, réunions d’équipes, projets impliquant des débats et conférences. L’IS affiche une croissance annuelle de 10 % dans le secteur de l’assistance médicale, de 20

Tree thermometers and commodities: historic climate indicators

International Nuclear Information System (INIS)

Libby, L.M.; Pandolfi, L.J.

1979-01-01

In four modern trees, hydrogen and oxygen isotope ratios track the modern temperature records. In a 2000-yr sequence of a Japanese cedar, there are the same periodicities of variation of D/H and O 18 /O 16 as have been found in O 18 /O 16 in a Greenland ice well. The same periodicities are found in uranium and organic carbon concentrations versus depth in a sea core from the Santa Barbara Channel, and in carbon-14 variations in a sequence of Bristlecone pine from southern California. In a 2000-yr sequence of Japanese cedar and in a 1000-yr sequence of European oak D/H and O 18 /O 16 are related to each other by a slope of 8, just as they are in world-wide precipitation. In a 72-yr sequence of Sequoia gigantea, measured year by year for its oxygen isotope ratios, the 10.5-yr cycle of sunspot numbers found, but not the 21-yr cycle of sunspot magnetism; this we believe indicates that the sun is affecting the earth's climate with non-magnetic particles, probably photons. All these phenomena are related to periodic changes in sea surface temperature caused by periodic changes in the sun. (author)

A comparison of effects from prescribed fires and wildfires managed for resource objectives in Sequoia and Kings Canyon National Parks

Science.gov (United States)

Nesmith, C.B.; Caprio, Anthony C.; Pfaff, Anne H.; McGinnis, Thomas W.; Keeley, Jon E.

2011-01-01

Current goals for prescription burning are focused on measures of fuel consumption and changes in forest density. These benchmarks, however, do not address the extent to which prescription burning meets perceived ecosystem needs of heterogeneity in burning, both for overstory trees and understory herbs and shrubs. There are still questions about how closely prescribed fires mimic these patterns compared to natural wildfires. This study compared burn patterns of prescribed fires and managed unplanned wildfires to understand how the differing burning regimes affect ecosystem properties. Measures of forest structure and fire severity were sampled in three recent prescribed fires and three wildfires managed for resource objectives in Sequoia and Kings Canyon National Parks. Fine scale patterns of fire severity and heterogeneity were compared between fire types using ground-based measures of fire effects on fuels and overstory and understory vegetation. Prescribed fires and wildfires managed for resource objectives displayed similar patterns of overstory and understory fire severity, heterogeneity, and seedling and sapling survival. Variation among plots within the same fire was always greater than between fire types. Prescribed fires can provide burned landscapes that approximate natural fires in many ways. It is recognized that constraints placed on when wildfires managed for resource objectives are allowed to burn freely may bias the range of conditions that might have been experienced under more natural conditions. Therefore they may not exactly mimic natural wildfires. Overall, the similarity in fire effects that we observed between prescribed fires and managed wildfires indicate that despite the restrictions that are often placed on prescribed fires, they appear to be creating post-fire conditions that approximate natural fires when assessed on a fine spatial scale.

The right tree for the job? perceptions of species suitability for the provision of ecosystem services.

Science.gov (United States)

Smaill, Simeon J; Bayne, Karen M; Coker, Graham W R; Paul, Thomas S H; Clinton, Peter W

2014-04-01

Stakeholders in plantation forestry are increasingly aware of the importance of the ecosystem services and non-market values associated with forests. In New Zealand, there is significant interest in establishing species other than Pinus radiata D. Don (the dominant plantation species) in the belief that alternative species are better suited to deliver these services. Significant risk is associated with this position as there is little objective data to support these views. To identify which species were likely to be planted to deliver ecosystem services, a survey was distributed to examine stakeholder perceptions. Stakeholders were asked which of 15 tree attributes contributed to the provision of five ecosystem services (amenity value, bioenergy production, carbon capture, the diversity of native habitat, and erosion control/water quality) and to identify which of 22 candidate tree species possessed those attributes. These data were combined to identify the species perceived most suitable for the delivery of each ecosystem service. Sequoia sempervirens (D.Don) Endl. closely matched the stakeholder derived ideotypes associated with all five ecosystem services. Comparisons to data from growth, physiological and ecological studies demonstrated that many of the opinions held by stakeholders were inaccurate, leading to erroneous assumptions regarding the suitability of most candidate species. Stakeholder perceptions substantially influence tree species selection, and plantations established on the basis of inaccurate opinions are unlikely to deliver the desired outcomes. Attitudinal surveys associated with engagement campaigns are essential to improve stakeholder knowledge, advancing the development of fit-for-purpose forest management that provides the required ecosystem services.

Produção de painéis compensados fenólicos com lâminas de madeira de Sequoia sempervirens

Directory of Open Access Journals (Sweden)

Setsuo Iwakiri

Full Text Available Esta pesquisa teve como objetivo avaliar a qualidade dos painéis compensados multilaminados produzidos com lâminas de madeira de Sequoia sempervirens. Foram produzidos em laboratório compensados com cinco lâminas de 2,0 mm de espessura, coladas com resina fenol-formaldeído, com duas diferentes formulações: (A FF = 100; E = 5; CC = 5; A = 5, e (B FF = 100; E = 15; CC = 15; A = 15, e duas gramaturas: 280g/m² e 320 g/m². Os painéis foram prensados com pressão específica de 10 kgf/cm², temperatura de 130 ºC e tempo de prensagem de dez minutos. Foram avaliadas as propriedades de resistência da linha de cola aos esforços de cisalhamento e de flexão estática (módulo de elasticidade e módulo de ruptura, paralelo e perpendicular às fibras. De uma forma geral, as diferentes formulações de cola e gramaturas não afetaram significativamente as propriedades dos painéis, o que representa um aspecto importante sob o ponto de vista econômico. A resistência ao cisalhamento e a percentagem de falhas na madeira dos painéis produzidos com a formulação (B atenderam aos requisitos mínimos da norma EN 314-2 (1993 para painéis de uso externo. Os resultados indicam que as lâminas de Sequoia sempervirens podem ser utilizadas para compor o miolo de painéis compensados para uso externo.

Digital gene expression analysis of male and female bud transition in Metasequoia reveals high activity of MADS-box transcription factors and hormone-mediated sugar pathways

OpenAIRE

Zhao, Ying; Liang, Haiying; Li, Lan; Tang, Sha; Han, Xiao; Wang, Congpeng; Xia, Xinli; Yin, Weilun

2015-01-01

Metasequoia glyptostroboides is a famous redwood tree of ecological and economic importance, and requires more than 20 years of juvenile-to-adult transition before producing female and male cones. Previously, we induced reproductive buds using a hormone solution in juvenile Metasequoia trees as young as 5-to-7 years old. In the current study, hormone-treated shoots found in female and male buds were used to identify candidate genes involved in reproductive bud transition in Metasequoia. Sampl...

Attività sperimentale di agricoltura di precisione su vigneto Confronto tra i sensori Mapir Survey2 e Parrot Sequoia

Directory of Open Access Journals (Sweden)

Simone Kartsiotis

2018-01-01

Full Text Available This report presents a comparison via field-testing between Parrot Sequoia and Mapir Survey2 multispectral cameras. Both sensors are commonly used in precision farming activities conducted by micro-RPAS (drones, thanks to their small size and light weight. The experimental activity was performed in summer on the vineyards of the Savignola Paolina agricultural holding in Tuscany. The sensors were taken on board the EXOS drone, a hexacopter developed by Zephyr S.r.l. company and specifically designed for precision farming operations. Good and bad qualities for each cameras are examined by a comprehensive approach, starting from technical specifications and continuing with a comparison of the results obtained on field. All the activity was performed by a partnership between the companies DroneBee and Zephyr S.r.l. .

Preferences of Coptotermes formosanus Shiraki and Coptotermes gestroi (Wasmann (Blattodea: Rhinotermitidae among Three Commercial Wood Species

Directory of Open Access Journals (Sweden)

Nirmala K. Hapukotuwa

2011-11-01

Full Text Available The Formosan subterranean termite, Coptotermes formosanus Shiraki, and the Asian subterranean termite, Coptotermes gestroi (Wasmann, are both pests of wood in service in Hawaii and Florida. We conducted a laboratory study using method modified from those described in standard E1-09 of the American Wood Protection Association (AWPA 2009 to assess the termite resistance of three commercially available wood species used in regions of the USA where both termite species occur: Douglas fir, Pseudotsuga menziessii, southern yellow pine, Pinus spp. and redwood, Sequoia sempervirens. A multiple-choice (three-choice assay was used for four weeks (28 days in order to simulate field conditions of food choice and assess termite feeding preferences under 28 °C and 72–80% RH. 400 termites (360 workers: 40 soldiers were released into each test jar. Five replicates and two controls of each wood species were used with each termite species. Termite mortality was recorded at the end of the test; and wood wafers were oven-dried and weighed before and after termite exposure to determine the mass loss due to termite feeding, and rated visually on a 0 (failure to 10 (sound scale. There were significant differences in mean mass loss values among the three wood species and between two termite species. The mean mass loss value for redwood was significantly lower than Douglas fir and southern yellow pine with both termite species. However, C. formosanus showed increased feeding on Douglas fir and southern yellow pine compared to C. gestroi.

Fostering personal relationships with the wild: Oral history's role in recreation management

Science.gov (United States)

Alison Steiner; Daniel R. Williams

2017-01-01

Sequoia and Kings Canyon National Parks (SEKI) encompass much of central California's most stunning scenery. Dramatic peaks and passes, perennial snowfields, remote lake basins, alpine meadows, steep canyons, and shockingly big trees characterize the more than 800,000 acres of wild land that lie within the parks. Drought-resistant chaparral and blue oak woodlands...

[Phylogenetic relationships among the genera of Taxodiaceae and Cupressaceae from 28S rDNA sequences].

Science.gov (United States)

Li, Chun-Xiang; Yang, Qun

2003-03-01

DNA sequences from 28S rDNA were used to assess relationships between and within traditional Taxodiaceae and Cupressaceae s.s. The MP tree and NJ tree generally are similar to one another. The results show that Taxodiaceae and Cupressaceae s.s. form a monophyletic conifer lineage excluding Sciadopitys. In the Taxodiaceae-Cupressaceae s.s. monophyletic group, the Taxodiaceae is paraphyletic. Taxodium, Glyptostrobus and Cryptomeria forming a clade(Taxodioideae), in which Glyptostrobus and Taxodium are closely related and sister to Cryptomeria; Sequoia, Sequoiadendron and Metasequoia are closely related to each other, forming another clade (Sequoioideae), in which Sequoia and Sequoiadendron are closely related and sister to Metasequoia; the seven genera of Cupressaceae s.s. are found to be closely related to form a monophyletic lineage (Cupressoideae). These results are basically similar to analyses from chloroplast gene data. But the relationships among Taiwania, Sequoioideae, Taxodioideae, and Cupressoideae remain unclear because of the slow evolution rate of 28S rDNA, which might best be answered by sequencing more rapidly evolving nuclear genes.

Large woody debris budgets in the Caspar Creek Experimental Watersheds

Science.gov (United States)

Sue Hilton

2012-01-01

Monitoring of large woody debris (LWD) in the two mainstem channels of the Caspar Creek Experimental Watersheds since 1998, combined with older data from other work in the watersheds, gives estimates of channel wood input rates, survival, and outputs in intermediate-sized channels in coastal redwood forests. Input rates from standing trees for the two reaches over a 15...

In vitro foliage susceptibility of canary islands laurel forests: a model for better understanding the ecology of Phytophthora ramorum

Science.gov (United States)

Eduardo Moralejo; Enrique Descals

2008-01-01

The tree species that dominate the cloud-zone forests of Macaronesia, the coastal redwoods of California, the Valdivian forests of Chile, the Atlantic forests of Brazil and the podocarp forests of New Zealand are all examples of paleoendemic species that once had a much wider distribution. They appear to owe their survival to the particular environmental conditions...

Determining baseline element composition of lichens. II. Hypogymnia enteromorpha and Usnea spp. at Redwood National Park, California

Science.gov (United States)

Gough, L.P.; Jackson, L.L.; Sacklin, J.A.

1988-01-01

Hypogymnia enteromorpha and Usnea spp. were collected in the Little Bald Hills ultramafic region of Redwood National Park, California, to establish element-concentration norms. Baselines are presented for Ba, Ca, Cu, Mn, Ni, P, Sr, V, and Zn for both lichen species; for Li, Mg, and K for H. enteromorpha; and for Al, Ce, Cr, Co, Fe, Na, and Ti for Usnea. Element concentrations of future collections of this same material can be used to monitor possible air quality changes anticipated from mining activities planned nearby. The variability in the element concentrations was partitioned between geographical distance increments and sample preparation and analysis procedures. In general, most of this variability was found in samples less than a few hundreds of meters apart rather than those at about 1 km apart. Therefore, except for Ba and Co, no large geographical element-concentration trends were observed. Samples of both species contained elevated levels of Ni and Mg, which probably reflect the ultramafic terrain over which they occur.

Utilization of silicifed Tertiary wood as raw material for the natural stone industry. [German Democratic Republic

Energy Technology Data Exchange (ETDEWEB)

Bellmann, H J; Schuettler, J; Jakisch, E

1981-11-01

This paper discusses the occurrence of silicified tree trunks and stumps in the Boehlen brown coal field. The trees, mainly Taxodium and Sequoia 25 million years old, are located within the top brown coal seam of the deposit and present a major obstacle to excavator operation, together with other forms of so-called 'brown coal quartzite'. The quartz of the silicified trees occurs as opal, cryptocrystalline quartz and low temperature quartz. The separate removal and disposal of this wood as well as efforts made to use selected wood as raw material are briefly summarized. Various products for interior house decoration have been manufactured from the wood. (4 refs.)

Categorizing ideas about trees: a tree of trees.

Science.gov (United States)

Fisler, Marie; Lecointre, Guillaume

2013-01-01

The aim of this study is to explore whether matrices and MP trees used to produce systematic categories of organisms could be useful to produce categories of ideas in history of science. We study the history of the use of trees in systematics to represent the diversity of life from 1766 to 1991. We apply to those ideas a method inspired from coding homologous parts of organisms. We discretize conceptual parts of ideas, writings and drawings about trees contained in 41 main writings; we detect shared parts among authors and code them into a 91-characters matrix and use a tree representation to show who shares what with whom. In other words, we propose a hierarchical representation of the shared ideas about trees among authors: this produces a "tree of trees." Then, we categorize schools of tree-representations. Classical schools like "cladists" and "pheneticists" are recovered but others are not: "gradists" are separated into two blocks, one of them being called here "grade theoreticians." We propose new interesting categories like the "buffonian school," the "metaphoricians," and those using "strictly genealogical classifications." We consider that networks are not useful to represent shared ideas at the present step of the study. A cladogram is made for showing who is sharing what with whom, but also heterobathmy and homoplasy of characters. The present cladogram is not modelling processes of transmission of ideas about trees, and here it is mostly used to test for proximity of ideas of the same age and for categorization.

A lightning multiple casualty incident in Sequoia and Kings Canyon National Parks.

Science.gov (United States)

Spano, Susanne J; Campagne, Danielle; Stroh, Geoff; Shalit, Marc

2015-03-01

Multiple casualty incidents (MCIs) are uncommon in remote wilderness settings. This is a case report of a lightning strike on a Boy Scout troop hiking through Sequoia and Kings Canyon National Parks (SEKI), in which the lightning storm hindered rescue efforts. The purpose of this study was to review the response to a lightning-caused MCI in a wilderness setting, address lightning injury as it relates to field management, and discuss evacuation options in inclement weather incidents occurring in remote locations. An analysis of SEKI search and rescue data and a review of current literature were performed. A lightning strike at 10,600 feet elevation in the Sierra Nevada Mountains affected a party of 5 adults and 7 Boy Scouts (age range 12 to 17 years old). Resources mobilized for the rescue included 5 helicopters, 2 ambulances, 2 hospitals, and 15 field and 14 logistical support personnel. The incident was managed from strike to scene clearance in 4 hours and 20 minutes. There were 2 fatalities, 1 on scene and 1 in the hospital. Storm conditions complicated on-scene communication and evacuation efforts. Exposure to ongoing lightning and a remote wilderness location affected both victims and rescuers in a lightning MCI. Helicopters, the main vehicles of wilderness rescue in SEKI, can be limited by weather, daylight, and terrain. Redundancies in communication systems are vital for episodes of radio failure. Reverse triage should be implemented in lightning injury MCIs. Education of both wilderness travelers and rescuers regarding these issues should be pursued. Copyright © 2015 Wilderness Medical Society. Published by Elsevier Inc. All rights reserved.

Supporting data for hydrologic studies in San Francisco Bay, California : meteorological measurements at the Port of Redwood City during 1998-2001

Science.gov (United States)

Schemel, Laurence E.

2002-01-01

Meteorological data were collected during 1998-2001 at the Port of Redwood City, California, to support hydrologic studies in South San Francisco Bay. The measured meteorological variables were air temperature, atmospheric pressure, quantum flux (insolation), and four parameters of wind speed and direction: scalar mean horizontal wind speed, (vector) resultant horizontal wind speed, resultant wind direction, and standard deviation of the wind direction. Hourly mean values based on measurements at five-minute intervals were logged at the site. Daily mean values were computed for temperature, infolation, pressure, and scalar wind speed. Daily mean values for 1998-2001 are described in this report, and a short record of hourly mean values is compared to data from another near-by station. Data (hourly and daily mean) from the entire period of record (starting in April 1992) and reports describing data prior to 1998 are provided.

Tree compression with top trees

DEFF Research Database (Denmark)

Bille, Philip; Gørtz, Inge Li; Landau, Gad M.

2013-01-01

We introduce a new compression scheme for labeled trees based on top trees [3]. Our compression scheme is the first to simultaneously take advantage of internal repeats in the tree (as opposed to the classical DAG compression that only exploits rooted subtree repeats) while also supporting fast...

Tree compression with top trees

DEFF Research Database (Denmark)

Bille, Philip; Gørtz, Inge Li; Landau, Gad M.

2015-01-01

We introduce a new compression scheme for labeled trees based on top trees. Our compression scheme is the first to simultaneously take advantage of internal repeats in the tree (as opposed to the classical DAG compression that only exploits rooted subtree repeats) while also supporting fast...

Generalising tree traversals and tree transformations to DAGs

DEFF Research Database (Denmark)

Bahr, Patrick; Axelsson, Emil

2017-01-01

We present a recursion scheme based on attribute grammars that can be transparently applied to trees and acyclic graphs. Our recursion scheme allows the programmer to implement a tree traversal or a tree transformation and then apply it to compact graph representations of trees instead. The resul......We present a recursion scheme based on attribute grammars that can be transparently applied to trees and acyclic graphs. Our recursion scheme allows the programmer to implement a tree traversal or a tree transformation and then apply it to compact graph representations of trees instead...... as the complementing theory with a number of examples....

Surface tree languages and parallel derivation trees

NARCIS (Netherlands)

Engelfriet, Joost

1976-01-01

The surface tree languages obtained by top-down finite state transformation of monadic trees are exactly the frontier-preserving homomorphic images of sets of derivation trees of ETOL systems. The corresponding class of tree transformation languages is therefore equal to the class of ETOL languages.

Critical Loads of Atmospheric Nitrogen Deposition for Aquatic Ecosystems in Yosemite and Sequoia and Kings Canyon National Parks

Science.gov (United States)

Nanus, L.; Clow, D. W.; Sickman, J. O.

2016-12-01

High-elevation aquatic ecosystems in Yosemite (YOSE) and Sequoia and Kings Canyon (SEKI) National Parks are impacted by atmospheric nitrogen (N) deposition associated with local and regional air pollution. Documented effects include elevated surface water nitrate concentrations, increased algal productivity, and changes in diatom species assemblages. Annual wet inorganic N deposition maps, developed at 1-km resolution for YOSE and SEKI to quantify N deposition to sensitive high-elevation ecosystems, range from 1.0 to over 5.0 kg N ha-1 yr-1. Critical loads of N deposition for nutrient enrichment of aquatic ecosystems were quantified and mapped using a geostatistical approach, with N deposition, topography, vegetation, geology, and climate as potential explanatory variables. Multiple predictive models were created using various combinations of explanatory variables; this approach allowed us to better quantify uncertainty and more accurately identify the areas most sensitive to atmospherically deposited N. The lowest critical loads estimates and highest exceedances identified within YOSE and SEKI occurred in high-elevation basins with steep slopes, sparse vegetation, and areas of neoglacial till and talus. These results are consistent with previous analyses in the Rocky Mountains, and highlight the sensitivity of alpine ecosystems to atmospheric N deposition.

TreePics: visualizing trees with pictures

Directory of Open Access Journals (Sweden)

Nicolas Puillandre

2017-09-01

Full Text Available While many programs are available to edit phylogenetic trees, associating pictures with branch tips in an efficient and automatic way is not an available option. Here, we present TreePics, a standalone software that uses a web browser to visualize phylogenetic trees in Newick format and that associates pictures (typically, pictures of the voucher specimens to the tip of each branch. Pictures are visualized as thumbnails and can be enlarged by a mouse rollover. Further, several pictures can be selected and displayed in a separate window for visual comparison. TreePics works either online or in a full standalone version, where it can display trees with several thousands of pictures (depending on the memory available. We argue that TreePics can be particularly useful in a preliminary stage of research, such as to quickly detect conflicts between a DNA-based phylogenetic tree and morphological variation, that may be due to contamination that needs to be removed prior to final analyses, or the presence of species complexes.

Refining age estimates for three historic ground rupturing earthquakes in the Santa Cruz Mountains: 14C Wiggle-matching and Non-Native Pollen as age indicators (or not!)

Science.gov (United States)

Streig, A. R.; Weldon, R. J.; Dawson, T. E.; Guilderson, T.; Gavin, D. G.; Reidy, L.

2013-12-01

The Hazel Dell site provides the first definitive paleoseismic evidence of two pre-1906 19th century events on the Santa Cruz Mountains section based on the presence of anthropogenic artifacts. Hundreds of pieces of cut redwood chips were found in a stratigraphic horizon just below the ante-penultimate (E3) earthquake surface, suggesting that redwood trees at the site were cut down right before earthquake E3. We correlate our paleoseismic findings with the historic record and the onset of redwood logging in the area by determining the felling date of a buried redwood tree stump at the site and the age of the woodchips. We wiggle match 14 radiocarbon dates sampled from annual growth rings taken from the stump and the known interval between growth rings, with the intercepts of the INTCAL04 terrestrial 14C calibration curve. Pending 13C measurements, we find that the youngest ring we have identified in the tree is A.D. 1800. We also wiggle match 2 radiocarbon dates from inner and outer growth rings from two wood chips (with bark); their ages are consistent with the tree and the youngest woodchip ring is dated to 1813 A.D. There are no known ethnographic or historical accounts of pre-contact native people felling large trees in the way that European colonists did. The first record of European land use was for pasture in 1803. The property became a Spanish land grant in 1827, soon after which a whip-saw lumber mill is documented to have begun operation in the upper Corralitos area. We combine these paleoseismic results with historical earthquake accounts for the area and conclude that the San Andreas fault ruptured in 1838, 1890 and 1906. The Hazel Dell results are in contrast with findings from earlier paleoseismic studies in the Santa Cruz Mountains. The Grizzly Flat site, 6 km to the north, found evidence of 1906 and one 17th century earthquake. Two historic earthquakes were observed at the Mill Canyon site 8 km to the south and at the Arano Flat site 9.5 km south of

ColorTree: a batch customization tool for phylogenic trees.

Science.gov (United States)

Chen, Wei-Hua; Lercher, Martin J

2009-07-31

Genome sequencing projects and comparative genomics studies typically aim to trace the evolutionary history of large gene sets, often requiring human inspection of hundreds of phylogenetic trees. If trees are checked for compatibility with an explicit null hypothesis (e.g., the monophyly of certain groups), this daunting task is greatly facilitated by an appropriate coloring scheme. In this note, we introduce ColorTree, a simple yet powerful batch customization tool for phylogenic trees. Based on pattern matching rules, ColorTree applies a set of customizations to an input tree file, e.g., coloring labels or branches. The customized trees are saved to an output file, which can then be viewed and further edited by Dendroscope (a freely available tree viewer). ColorTree runs on any Perl installation as a stand-alone command line tool, and its application can thus be easily automated. This way, hundreds of phylogenic trees can be customized for easy visual inspection in a matter of minutes. ColorTree allows efficient and flexible visual customization of large tree sets through the application of a user-supplied configuration file to multiple tree files.

Cenozoic climate change shaped the evolutionary ecophysiology of the Cupressaceae conifers

OpenAIRE

Pittermann, Jarmila; Stuart, Stephanie A.; Dawson, Todd E.; Moreau, Astrid

2012-01-01

The Cupressaceae clade has the broadest diversity in habitat and morphology of any conifer family. This clade is characterized by highly divergent physiological strategies, with deciduous swamp-adapted genera-like Taxodium at one extreme, and evergreen desert genera-like Cupressus at the other. The size disparity within the Cupressaceae is equally impressive, with members ranging from 5-m-tall juniper shrubs to 100-m-tall redwood trees. Phylogenetic studies demonstrate that despite this varia...

Linking Forests and Fish: The Relationship Between Productivities of Salmonids and Forest Stands in Northern California

Science.gov (United States)

Wilzbach, P.; Frazey, S.

2005-05-01

Productivities of resident salmonid populations, upland, and riparian areas in 25 small watersheds of coastal northern California were estimated and compared to determine if: 1) upland site productivity predicted riparian site productivity; 2) either upland or riparian site productivity predicted salmonid productivity; and 3) other parameters explained more of the variance in salmonid productivity than upland or riparian site productivity. Salmonid productivity was indexed by total salmonid biomass, length of age 1 fish, and percent habitat saturation. Upland and riparian site productivities were estimated using site indices for redwood (Sequoia sempervirens) and red alder (Alnus rubra), respectively. Upland and riparian site indices were correlated, but neither factor contributed to the best approximating models of salmonid biomass or fish length at age one. Salmonid biomass was best described by a positive relationship with drainage area, and length at age was best described by a positive relationship with percent of riparian hardwoods. Percent habitat saturation was not well described by any of the models constructed. Lack of a relationship between upland conifer and salmonid productivity suggests that management of land for timber productivity and component streams for salmonid production in these sites will require separate, albeit integrated, strategies.

Tree Colors: Color Schemes for Tree-Structured Data.

Science.gov (United States)

Tennekes, Martijn; de Jonge, Edwin

2014-12-01

We present a method to map tree structures to colors from the Hue-Chroma-Luminance color model, which is known for its well balanced perceptual properties. The Tree Colors method can be tuned with several parameters, whose effect on the resulting color schemes is discussed in detail. We provide a free and open source implementation with sensible parameter defaults. Categorical data are very common in statistical graphics, and often these categories form a classification tree. We evaluate applying Tree Colors to tree structured data with a survey on a large group of users from a national statistical institute. Our user study suggests that Tree Colors are useful, not only for improving node-link diagrams, but also for unveiling tree structure in non-hierarchical visualizations.

TreePOD: Sensitivity-Aware Selection of Pareto-Optimal Decision Trees.

Science.gov (United States)

Muhlbacher, Thomas; Linhardt, Lorenz; Moller, Torsten; Piringer, Harald

2018-01-01

Balancing accuracy gains with other objectives such as interpretability is a key challenge when building decision trees. However, this process is difficult to automate because it involves know-how about the domain as well as the purpose of the model. This paper presents TreePOD, a new approach for sensitivity-aware model selection along trade-offs. TreePOD is based on exploring a large set of candidate trees generated by sampling the parameters of tree construction algorithms. Based on this set, visualizations of quantitative and qualitative tree aspects provide a comprehensive overview of possible tree characteristics. Along trade-offs between two objectives, TreePOD provides efficient selection guidance by focusing on Pareto-optimal tree candidates. TreePOD also conveys the sensitivities of tree characteristics on variations of selected parameters by extending the tree generation process with a full-factorial sampling. We demonstrate how TreePOD supports a variety of tasks involved in decision tree selection and describe its integration in a holistic workflow for building and selecting decision trees. For evaluation, we illustrate a case study for predicting critical power grid states, and we report qualitative feedback from domain experts in the energy sector. This feedback suggests that TreePOD enables users with and without statistical background a confident and efficient identification of suitable decision trees.

Two Trees: Migrating Fault Trees to Decision Trees for Real Time Fault Detection on International Space Station

Science.gov (United States)

Lee, Charles; Alena, Richard L.; Robinson, Peter

2004-01-01

We started from ISS fault trees example to migrate to decision trees, presented a method to convert fault trees to decision trees. The method shows that the visualizations of root cause of fault are easier and the tree manipulating becomes more programmatic via available decision tree programs. The visualization of decision trees for the diagnostic shows a format of straight forward and easy understands. For ISS real time fault diagnostic, the status of the systems could be shown by mining the signals through the trees and see where it stops at. The other advantage to use decision trees is that the trees can learn the fault patterns and predict the future fault from the historic data. The learning is not only on the static data sets but also can be online, through accumulating the real time data sets, the decision trees can gain and store faults patterns in the trees and recognize them when they come.

Tree Nut Allergies

Science.gov (United States)

... Blog Vision Awards Common Allergens Tree Nut Allergy Tree Nut Allergy Learn about tree nut allergy, how ... a Tree Nut Label card . Allergic Reactions to Tree Nuts Tree nuts can cause a severe and ...

Big trees, old trees, and growth factor tables

Science.gov (United States)

Kevin T. Smith

2018-01-01

The potential for a tree to reach a great size and to live a long life frequently captures the public's imagination. Sometimes the desire to know the age of an impressively large tree is simple curiosity. For others, the date-of-tree establishment can make a big diff erence for management, particularly for trees at historic sites or those mentioned in property...

A Suffix Tree Or Not a Suffix Tree?

DEFF Research Database (Denmark)

Starikovskaya, Tatiana; Vildhøj, Hjalte Wedel

2015-01-01

In this paper we study the structure of suffix trees. Given an unlabeled tree r on n nodes and suffix links of its internal nodes, we ask the question “Is r a suffix tree?”, i.e., is there a string S whose suffix tree has the same topological structure as r? We place no restrictions on S, in part...

Tree-growth analyses to estimate tree species' drought tolerance

NARCIS (Netherlands)

Eilmann, B.; Rigling, A.

2012-01-01

Climate change is challenging forestry management and practices. Among other things, tree species with the ability to cope with more extreme climate conditions have to be identified. However, while environmental factors may severely limit tree growth or even cause tree death, assessing a tree

TreeNetViz: revealing patterns of networks over tree structures.

Science.gov (United States)

Gou, Liang; Zhang, Xiaolong Luke

2011-12-01

Network data often contain important attributes from various dimensions such as social affiliations and areas of expertise in a social network. If such attributes exhibit a tree structure, visualizing a compound graph consisting of tree and network structures becomes complicated. How to visually reveal patterns of a network over a tree has not been fully studied. In this paper, we propose a compound graph model, TreeNet, to support visualization and analysis of a network at multiple levels of aggregation over a tree. We also present a visualization design, TreeNetViz, to offer the multiscale and cross-scale exploration and interaction of a TreeNet graph. TreeNetViz uses a Radial, Space-Filling (RSF) visualization to represent the tree structure, a circle layout with novel optimization to show aggregated networks derived from TreeNet, and an edge bundling technique to reduce visual complexity. Our circular layout algorithm reduces both total edge-crossings and edge length and also considers hierarchical structure constraints and edge weight in a TreeNet graph. These experiments illustrate that the algorithm can reduce visual cluttering in TreeNet graphs. Our case study also shows that TreeNetViz has the potential to support the analysis of a compound graph by revealing multiscale and cross-scale network patterns. © 2011 IEEE

TREE SELECTING AND TREE RING MEASURING IN DENDROCHRONOLOGICAL INVESTIGATIONS

Directory of Open Access Journals (Sweden)

Sefa Akbulut

2004-04-01

Full Text Available Dendrochronology is a method of dating which makes use of the annual nature of tree growth. Dendrochronology may be divided into a number of subfields, each of which covers one or more aspects of the use of tree ring data: dendroclimatology, dendrogeomorphology, dendrohydrology, dendroecology, dendroarchaelogy, and dendrogylaciology. Basic of all form the analysis of the tree rings. The wood or tree rings can aid to dating past events about climatology, ecology, geology, hydrology. Dendrochronological studies are conducted either on increment cores or on discs. It may be seen abnormalities on tree rings during the measurement like that false rings, missing rings, reaction wood. Like that situation, increment cores must be extracted from four different sides of each tree and be studied as more as on tree.

Visualizing Individual Tree Differences in Tree-Ring Studies

Directory of Open Access Journals (Sweden)

Mario Trouillier

2018-04-01

Full Text Available Averaging tree-ring measurements from multiple individuals is one of the most common procedures in dendrochronology. It serves to filter out noise from individual differences between trees, such as competition, height, and micro-site effects, which ideally results in a site chronology sensitive to regional scale factors such as climate. However, the climate sensitivity of individual trees can be modulated by factors like competition, height, and nitrogen deposition, calling attention to whether average chronologies adequately assess climatic growth-control. In this study, we demonstrate four simple but effective methods to visually assess differences between individual trees. Using individual tree climate-correlations we: (1 employed jitter plots with superimposed metadata to assess potential causes for these differences; (2 plotted the frequency distributions of climate correlations over time as heat maps; (3 mapped the spatial distribution of climate sensitivity over time to assess spatio-temporal dynamics; and (4 used t-distributed Stochastic Neighborhood Embedding (t-SNE to assess which trees were generally more similar in terms of their tree-ring pattern and their correlation with climate variables. This suite of exploratory methods can indicate if individuals in tree-ring datasets respond differently to climate variability, and therefore, should not solely be explored with climate correlations of the mean population chronology.

Fault tree handbook

International Nuclear Information System (INIS)

Haasl, D.F.; Roberts, N.H.; Vesely, W.E.; Goldberg, F.F.

1981-01-01

This handbook describes a methodology for reliability analysis of complex systems such as those which comprise the engineered safety features of nuclear power generating stations. After an initial overview of the available system analysis approaches, the handbook focuses on a description of the deductive method known as fault tree analysis. The following aspects of fault tree analysis are covered: basic concepts for fault tree analysis; basic elements of a fault tree; fault tree construction; probability, statistics, and Boolean algebra for the fault tree analyst; qualitative and quantitative fault tree evaluation techniques; and computer codes for fault tree evaluation. Also discussed are several example problems illustrating the basic concepts of fault tree construction and evaluation

Modular tree automata

DEFF Research Database (Denmark)

Bahr, Patrick

2012-01-01

Tree automata are traditionally used to study properties of tree languages and tree transformations. In this paper, we consider tree automata as the basis for modular and extensible recursion schemes. We show, using well-known techniques, how to derive from standard tree automata highly modular...

Rate of tree carbon accumulation increases continuously with tree size.

Science.gov (United States)

Stephenson, N L; Das, A J; Condit, R; Russo, S E; Baker, P J; Beckman, N G; Coomes, D A; Lines, E R; Morris, W K; Rüger, N; Alvarez, E; Blundo, C; Bunyavejchewin, S; Chuyong, G; Davies, S J; Duque, A; Ewango, C N; Flores, O; Franklin, J F; Grau, H R; Hao, Z; Harmon, M E; Hubbell, S P; Kenfack, D; Lin, Y; Makana, J-R; Malizia, A; Malizia, L R; Pabst, R J; Pongpattananurak, N; Su, S-H; Sun, I-F; Tan, S; Thomas, D; van Mantgem, P J; Wang, X; Wiser, S K; Zavala, M A

2014-03-06

Forests are major components of the global carbon cycle, providing substantial feedback to atmospheric greenhouse gas concentrations. Our ability to understand and predict changes in the forest carbon cycle--particularly net primary productivity and carbon storage--increasingly relies on models that represent biological processes across several scales of biological organization, from tree leaves to forest stands. Yet, despite advances in our understanding of productivity at the scales of leaves and stands, no consensus exists about the nature of productivity at the scale of the individual tree, in part because we lack a broad empirical assessment of whether rates of absolute tree mass growth (and thus carbon accumulation) decrease, remain constant, or increase as trees increase in size and age. Here we present a global analysis of 403 tropical and temperate tree species, showing that for most species mass growth rate increases continuously with tree size. Thus, large, old trees do not act simply as senescent carbon reservoirs but actively fix large amounts of carbon compared to smaller trees; at the extreme, a single big tree can add the same amount of carbon to the forest within a year as is contained in an entire mid-sized tree. The apparent paradoxes of individual tree growth increasing with tree size despite declining leaf-level and stand-level productivity can be explained, respectively, by increases in a tree's total leaf area that outpace declines in productivity per unit of leaf area and, among other factors, age-related reductions in population density. Our results resolve conflicting assumptions about the nature of tree growth, inform efforts to undertand and model forest carbon dynamics, and have additional implications for theories of resource allocation and plant senescence.

A bijection between phylogenetic trees and plane oriented recursive trees

OpenAIRE

Prodinger, Helmut

2017-01-01

Phylogenetic trees are binary nonplanar trees with labelled leaves, and plane oriented recursive trees are planar trees with an increasing labelling. Both families are enumerated by double factorials. A bijection is constructed, using the respective representations a 2-partitions and trapezoidal words.

Rate of tree carbon accumulation increases continuously with tree size

Science.gov (United States)

Stephenson, N.L.; Das, A.J.; Condit, R.; Russo, S.E.; Baker, P.J.; Beckman, N.G.; Coomes, D.A.; Lines, E.R.; Morris, W.K.; Rüger, N.; Álvarez, E.; Blundo, C.; Bunyavejchewin, S.; Chuyong, G.; Davies, S.J.; Duque, Á.; Ewango, C.N.; Flores, O.; Franklin, J.F.; Grau, H.R.; Hao, Z.; Harmon, M.E.; Hubbell, S.P.; Kenfack, D.; Lin, Y.; Makana, J.-R.; Malizia, A.; Malizia, L.R.; Pabst, R.J.; Pongpattananurak, N.; Su, S.-H.; Sun, I-F.; Tan, S.; Thomas, D.; van Mantgem, P.J.; Wang, X.; Wiser, S.K.; Zavala, M.A.

2014-01-01

Forests are major components of the global carbon cycle, providing substantial feedback to atmospheric greenhouse gas concentrations. Our ability to understand and predict changes in the forest carbon cycle—particularly net primary productivity and carbon storage - increasingly relies on models that represent biological processes across several scales of biological organization, from tree leaves to forest stands. Yet, despite advances in our understanding of productivity at the scales of leaves and stands, no consensus exists about the nature of productivity at the scale of the individual tree, in part because we lack a broad empirical assessment of whether rates of absolute tree mass growth (and thus carbon accumulation) decrease, remain constant, or increase as trees increase in size and age. Here we present a global analysis of 403 tropical and temperate tree species, showing that for most species mass growth rate increases continuously with tree size. Thus, large, old trees do not act simply as senescent carbon reservoirs but actively fix large amounts of carbon compared to smaller trees; at the extreme, a single big tree can add the same amount of carbon to the forest within a year as is contained in an entire mid-sized tree. The apparent paradoxes of individual tree growth increasing with tree size despite declining leaf-level and stand-level productivity can be explained, respectively, by increases in a tree’s total leaf area that outpace declines in productivity per unit of leaf area and, among other factors, age-related reductions in population density. Our results resolve conflicting assumptions about the nature of tree growth, inform efforts to understand and model forest carbon dynamics, and have additional implications for theories of resource allocation and plant senescence.

IcyTree: rapid browser-based visualization for phylogenetic trees and networks.

Science.gov (United States)

Vaughan, Timothy G

2017-08-01

IcyTree is an easy-to-use application which can be used to visualize a wide variety of phylogenetic trees and networks. While numerous phylogenetic tree viewers exist already, IcyTree distinguishes itself by being a purely online tool, having a responsive user interface, supporting phylogenetic networks (ancestral recombination graphs in particular), and efficiently drawing trees that include information such as ancestral locations or trait values. IcyTree also provides intuitive panning and zooming utilities that make exploring large phylogenetic trees of many thousands of taxa feasible. IcyTree is a web application and can be accessed directly at http://tgvaughan.github.com/icytree . Currently supported web browsers include Mozilla Firefox and Google Chrome. IcyTree is written entirely in client-side JavaScript (no plugin required) and, once loaded, does not require network access to run. IcyTree is free software, and the source code is made available at http://github.com/tgvaughan/icytree under version 3 of the GNU General Public License. tgvaughan@gmail.com. © The Author(s) 2017. Published by Oxford University Press.

TreeScaper: Visualizing and Extracting Phylogenetic Signal from Sets of Trees.

Science.gov (United States)

Huang, Wen; Zhou, Guifang; Marchand, Melissa; Ash, Jeremy R; Morris, David; Van Dooren, Paul; Brown, Jeremy M; Gallivan, Kyle A; Wilgenbusch, Jim C

2016-12-01

Modern phylogenomic analyses often result in large collections of phylogenetic trees representing uncertainty in individual gene trees, variation across genes, or both. Extracting phylogenetic signal from these tree sets can be challenging, as they are difficult to visualize, explore, and quantify. To overcome some of these challenges, we have developed TreeScaper, an application for tree set visualization as well as the identification of distinct phylogenetic signals. GUI and command-line versions of TreeScaper and a manual with tutorials can be downloaded from https://github.com/whuang08/TreeScaper/releases TreeScaper is distributed under the GNU General Public License. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The political ecology of forest health in the redwood region

Science.gov (United States)

Chris Lee; Yana Valachovic; Dan Stark

2017-01-01

Imported forest pests have changed North American forests and caused staggering monetary losses in the centuries since the country was founded. Since most problem-causing non-native pests are innocuous in their home ranges, where they have coevolved with their host trees, experts cannot predict which pathogens or insects will have lethal effect on other continents....

Flowering Trees

Indian Academy of Sciences (India)

IAS Admin

Flowering Trees. Ailanthus excelsa Roxb. (INDIAN TREE OF. HEAVEN) of Simaroubaceae is a lofty tree with large pinnately compound alternate leaves, which are ... inflorescences, unisexual and greenish-yellow. Fruits are winged, wings many-nerved. Wood is used in making match sticks. 1. Male flower; 2. Female flower.

Why do trees die? Characterizing the drivers of background tree mortality

Science.gov (United States)

Das, Adrian J.; Stephenson, Nathan L.; Davis, Kristin P.

2016-01-01

The drivers of background tree mortality rates—the typical low rates of tree mortality found in forests in the absence of acute stresses like drought—are central to our understanding of forest dynamics, the effects of ongoing environmental changes on forests, and the causes and consequences of geographical gradients in the nature and strength of biotic interactions. To shed light on factors contributing to background tree mortality, we analyzed detailed pathological data from 200,668 tree-years of observation and 3,729 individual tree deaths, recorded over a 13-yr period in a network of old-growth forest plots in California's Sierra Nevada mountain range. We found that: (1) Biotic mortality factors (mostly insects and pathogens) dominated (58%), particularly in larger trees (86%). Bark beetles were the most prevalent (40%), even though there were no outbreaks during the study period; in contrast, the contribution of defoliators was negligible. (2) Relative occurrences of broad classes of mortality factors (biotic, 58%; suppression, 51%; and mechanical, 25%) are similar among tree taxa, but may vary with tree size and growth rate. (3) We found little evidence of distinct groups of mortality factors that predictably occur together on trees. Our results have at least three sets of implications. First, rather than being driven by abiotic factors such as lightning or windstorms, the “ambient” or “random” background mortality that many forest models presume to be independent of tree growth rate is instead dominated by biotic agents of tree mortality, with potentially critical implications for forecasting future mortality. Mechanistic models of background mortality, even for healthy, rapidly growing trees, must therefore include the insects and pathogens that kill trees. Second, the biotic agents of tree mortality, instead of occurring in a few predictable combinations, may generally act opportunistically and with a relatively large degree of independence from

Flowering Trees

Indian Academy of Sciences (India)

Flowering Trees. Gyrocarpus americanus Jacq. (Helicopter Tree) of Hernandiaceae is a moderate size deciduous tree that grows to about 12 m in height with a smooth, shining, greenish-white bark. The leaves are ovate, rarely irregularly ... flowers which are unpleasant smelling. Fruit is a woody nut with two long thin wings.

Cache-Oblivious Search Trees via Binary Trees of Small Height

DEFF Research Database (Denmark)

Brodal, G.S.; Fagerberg, R.; Jacob, R.

2002-01-01

We propose a version of cache oblivious search trees which is simpler than the previous proposal of Bender, Demaine and Farach-Colton and has the same complexity bounds. In particular, our data structure avoids the use of weight balanced B-trees, and can be implemented as just a single array......, and range queries in worst case O(logB n + k/B) memory transfers, where k is the size of the output.The basic idea of our data structure is to maintain a dynamic binary tree of height log n+O(1) using existing methods, embed this tree in a static binary tree, which in turn is embedded in an array in a cache...... oblivious fashion, using the van Emde Boas layout of Prokop.We also investigate the practicality of cache obliviousness in the area of search trees, by providing an empirical comparison of different methods for laying out a search tree in memory....

Flowering Trees

Indian Academy of Sciences (India)

Flowering Trees. Boswellia serrata Roxb. ex Colebr. (Indian Frankincense tree) of Burseraceae is a large-sized deciduous tree that is native to India. Bark is thin, greenish-ash-coloured that exfoliates into smooth papery flakes. Stem exudes pinkish resin ... Fruit is a three-valved capsule. A green gum-resin exudes from the ...

Systolic trees and systolic language recognition by tree automata

Energy Technology Data Exchange (ETDEWEB)

Steinby, M

1983-01-01

K. Culik II, J. Gruska, A. Salomaa and D. Wood have studied the language recognition capabilities of certain types of systolically operating networks of processors (see research reports Cs-81-32, Cs-81-36 and Cs-82-01, Univ. of Waterloo, Ontario, Canada). In this paper, their model for systolic VLSI trees is formalised in terms of standard tree automaton theory, and the way in which some known facts about recognisable forests and tree transductions can be applied in VLSI tree theory is demonstrated. 13 references.

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.

Science.gov (United States)

Wehe, André; Bansal, Mukul S; Burleigh, J Gordon; Eulenstein, Oliver

2008-07-01

DupTree is a new software program for inferring rooted species trees from collections of gene trees using the gene tree parsimony approach. The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses. In addition, DupTree allows users to examine alternate rootings and to weight the reconciliation costs for gene trees. DupTree is an open source project written in C++. DupTree for Mac OS X, Windows, and Linux along with a sample dataset and an on-line manual are available at http://genome.cs.iastate.edu/CBL/DupTree

Flowering Trees

Indian Academy of Sciences (India)

More Details Fulltext PDF. Volume 8 Issue 8 August 2003 pp 112-112 Flowering Trees. Zizyphus jujuba Lam. of Rhamnaceae · More Details Fulltext PDF. Volume 8 Issue 9 September 2003 pp 97-97 Flowering Trees. Moringa oleifera · More Details Fulltext PDF. Volume 8 Issue 10 October 2003 pp 100-100 Flowering Trees.

Embedding complete ternary tree in hypercubes using AVL trees

NARCIS (Netherlands)

S.A. Choudum; I. Raman (Indhumathi)

2008-01-01

htmlabstractA complete ternary tree is a tree in which every non-leaf vertex has exactly three children. We prove that a complete ternary tree of height h, TTh, is embeddable in a hypercube of dimension . This result coincides with the result of [2]. However, in this paper, the embedding utilizes

Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses.

Science.gov (United States)

Fouquier, Jennifer; Rideout, Jai Ram; Bolyen, Evan; Chase, John; Shiffer, Arron; McDonald, Daniel; Knight, Rob; Caporaso, J Gregory; Kelley, Scott T

2016-02-24

Fungi play critical roles in many ecosystems, cause serious diseases in plants and animals, and pose significant threats to human health and structural integrity problems in built environments. While most fungal diversity remains unknown, the development of PCR primers for the internal transcribed spacer (ITS) combined with next-generation sequencing has substantially improved our ability to profile fungal microbial diversity. Although the high sequence variability in the ITS region facilitates more accurate species identification, it also makes multiple sequence alignment and phylogenetic analysis unreliable across evolutionarily distant fungi because the sequences are hard to align accurately. To address this issue, we created ghost-tree, a bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach starts with a "foundation" phylogeny based on one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families). Then, "extension" phylogenies are built for more closely related organisms (e.g., fungal species or strains) using a second more rapidly evolving genetic marker. These smaller phylogenies are then grafted onto the foundation tree by mapping taxonomic names such that each corresponding foundation-tree tip would branch into its new "extension tree" child. We applied ghost-tree to graft fungal extension phylogenies derived from ITS sequences onto a foundation phylogeny derived from fungal 18S sequences. Our analysis of simulated and real fungal ITS data sets found that phylogenetic distances between fungal communities computed using ghost-tree phylogenies explained significantly more variance than non-phylogenetic distances. The phylogenetic metrics also improved our ability to distinguish small differences (effect sizes) between microbial communities, though results were similar to non

Trees are good, but…

Science.gov (United States)

E.G. McPherson; F. Ferrini

2010-01-01

We know that “trees are good,” and most people believe this to be true. But if this is so, why are so many trees neglected, and so many tree wells empty? An individual’s attitude toward trees may result from their firsthand encounters with specific trees. Understanding how attitudes about trees are shaped, particularly aversion to trees, is critical to the business of...

Multiple-purpose trees for pastoral farming in New Zealand: with emphasis on tree legumes. [Lucerne Tree: Medick Tree

Energy Technology Data Exchange (ETDEWEB)

Davies, D J.G.; Macfarlane, R P

1979-01-01

The potential for soil conservation and agroforestry of several native and exotic legumes is discussed. Flowering period, chemical composition of leaves/pods, hardiness to frost and drought, timber value, forage potential for livestock and bees, ornamental value and other products are tabulated with information on up to 38 species. Two low-growing species that have proved useful for slope stabilization as well as forage are tree lucerne (Cytisus palmensis) and tree medick (Medicago arborea), the latter being shrubby and more suitable for cold districts. Gleditsia triacanthos is recommended as a shade and fodder tree for farm pasture.

Estimation the remaining service-lifetime of wooden structure of geothermal cooling tower

Directory of Open Access Journals (Sweden)

Effendi Tri Bahtiar

2017-06-01

Full Text Available Similar with other construction materials, wood strength is decreasing when applied by long term loading. Wooden cooling tower structure at Star Energy Geothermal (Wayang Windu Ltd was built in 1998 and it should be evaluated to avoid sudden structural failure. Evaluation conducted through several steps: wood species identification, the physical and mechanical properties testing, and estimation for remaining service-lifetime by generating mathematical models derived from creep test and reduction of cross sectional area of the wood. Identification result that the wood are redwood (Sequoia sempervirens and Douglas fir (Pseudotsuga menziesii. The wood density value has degraded from the surface until 0.25 cm depth. Strength characteristics of the wood have considerably decreased, but the allowable stress for bending, tension parallel to grain, and shear were still higher than NDS2005 requirements. The allowable stress for compression parallel to grain was slightly lower than NDS, while compression perpendicular to grain was much lower. Average modulus of elasticity reduces become lower than the value stated by the code, but the minimum value of modulus of elasticity (Emin of redwood was still higher than the code value, while Emin of Douglas fir is slightly lower. Then, in accordance with those findings, the construction would not failure yet but the deformation and vibration will occur in higher rate than design planning. This research develops mathematical models for estimating the remaining service-lifetime of the wooden cooling tower structure in geothermal power plant based on the wood performance in resisting long term loading and its deterioration rate. The deterioration rate of wood member of cooling tower structure at Star Energy Geothermal (Wayang Windu Ltd is 0.0147 cm depth per year, so equation for the residual service life estimation is σlaterσtoday=bh2(b−0.0147T(h−0.0147T2, and σlater must be lower than allowable stress.

Shedding light on tree growth : ring analysis of juvenile tropical trees

NARCIS (Netherlands)

Soliz Gamboa, C.C.

2010-01-01

In the understory of tropical forests light is believed to be the main limiting growth factor for the newly established trees. Trees growing in shade of the understory may experience periods of slow radial growth. It is expected that gaps created by tree or branch fall will provoke tree growth

Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance

Science.gov (United States)

2013-01-01

Background Constructing species trees from multi-copy gene trees remains a challenging problem in phylogenetics. One difficulty is that the underlying genes can be incongruent due to evolutionary processes such as gene duplication and loss, deep coalescence, or lateral gene transfer. Gene tree estimation errors may further exacerbate the difficulties of species tree estimation. Results We present a new approach for inferring species trees from incongruent multi-copy gene trees that is based on a generalization of the Robinson-Foulds (RF) distance measure to multi-labeled trees (mul-trees). We prove that it is NP-hard to compute the RF distance between two mul-trees; however, it is easy to calculate this distance between a mul-tree and a singly-labeled species tree. Motivated by this, we formulate the RF problem for mul-trees (MulRF) as follows: Given a collection of multi-copy gene trees, find a singly-labeled species tree that minimizes the total RF distance from the input mul-trees. We develop and implement a fast SPR-based heuristic algorithm for the NP-hard MulRF problem. We compare the performance of the MulRF method (available at http://genome.cs.iastate.edu/CBL/MulRF/) with several gene tree parsimony approaches using gene tree simulations that incorporate gene tree error, gene duplications and losses, and/or lateral transfer. The MulRF method produces more accurate species trees than gene tree parsimony approaches. We also demonstrate that the MulRF method infers in minutes a credible plant species tree from a collection of nearly 2,000 gene trees. Conclusions Our new phylogenetic inference method, based on a generalized RF distance, makes it possible to quickly estimate species trees from large genomic data sets. Since the MulRF method, unlike gene tree parsimony, is based on a generic tree distance measure, it is appealing for analyses of genomic data sets, in which many processes such as deep coalescence, recombination, gene duplication and losses as

Trees

Science.gov (United States)

Al-Khaja, Nawal

2007-01-01

This is a thematic lesson plan for young learners about palm trees and the importance of taking care of them. The two part lesson teaches listening, reading and speaking skills. The lesson includes parts of a tree; the modal auxiliary, can; dialogues and a role play activity.

Spectra of chemical trees

International Nuclear Information System (INIS)

Balasubramanian, K.

1982-01-01

A method is developed for obtaining the spectra of trees of NMR and chemical interests. The characteristic polynomials of branched trees can be obtained in terms of the characteristic polynomials of unbranched trees and branches by pruning the tree at the joints. The unbranched trees can also be broken down further until a tree containing just two vertices is obtained. The effectively reduces the order of the secular determinant of the tree used at the beginning to determinants of orders atmost equal to the number of vertices in the branch containing the largest number of vertices. An illustrative example of a NMR graph is given for which the 22 x 22 secular determinant is reduced to determinants of orders atmost 4 x 4 in just the second step of the algorithm. The tree pruning algorithm can be applied even to trees with no symmetry elements and such a factoring can be achieved. Methods developed here can be elegantly used to find if two trees are cospectral and to construct cospectral trees

Estimating the spatial and temporal distribution of species richness within Sequoia and Kings Canyon National Parks.

Directory of Open Access Journals (Sweden)

Steve Wathen

Full Text Available Evidence for significant losses of species richness or biodiversity, even within protected natural areas, is mounting. Managers are increasingly being asked to monitor biodiversity, yet estimating biodiversity is often prohibitively expensive. As a cost-effective option, we estimated the spatial and temporal distribution of species richness for four taxonomic groups (birds, mammals, herpetofauna (reptiles and amphibians, and plants within Sequoia and Kings Canyon National Parks using only existing biological studies undertaken within the Parks and the Parks' long-term wildlife observation database. We used a rarefaction approach to model species richness for the four taxonomic groups and analyzed those groups by habitat type, elevation zone, and time period. We then mapped the spatial distributions of species richness values for the four taxonomic groups, as well as total species richness, for the Parks. We also estimated changes in species richness for birds, mammals, and herpetofauna since 1980. The modeled patterns of species richness either peaked at mid elevations (mammals, plants, and total species richness or declined consistently with increasing elevation (herpetofauna and birds. Plants reached maximum species richness values at much higher elevations than did vertebrate taxa, and non-flying mammals reached maximum species richness values at higher elevations than did birds. Alpine plant communities, including sagebrush, had higher species richness values than did subalpine plant communities located below them in elevation. These results are supported by other papers published in the scientific literature. Perhaps reflecting climate change: birds and herpetofauna displayed declines in species richness since 1980 at low and middle elevations and mammals displayed declines in species richness since 1980 at all elevations.

MeshTree: A Delay optimised Overlay Multicast Tree Building Protocol

OpenAIRE

Tan, Su-Wei; Waters, A. Gill; Crawford, John

2005-01-01

We study decentralised low delay degree-constrained overlay multicast tree construction for single source real-time applications. This optimisation problem is NP-hard even if computed centrally. We identify two problems in traditional distributed solutions, namely the greedy problem and delay-cost trade-off. By offering solutions to these problems, we propose a new self-organising distributed tree building protocol called MeshTree. The main idea is to embed the delivery tree in a degree-bound...

Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction.

Science.gov (United States)

Mai, Uyen; Sayyari, Erfan; Mirarab, Siavash

2017-01-01

Phylogenetic trees inferred using commonly-used models of sequence evolution are unrooted, but the root position matters both for interpretation and downstream applications. This issue has been long recognized; however, whether the potential for discordance between the species tree and gene trees impacts methods of rooting a phylogenetic tree has not been extensively studied. In this paper, we introduce a new method of rooting a tree based on its branch length distribution; our method, which minimizes the variance of root to tip distances, is inspired by the traditional midpoint rerooting and is justified when deviations from the strict molecular clock are random. Like midpoint rerooting, the method can be implemented in a linear time algorithm. In extensive simulations that consider discordance between gene trees and the species tree, we show that the new method is more accurate than midpoint rerooting, but its relative accuracy compared to using outgroups to root gene trees depends on the size of the dataset and levels of deviations from the strict clock. We show high levels of error for all methods of rooting estimated gene trees due to factors that include effects of gene tree discordance, deviations from the clock, and gene tree estimation error. Our simulations, however, did not reveal significant differences between two equivalent methods for species tree estimation that use rooted and unrooted input, namely, STAR and NJst. Nevertheless, our results point to limitations of existing scalable rooting methods.

TreePlus: interactive exploration of networks with enhanced tree layouts.

Science.gov (United States)

Lee, Bongshin; Parr, Cynthia S; Plaisant, Catherine; Bederson, Benjamin B; Veksler, Vladislav D; Gray, Wayne D; Kotfila, Christopher

2006-01-01

Despite extensive research, it is still difficult to produce effective interactive layouts for large graphs. Dense layout and occlusion make food webs, ontologies, and social networks difficult to understand and interact with. We propose a new interactive Visual Analytics component called TreePlus that is based on a tree-style layout. TreePlus reveals the missing graph structure with visualization and interaction while maintaining good readability. To support exploration of the local structure of the graph and gathering of information from the extensive reading of labels, we use a guiding metaphor of "Plant a seed and watch it grow." It allows users to start with a node and expand the graph as needed, which complements the classic overview techniques that can be effective at (but often limited to) revealing clusters. We describe our design goals, describe the interface, and report on a controlled user study with 28 participants comparing TreePlus with a traditional graph interface for six tasks. In general, the advantage of TreePlus over the traditional interface increased as the density of the displayed data increased. Participants also reported higher levels of confidence in their answers with TreePlus and most of them preferred TreePlus.

Refining discordant gene trees.

Science.gov (United States)

Górecki, Pawel; Eulenstein, Oliver

2014-01-01

Evolutionary studies are complicated by discordance between gene trees and the species tree in which they evolved. Dealing with discordant trees often relies on comparison costs between gene and species trees, including the well-established Robinson-Foulds, gene duplication, and deep coalescence costs. While these costs have provided credible results for binary rooted gene trees, corresponding cost definitions for non-binary unrooted gene trees, which are frequently occurring in practice, are challenged by biological realism. We propose a natural extension of the well-established costs for comparing unrooted and non-binary gene trees with rooted binary species trees using a binary refinement model. For the duplication cost we describe an efficient algorithm that is based on a linear time reduction and also computes an optimal rooted binary refinement of the given gene tree. Finally, we show that similar reductions lead to solutions for computing the deep coalescence and the Robinson-Foulds costs. Our binary refinement of Robinson-Foulds, gene duplication, and deep coalescence costs for unrooted and non-binary gene trees together with the linear time reductions provided here for computing these costs significantly extends the range of trees that can be incorporated into approaches dealing with discordance.

Simple street tree sampling

Science.gov (United States)

David J. Nowak; Jeffrey T. Walton; James Baldwin; Jerry. Bond

2015-01-01

Information on street trees is critical for management of this important resource. Sampling of street tree populations provides an efficient means to obtain street tree population information. Long-term repeat measures of street tree samples supply additional information on street tree changes and can be used to report damages from catastrophic events. Analyses of...

TreeFam: a curated database of phylogenetic trees of animal gene families

DEFF Research Database (Denmark)

Li, Heng; Coghlan, Avril; Ruan, Jue

2006-01-01

TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. Curated families are being added progressively......, based on seed alignments and trees in a similar fashion to Pfam. Release 1.1 of TreeFam contains curated trees for 690 families and automatically generated trees for another 11 646 families. These represent over 128 000 genes from nine fully sequenced animal genomes and over 45 000 other animal proteins...

Tree-space statistics and approximations for large-scale analysis of anatomical trees

DEFF Research Database (Denmark)

Feragen, Aasa; Owen, Megan; Petersen, Jens

2013-01-01

parametrize the relevant parts of tree-space well. Using the developed approximate statistics, we illustrate how the structure and geometry of airway trees vary across a population and show that airway trees with Chronic Obstructive Pulmonary Disease come from a different distribution in tree-space than...

Relating phylogenetic trees to transmission trees of infectious disease outbreaks.

Science.gov (United States)

Ypma, Rolf J F; van Ballegooijen, W Marijn; Wallinga, Jacco

2013-11-01

Transmission events are the fundamental building blocks of the dynamics of any infectious disease. Much about the epidemiology of a disease can be learned when these individual transmission events are known or can be estimated. Such estimations are difficult and generally feasible only when detailed epidemiological data are available. The genealogy estimated from genetic sequences of sampled pathogens is another rich source of information on transmission history. Optimal inference of transmission events calls for the combination of genetic data and epidemiological data into one joint analysis. A key difficulty is that the transmission tree, which describes the transmission events between infected hosts, differs from the phylogenetic tree, which describes the ancestral relationships between pathogens sampled from these hosts. The trees differ both in timing of the internal nodes and in topology. These differences become more pronounced when a higher fraction of infected hosts is sampled. We show how the phylogenetic tree of sampled pathogens is related to the transmission tree of an outbreak of an infectious disease, by the within-host dynamics of pathogens. We provide a statistical framework to infer key epidemiological and mutational parameters by simultaneously estimating the phylogenetic tree and the transmission tree. We test the approach using simulations and illustrate its use on an outbreak of foot-and-mouth disease. The approach unifies existing methods in the emerging field of phylodynamics with transmission tree reconstruction methods that are used in infectious disease epidemiology.

Decision-Tree Program

Science.gov (United States)

Buntine, Wray

1994-01-01

IND computer program introduces Bayesian and Markov/maximum-likelihood (MML) methods and more-sophisticated methods of searching in growing trees. Produces more-accurate class-probability estimates important in applications like diagnosis. Provides range of features and styles with convenience for casual user, fine-tuning for advanced user or for those interested in research. Consists of four basic kinds of routines: data-manipulation, tree-generation, tree-testing, and tree-display. Written in C language.

Tree-growth analyses to estimate tree species' drought tolerance.

Science.gov (United States)

Eilmann, Britta; Rigling, Andreas

2012-02-01

Climate change is challenging forestry management and practices. Among other things, tree species with the ability to cope with more extreme climate conditions have to be identified. However, while environmental factors may severely limit tree growth or even cause tree death, assessing a tree species' potential for surviving future aggravated environmental conditions is rather demanding. The aim of this study was to find a tree-ring-based method suitable for identifying very drought-tolerant species, particularly potential substitute species for Scots pine (Pinus sylvestris L.) in Valais. In this inner-Alpine valley, Scots pine used to be the dominating species for dry forests, but today it suffers from high drought-induced mortality. We investigate the growth response of two native tree species, Scots pine and European larch (Larix decidua Mill.), and two non-native species, black pine (Pinus nigra Arnold) and Douglas fir (Pseudotsuga menziesii Mirb. var. menziesii), to drought. This involved analysing how the radial increment of these species responded to increasing water shortage (abandonment of irrigation) and to increasingly frequent drought years. Black pine and Douglas fir are able to cope with drought better than Scots pine and larch, as they show relatively high radial growth even after irrigation has been stopped and a plastic growth response to drought years. European larch does not seem to be able to cope with these dry conditions as it lacks the ability to recover from drought years. The analysis of trees' short-term response to extreme climate events seems to be the most promising and suitable method for detecting how tolerant a tree species is towards drought. However, combining all the methods used in this study provides a complete picture of how water shortage could limit species.

Are trees long-lived?

Science.gov (United States)

Kevin T. Smith

2009-01-01

Trees and tree care can capture the best of people's motivations and intentions. Trees are living memorials that help communities heal at sites of national tragedy, such as Oklahoma City and the World Trade Center. We mark the places of important historical events by the trees that grew nearby even if the original tree, such as the Charter Oak in Connecticut or...

There's Life in Hazard Trees

Science.gov (United States)

Mary Torsello; Toni McLellan

The goals of hazard tree management programs are to maximize public safety and maintain a healthy sustainable tree resource. Although hazard tree management frequently targets removal of trees or parts of trees that attract wildlife, it can take into account a diversity of tree values. With just a little extra planning, hazard tree management can be highly beneficial...

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Energy Technology Data Exchange (ETDEWEB)

N. Price, Morgan; S. Dehal, Paramvir; P. Arkin, Adam

2009-07-31

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

A natural resource condition assessment for Sequoia and Kings Canyon National Parks: Appendix 22: climatic change

Science.gov (United States)

Das, Adrian J.; Stephenson, Nathan L.

2013-01-01

Climate is a master controller of the structure, composition, and function of biotic communities, affecting them both directly, through physiological effects, and indirectly, by mediating biotic interactions and by influencing disturbance regimes. Sequoia and Kings Canyon National Park’s (SEKI’s) dramatic elevational changes in biotic communities -- from warm mediterranean to cold alpine -- are but one manifestation of climate’s overarching importance in shaping SEKI’s landscape. Yet humans are now altering the global climate, with measurable effects on ecosystems (IPCC 2007). Over the last few decades across the western United States, human-induced climatic changes have likely contributed to observed declines in fraction of precipitation falling as snow and snowpack water content (Mote et al. 2005, Knowles et al. 2006), advance in spring snowmelt (Stewart et al. 2005, Barnett et al. 2008), and consequent increase in area burned in wildfires (Westerling et al. 2006). In the Sierra Nevada, warming temperatures have likely contributed to observed glacial recession (Basagic 2008), uphill migration of small mammals (Moritz et al. 2008), and increasing tree mortality rates (van Mantgem and Stephenson 2007, van Mantgem et al. 2009). More substantial changes can be expected for the future (e.g., IPCC 2007). Given the central importance of climate and climatic changes, we sought to describe long-term trends in temperature and precipitation at SEKI. Time and budget constraints limited us to analyses of mean annual temperature and mean annual precipitation, using readily-available data. If funds become available in the future, further analyses will be needed to analyze trends by season, trends in daily minimum and maximum temperatures, and so on. We chose to analyze data from individual weather stations rather than use interpolated climatic data from sources such as PRISM (http://www.prism.oregonstate.edu/). In topographically complex mountainous regions with few

TreeRipper web application: towards a fully automated optical tree recognition software

Directory of Open Access Journals (Sweden)

Hughes Joseph

2011-05-01

Full Text Available Abstract Background Relationships between species, genes and genomes have been printed as trees for over a century. Whilst this may have been the best format for exchanging and sharing phylogenetic hypotheses during the 20th century, the worldwide web now provides faster and automated ways of transferring and sharing phylogenetic knowledge. However, novel software is needed to defrost these published phylogenies for the 21st century. Results TreeRipper is a simple website for the fully-automated recognition of multifurcating phylogenetic trees (http://linnaeus.zoology.gla.ac.uk/~jhughes/treeripper/. The program accepts a range of input image formats (PNG, JPG/JPEG or GIF. The underlying command line c++ program follows a number of cleaning steps to detect lines, remove node labels, patch-up broken lines and corners and detect line edges. The edge contour is then determined to detect the branch length, tip label positions and the topology of the tree. Optical Character Recognition (OCR is used to convert the tip labels into text with the freely available tesseract-ocr software. 32% of images meeting the prerequisites for TreeRipper were successfully recognised, the largest tree had 115 leaves. Conclusions Despite the diversity of ways phylogenies have been illustrated making the design of a fully automated tree recognition software difficult, TreeRipper is a step towards automating the digitization of past phylogenies. We also provide a dataset of 100 tree images and associated tree files for training and/or benchmarking future software. TreeRipper is an open source project licensed under the GNU General Public Licence v3.

MixtureTree annotator: a program for automatic colorization and visual annotation of MixtureTree.

Directory of Open Access Journals (Sweden)

Shu-Chuan Chen

Full Text Available The MixtureTree Annotator, written in JAVA, allows the user to automatically color any phylogenetic tree in Newick format generated from any phylogeny reconstruction program and output the Nexus file. By providing the ability to automatically color the tree by sequence name, the MixtureTree Annotator provides a unique advantage over any other programs which perform a similar function. In addition, the MixtureTree Annotator is the only package that can efficiently annotate the output produced by MixtureTree with mutation information and coalescent time information. In order to visualize the resulting output file, a modified version of FigTree is used. Certain popular methods, which lack good built-in visualization tools, for example, MEGA, Mesquite, PHY-FI, TreeView, treeGraph and Geneious, may give results with human errors due to either manually adding colors to each node or with other limitations, for example only using color based on a number, such as branch length, or by taxonomy. In addition to allowing the user to automatically color any given Newick tree by sequence name, the MixtureTree Annotator is the only method that allows the user to automatically annotate the resulting tree created by the MixtureTree program. The MixtureTree Annotator is fast and easy-to-use, while still allowing the user full control over the coloring and annotating process.

On Determining if Tree-based Networks Contain Fixed Trees.

Science.gov (United States)

Anaya, Maria; Anipchenko-Ulaj, Olga; Ashfaq, Aisha; Chiu, Joyce; Kaiser, Mahedi; Ohsawa, Max Shoji; Owen, Megan; Pavlechko, Ella; St John, Katherine; Suleria, Shivam; Thompson, Keith; Yap, Corrine

2016-05-01

We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is N based on T? We show that it is [Formula: see text]-hard to decide, by reduction from 3-Dimensional Matching (3DM) and further that the problem is fixed-parameter tractable.

Whole-tree distribution and temporal variation of non-structural carbohydrates in broadleaf evergreen trees.

Science.gov (United States)

Smith, Merryn G; Miller, Rebecca E; Arndt, Stefan K; Kasel, Sabine; Bennett, Lauren T

2018-04-01

Non-structural carbohydrates (NSCs) form a fundamental yet poorly quantified carbon pool in trees. Studies of NSC seasonality in forest trees have seldom measured whole-tree NSC stocks and allocation among organs, and are not representative of all tree functional types. Non-structural carbohydrate research has primarily focussed on broadleaf deciduous and coniferous evergreen trees with distinct growing seasons, while broadleaf evergreen trees remain under-studied despite their different growth phenology. We measured whole-tree NSC allocation and temporal variation in Eucalyptus obliqua L'Hér., a broadleaf evergreen tree species typically occurring in mixed-age temperate forests, which has year-round growth and the capacity to resprout after fire. Our overarching objective was to improve the empirical basis for understanding the functional importance of NSC allocation and stock changes at the tree- and organ-level in this tree functional type. Starch was the principal storage carbohydrate and was primarily stored in the stem and roots of young (14-year-old) trees rather than the lignotuber, which did not appear to be a specialized starch storage organ. Whole-tree NSC stocks were depleted during spring and summer due to significant decreases in starch mass in the roots and stem, seemingly to support root and crown growth but potentially exacerbated by water stress in summer. Seasonality of stem NSCs differed between young and mature trees, and was not synchronized with stem basal area increments in mature trees. Our results suggest that the relative magnitude of seasonal NSC stock changes could vary with tree growth stage, and that the main drivers of NSC fluctuations in broadleaf evergreen trees in temperate biomes could be periodic disturbances such as summer drought and fire, rather than growth phenology. These results have implications for understanding post-fire tree recovery via resprouting, and for incorporating NSC pools into carbon models of mixed

The effect of contaminated groundwater on tree growth: A tree-ring analysis

International Nuclear Information System (INIS)

LeBlanc, D.C.; Loehle, C.

1990-10-01

A study was conducted on the effect of contaminated groundwater seepage on tree growth downslope from F- and H-Area seepage basins of the Savannah River Site. Trees in wetlands along Four Mile Creek began to show localized stress and mortality in the late 1970s. Extreme winter temperatures and high rainfall were ruled out as potential causal factors of tree stress. Drought was shown to affect trees in both contaminated and uncontaminated zones, but trees in uncontaminated areas exhibit better recovery after drought than trees in contaminated areas. Pollution-mediated alteration of soil acidity and aluminum, sodium, and heavy metal concentrations likely acted to predispose trees to decline, with severe drought acting as the trigger for decline initiation and tree death. Thus, a moderate pollution loading, not sufficient to cause visible damage of itself, may create conditions in which sudden, severe decline could result from natural stresses. This mechanism of forest decline is common, and should be considered in evaluations of the impact of pollution on wetland forest systems. 28 refs., 4 figs., 6 tabs

SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees.

Science.gov (United States)

Beccati, Alan; Gerken, Jan; Quast, Christian; Yilmaz, Pelin; Glöckner, Frank Oliver

2017-09-30

Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the taxonomic framework. The SILVA Tree Viewer is a web application designed for visualizing large phylogenetic trees without requiring the download of any software tool or data files. The SILVA Tree Viewer is based on Web Geographic Information Systems (Web-GIS) technology with a PostgreSQL backend. It enables zoom and pan functionalities similar to Google Maps. The SILVA Tree Viewer enables access to two phylogenetic (guide) trees provided by the SILVA database: the SSU Ref NR99 inferred from high-quality, full-length small subunit sequences, clustered at 99% sequence identity and the LSU Ref inferred from high-quality, full-length large subunit sequences. The Tree Viewer provides tree navigation, search and browse tools as well as an interactive feedback system to collect any kinds of requests ranging from taxonomy to data curation and improving the tool itself.

D2-tree

DEFF Research Database (Denmark)

Brodal, Gerth Stølting; Sioutas, Spyros; Pantazos, Kostas

2015-01-01

We present a new overlay, called the Deterministic Decentralized tree (D2-tree). The D2-tree compares favorably to other overlays for the following reasons: (a) it provides matching and better complexities, which are deterministic for the supported operations; (b) the management of nodes (peers...

Tree felling 2014

CERN Multimedia

2014-01-01

With a view to creating new landscapes and making its population of trees safer and healthier, this winter CERN will complete the tree-felling campaign started in 2010.   Tree felling will take place between 15 and 22 November on the Swiss part of the Meyrin site. This work is being carried out above all for safety reasons. The trees to be cut down are at risk of falling as they are too old and too tall to withstand the wind. In addition, the roots of poplar trees are very powerful and spread widely, potentially damaging underground networks, pavements and roadways. Compensatory tree planting campaigns will take place in the future, subject to the availability of funding, with the aim of creating coherent landscapes while also respecting the functional constraints of the site. These matters are being considered in close collaboration with the Geneva nature and countryside directorate (Direction générale de la nature et du paysage, DGNP). GS-SE Group

Phylogenetic trees

OpenAIRE

Baños, Hector; Bushek, Nathaniel; Davidson, Ruth; Gross, Elizabeth; Harris, Pamela E.; Krone, Robert; Long, Colby; Stewart, Allen; Walker, Robert

2016-01-01

We introduce the package PhylogeneticTrees for Macaulay2 which allows users to compute phylogenetic invariants for group-based tree models. We provide some background information on phylogenetic algebraic geometry and show how the package PhylogeneticTrees can be used to calculate a generating set for a phylogenetic ideal as well as a lower bound for its dimension. Finally, we show how methods within the package can be used to compute a generating set for the join of any two ideals.

Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent.

Science.gov (United States)

Allman, Elizabeth S; Degnan, James H; Rhodes, John A

2011-06-01

Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals-each with many genes-splitting into new populations or species. The coalescent process, which models ancestry of gene copies within populations, is often used to model the probability distribution of gene trees given a fixed species tree. This multispecies coalescent model provides a framework for phylogeneticists to infer species trees from gene trees using maximum likelihood or Bayesian approaches. Because the coalescent models a branching process over time, all trees are typically assumed to be rooted in this setting. Often, however, gene trees inferred by traditional phylogenetic methods are unrooted. We investigate probabilities of unrooted gene trees under the multispecies coalescent model. We show that when there are four species with one gene sampled per species, the distribution of unrooted gene tree topologies identifies the unrooted species tree topology and some, but not all, information in the species tree edges (branch lengths). The location of the root on the species tree is not identifiable in this situation. However, for 5 or more species with one gene sampled per species, we show that the distribution of unrooted gene tree topologies identifies the rooted species tree topology and all its internal branch lengths. The length of any pendant branch leading to a leaf of the species tree is also identifiable for any species from which more than one gene is sampled.

Covering tree with stars

DEFF Research Database (Denmark)

Baumbach, Jan; Guo, Jiong; Ibragimov, Rashid

2015-01-01

We study the tree edit distance problem with edge deletions and edge insertions as edit operations. We reformulate a special case of this problem as Covering Tree with Stars (CTS): given a tree T and a set of stars, can we connect the stars in by adding edges between them such that the resulting...... tree is isomorphic to T? We prove that in the general setting, CST is NP-complete, which implies that the tree edit distance considered here is also NP-hard, even when both input trees having diameters bounded by 10. We also show that, when the number of distinct stars is bounded by a constant k, CTS...

Trees in the city: valuing street trees in Portland, Oregon

Science.gov (United States)

G.H. Donovan; D.T. Butry

2010-01-01

We use a hedonic price model to simultaneously estimate the effects of street trees on the sales price and the time-on-market (TOM) of houses in Portland. Oregon. On average, street trees add $8,870 to sales price and reduce TOM by 1.7 days. In addition, we found that the benefits of street trees spill over to neighboring houses. Because the provision and maintenance...

Urban tree growth modeling

Science.gov (United States)

E. Gregory McPherson; Paula J. Peper

2012-01-01

This paper describes three long-term tree growth studies conducted to evaluate tree performance because repeated measurements of the same trees produce critical data for growth model calibration and validation. Several empirical and process-based approaches to modeling tree growth are reviewed. Modeling is more advanced in the fields of forestry and...

Electron Tree

DEFF Research Database (Denmark)

Appelt, Ane L; Rønde, Heidi S

2013-01-01

The photo shows a close-up of a Lichtenberg figure – popularly called an “electron tree” – produced in a cylinder of polymethyl methacrylate (PMMA). Electron trees are created by irradiating a suitable insulating material, in this case PMMA, with an intense high energy electron beam. Upon discharge......, during dielectric breakdown in the material, the electrons generate branching chains of fractures on leaving the PMMA, producing the tree pattern seen. To be able to create electron trees with a clinical linear accelerator, one needs to access the primary electron beam used for photon treatments. We...... appropriated a linac that was being decommissioned in our department and dismantled the head to circumvent the target and ion chambers. This is one of 24 electron trees produced before we had to stop the fun and allow the rest of the accelerator to be disassembled....

Classification and regression trees

CERN Document Server

Breiman, Leo; Olshen, Richard A; Stone, Charles J

1984-01-01

The methodology used to construct tree structured rules is the focus of this monograph. Unlike many other statistical procedures, which moved from pencil and paper to calculators, this text's use of trees was unthinkable before computers. Both the practical and theoretical sides have been developed in the authors' study of tree methods. Classification and Regression Trees reflects these two sides, covering the use of trees as a data analysis method, and in a more mathematical framework, proving some of their fundamental properties.

FB-Tree: A B+-Tree for Flash-Based SSDs

DEFF Research Database (Denmark)

Jørgensen, Martin V.; Rasmussen, René B.; Saltenis, Simonas

2011-01-01

Due to their many advantages, flash-based SSDs (Solid-State Drives) have become a mainstream alternative to magnetic disks for database servers. Nevertheless, database systems, designed and optimized for magnetic disks, still do not fully exploit all the benefits of the new technology. We propose....... As a consequence, the FB-tree outperforms a regular B+-tree in all scenarios tested. For instance, the throughput of a random workload of 75% updates increases by a factor of three using only two times the space of the B+-tree....

Benefit-based tree valuation

Science.gov (United States)

E.G. McPherson

2007-01-01

Benefit-based tree valuation provides alternative estimates of the fair and reasonable value of trees while illustrating the relative contribution of different benefit types. This study compared estimates of tree value obtained using cost- and benefit-based approaches. The cost-based approach used the Council of Landscape and Tree Appraisers trunk formula method, and...

Fragmentation of random trees

International Nuclear Information System (INIS)

Kalay, Z; Ben-Naim, E

2015-01-01

We study fragmentation of a random recursive tree into a forest by repeated removal of nodes. The initial tree consists of N nodes and it is generated by sequential addition of nodes with each new node attaching to a randomly-selected existing node. As nodes are removed from the tree, one at a time, the tree dissolves into an ensemble of separate trees, namely, a forest. We study statistical properties of trees and nodes in this heterogeneous forest, and find that the fraction of remaining nodes m characterizes the system in the limit N→∞. We obtain analytically the size density ϕ s of trees of size s. The size density has power-law tail ϕ s ∼s −α with exponent α=1+(1/m). Therefore, the tail becomes steeper as further nodes are removed, and the fragmentation process is unusual in that exponent α increases continuously with time. We also extend our analysis to the case where nodes are added as well as removed, and obtain the asymptotic size density for growing trees. (paper)

FTAP, Minimal Cut Sets of Arbitrary Fault Trees. FRTPLT, Fault Tree Structure and Logical Gates Plot for Program FTAP. FRTGEN, Fault Trees by Sub-tree Generator from Parent Tree for Program FTAP

International Nuclear Information System (INIS)

Willie, Randall R.; Rabien, U.

1997-01-01

1 - Description of problem or function: FTAP is a general-purpose program for deriving minimal reliability cut and path set families from the fault tree for a complex system. The program has a number of useful features that make it well-suited to nearly all fault tree applications. An input fault tree may specify the system state as any logical function of subsystem or component state variables or complements of these variables; thus, for instance, 'exclusive-or' type relations may be formed. When fault tree logical relations involve complements of state variables, the analyst may instruct FTAP to produce a family of prime implicants, a generalization of the minimal cut set concept. The program offers the flexibility of several distinct methods of generating cut set families. FTAP can also identify certain subsystems as system modules and provide a collection of minimal cut set families that essentially expresses the system state as a function of these module state variables. Another feature allows a useful subfamily to be obtained when the family of minimal cut sets or prime implicants is too large to be found in its entirety; this subfamily may consist of only those sets not containing more than some fixed number of elements or only those sets 'interesting' to the analyst in some special sense. Finally, the analyst can modify the input fault tree in various ways by declaring state variables identically true or false. 2 - Method of solution: Fault tree methods are based on the observation that the system state, either working or failed, can usually be expressed as a Boolean relation between states of several large, readily identifiable subsystems. The state of each subsystem in turn depends on states of simpler subsystems and components which compose it, so that the state of the system itself is determined by a hierarchy of logical relationships between states of subsystems. A fault tree is a graphical representation of these relationships. 3 - Restrictions on the

REPP: A Case Study in Federal Financing--Long Term Fiscal and Instructional Implications. A Project Report.

Science.gov (United States)

Kistler, Kathleen M.

A study was conducted at the College of the Redwoods to analyze the fiscal, institutional, and instructional impact of the Redwood Employees Protection Plan (REPP) program, a federally funded retraining program for timber workers displaced by redwood park expansion. The study involved telephone interviews with 37 former and current students, 16…

Winter Birch Trees

Science.gov (United States)

Sweeney, Debra; Rounds, Judy

2011-01-01

Trees are great inspiration for artists. Many art teachers find themselves inspired and maybe somewhat obsessed with the natural beauty and elegance of the lofty tree, and how it changes through the seasons. One such tree that grows in several regions and always looks magnificent, regardless of the time of year, is the birch. In this article, the…

36 CFR 223.4 - Exchange of trees or portions of trees.

Science.gov (United States)

2010-07-01

... 36 Parks, Forests, and Public Property 2 2010-07-01 2010-07-01 false Exchange of trees or portions of trees. 223.4 Section 223.4 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF AGRICULTURE SALE AND DISPOSAL OF NATIONAL FOREST SYSTEM TIMBER General Provisions § 223.4 Exchange of trees or...

How many trees are enough? Tree death and the urban canopy

Science.gov (United States)

Lara A. Roman

2014-01-01

Massive city tree planting campaigns have invigorated the urban forestry movement, and engaged politicians, planners, and the public in urban greening. Million tree initiatives have been launched in Los Angeles, CA; Denver, CO; New York City, NY; Philadelphia, PA, and other cities. Sacramento, CA even has a five million tree program. These...

Keeping trees as assets

Science.gov (United States)

Kevin T. Smith

2009-01-01

Landscape trees have real value and contribute to making livable communities. Making the most of that value requires providing trees with the proper care and attention. As potentially large and long-lived organisms, trees benefit from commitment to regular care that respects the natural tree system. This system captures, transforms, and uses energy to survive, grow,...

Visualization of Uncertain Contour Trees

DEFF Research Database (Denmark)

Kraus, Martin

2010-01-01

Contour trees can represent the topology of large volume data sets in a relatively compact, discrete data structure. However, the resulting trees often contain many thousands of nodes; thus, many graph drawing techniques fail to produce satisfactory results. Therefore, several visualization methods...... were proposed recently for the visualization of contour trees. Unfortunately, none of these techniques is able to handle uncertain contour trees although any uncertainty of the volume data inevitably results in partially uncertain contour trees. In this work, we visualize uncertain contour trees...... by combining the contour trees of two morphologically filtered versions of a volume data set, which represent the range of uncertainty. These two contour trees are combined and visualized within a single image such that a range of potential contour trees is represented by the resulting visualization. Thus...

Forest FIRE and FIRE wood : tools for tree automata and tree algorithms

NARCIS (Netherlands)

Cleophas, L.G.W.A.; Piskorski, J.; Watson, B.W.; Yli-Jyrä, A.

2009-01-01

Pattern matching, acceptance, and parsing algorithms on node-labeled, ordered, ranked trees ('tree algorithms') are important for applications such as instruction selection and tree transformation/term rewriting. Many such algorithms have been developed. They often are based on results from such

Monitoring Million Trees LA: Tree performance during the early years and future benefits

Science.gov (United States)

E. Gregory McPherson

2014-01-01

Million Trees LA (MTLA) is one of several large-scale mayoral tree planting initiatives striving to create more livable cities through urban forestry. This study combined field sampling of tree survival and growth with numerical modeling of future benefits to assess performance of MTLA plantings. From 2006 to 2010 MTLA planted a diverse mix of 91,786 trees....

Skewed Binary Search Trees

DEFF Research Database (Denmark)

Brodal, Gerth Stølting; Moruz, Gabriel

2006-01-01

It is well-known that to minimize the number of comparisons a binary search tree should be perfectly balanced. Previous work has shown that a dominating factor over the running time for a search is the number of cache faults performed, and that an appropriate memory layout of a binary search tree...... can reduce the number of cache faults by several hundred percent. Motivated by the fact that during a search branching to the left or right at a node does not necessarily have the same cost, e.g. because of branch prediction schemes, we in this paper study the class of skewed binary search trees....... For all nodes in a skewed binary search tree the ratio between the size of the left subtree and the size of the tree is a fixed constant (a ratio of 1/2 gives perfect balanced trees). In this paper we present an experimental study of various memory layouts of static skewed binary search trees, where each...

The ghosts of trees past: savanna trees create enduring legacies in plant species composition.

Science.gov (United States)

Stahlheber, Karen A; Crispin, Kimberly L; Anton, Cassidy; D'Antonio, Carla M

2015-09-01

Isolated trees in savannas worldwide are known to modify their local environment and interact directly with neighboring plants. Less is known about how related tree species differ in their impacts on surrounding communities, how the effects of trees vary between years, and how composition might change following loss of the tree. To address these knowledge gaps, we explored the following questions: How do savanna trees influence the surrounding composition of herbaceous plants? Is the influence of trees consistent across different species and years? How does this change following the death of the tree? We surveyed herbaceous species composition and environmental attributes surrounding living and dead evergreen and deciduous Quercus trees in California (USA) savannas across several years that differed in their total precipitation. Oak trees of all species created distinct, homogenous understory communities dominated by exotic grasses across several sites. The composition of the low-diversity understory communities showed less interannual variation than open grassland, despite a two-fold difference in precipitation between the driest and wettest year. Vegetation composition was correlated with variation in soil properties, which were strongly affected by trees. Oaks also influenced the communities beyond the edge of the crown, but this depended on site and oak species. Low-diversity understory communities persisted up to 43 years following the death of the tree. A gradual decline in the effect of trees on the physical, environment following death did not result in vegetation becoming more similar to open grassland over time. The presence of long-lasting legacies of past tree crowns highlights the difficulty of assigning control of the current distribution of herbaceous species in grassland to their contemporary environment.

Barking up the wrong tree: injuries due to falls from trees in Solomon Islands.

Science.gov (United States)

Negin, Joel; Vizintin, Pavle; Houasia, Patrick; Martiniuk, Alexandra L C

2014-12-11

To investigate tree-related injuries in Solomon Islands by the types of trees involved, who is affected and the types of injuries caused. Descriptive case series of all cases of injuries related to trees presenting to the National Referral Hospital in Honiara from 1994 to 2011. Data were collected by the attending clinician using a Trauma Epidemiology form, which provides information on age, sex, cause of injury and type of fracture. Number of injuries by tree type, sex and age. Of the 7651 injuries in the database, 1107 (14%) were caused by falls from trees. Falls from coconut trees led to the highest number of injuries, followed by falls from mango, guava, apple and nut trees. Overall, 85% of injuries occurred in individuals aged trees, 77% of patients were aged tree types. Overall, 71% of injuries occurred among males. Of all injuries, 92% were fractures, 3% were dislocations and 5% were non-fracture, non-dislocation injuries. The arm (including wrist, elbow and hand) was the most common location of injury across all tree types. Distal radius fractures in the forearm were particularly common, as were ulna fractures. While mangos and guavas are undeniably delicious, the quest for their flesh can be hazardous. Children will always climb trees, but the search for food among children in lower-income settings may lead to higher rates of injury.

Recursive Trees for Practical ORAM

Directory of Open Access Journals (Sweden)

Moataz Tarik

2015-06-01

Full Text Available We present a new, general data structure that reduces the communication cost of recent tree-based ORAMs. Contrary to ORAM trees with constant height and path lengths, our new construction r-ORAM allows for trees with varying shorter path length. Accessing an element in the ORAM tree results in different communication costs depending on the location of the element. The main idea behind r-ORAM is a recursive ORAM tree structure, where nodes in the tree are roots of other trees. While this approach results in a worst-case access cost (tree height at most as any recent tree-based ORAM, we show that the average cost saving is around 35% for recent binary tree ORAMs. Besides reducing communication cost, r-ORAM also reduces storage overhead on the server by 4% to 20% depending on the ORAM’s client memory type. To prove r-ORAM’s soundness, we conduct a detailed overflow analysis. r-ORAM’s recursive approach is general in that it can be applied to all recent tree ORAMs, both constant and poly-log client memory ORAMs. Finally, we implement and benchmark r-ORAM in a practical setting to back up our theoretical claims.

Tree Transduction Tools for Cdec

Directory of Open Access Journals (Sweden)

Austin Matthews

2014-09-01

Full Text Available We describe a collection of open source tools for learning tree-to-string and tree-to-tree transducers and the extensions to the cdec decoder that enable translation with these. Our modular, easy-to-extend tools extract rules from trees or forests aligned to strings and trees subject to different structural constraints. A fast, multithreaded implementation of the Cohn and Blunsom (2009 model for extracting compact tree-to-string rules is also included. The implementation of the tree composition algorithm used by cdec is described, and translation quality and decoding time results are presented. Our experimental results add to the body of evidence suggesting that tree transducers are a compelling option for translation, particularly when decoding speed and translation model size are important.

City of Pittsburgh Trees

Data.gov (United States)

Allegheny County / City of Pittsburgh / Western PA Regional Data Center — Trees cared for and managed by the City of Pittsburgh Department of Public Works Forestry Division. Tree Benefits are calculated using the National Tree Benefit...

Flowering Trees

Indian Academy of Sciences (India)

user

Flowering Trees. Gliricidia sepium(Jacq.) Kunta ex Walp. (Quickstick) of Fabaceae is a small deciduous tree with. Pinnately compound leaves. Flower are prroduced in large number in early summer on terminal racemes. They are attractive, pinkish-white and typically like bean flowers. Fruit is a few-seeded flat pod.

Drawing Trees

DEFF Research Database (Denmark)

Halkjær From, Andreas; Schlichtkrull, Anders; Villadsen, Jørgen

2018-01-01

We formally prove in Isabelle/HOL two properties of an algorithm for laying out trees visually. The first property states that removing layout annotations recovers the original tree. The second property states that nodes are placed at least a unit of distance apart. We have yet to formalize three...

Interspecific variation in tree seedlings establishment in canopy gaps in relation to tree density

Energy Technology Data Exchange (ETDEWEB)

Reader, R.J.; Bonser, S.P.; Duralia, T.E.; Bricker, B.D. [Guelph Univ., ON (Canada). Dept. of Botany

1995-10-01

We tested whether interspecific variation in tree seedling establishment in canopy gaps was significantly related to interspecific variation in tree density, for seven deciduous forest tree species (Quercus alba, Hamamelis virginiana, Acer rubrum, Sassafras albidum, Quercus rubra, Prunus serotina, Ostrya virginiana). For each species, seedling establishment was calculated as the difference in seedling density before experimental gap creation versus three years after gap creation. In each of the six experimentally-created gap types (33% or 66% removal of tree basal area from 0.01ha, 0.05ha or 0.20ha patches), differences in seedling establishment among species were significantly related to differences in their density in the tree canopy. A regression model with log{sub e} tree density as the independent variable accounted for between 93% and 98% of interspecific variation in seedling establishment. Our results provide empirical support for models of tree dynamics in gaps that assume seedling establishment depends on canopy tree density. 17 refs, 1 fig, 3 tabs

Phylogenetic trees in bioinformatics

Energy Technology Data Exchange (ETDEWEB)

Burr, Tom L [Los Alamos National Laboratory

2008-01-01

Genetic data is often used to infer evolutionary relationships among a collection of viruses, bacteria, animal or plant species, or other operational taxonomic units (OTU). A phylogenetic tree depicts such relationships and provides a visual representation of the estimated branching order of the OTUs. Tree estimation is unique for several reasons, including: the types of data used to represent each OTU; the use ofprobabilistic nucleotide substitution models; the inference goals involving both tree topology and branch length, and the huge number of possible trees for a given sample of a very modest number of OTUs, which implies that fmding the best tree(s) to describe the genetic data for each OTU is computationally demanding. Bioinformatics is too large a field to review here. We focus on that aspect of bioinformatics that includes study of similarities in genetic data from multiple OTUs. Although research questions are diverse, a common underlying challenge is to estimate the evolutionary history of the OTUs. Therefore, this paper reviews the role of phylogenetic tree estimation in bioinformatics, available methods and software, and identifies areas for additional research and development.

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

OpenAIRE

N. Price, Morgan

2009-01-01

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor i...

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

OpenAIRE

Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P.

2009-01-01

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement Neighbor-Joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest neighbor in...

Flowering Trees

Indian Academy of Sciences (India)

Flowering Trees. Acrocarpus fraxinifolius Wight & Arn. (PINK CEDAR, AUSTRALIAN ASH) of. Caesalpiniaceae is a lofty unarmed deciduous native tree that attains a height of 30–60m with buttresses. Bark is thin and light grey. Leaves are compound and bright red when young. Flowers in dense, erect, axillary racemes.

On Tree-Based Phylogenetic Networks.

Science.gov (United States)

Zhang, Louxin

2016-07-01

A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree-based networks. We present a simple necessary and sufficient condition for tree-based networks and prove that a universal tree-based network exists for any number of taxa that contains as its base every phylogenetic tree on the same set of taxa. This answers two problems posted by Francis and Steel recently. A byproduct is a computer program for generating random binary phylogenetic networks under the uniform distribution model.

A Metric on Phylogenetic Tree Shapes.

Science.gov (United States)

Colijn, C; Plazzotta, G

2018-01-01

The shapes of evolutionary trees are influenced by the nature of the evolutionary process but comparisons of trees from different processes are hindered by the challenge of completely describing tree shape. We present a full characterization of the shapes of rooted branching trees in a form that lends itself to natural tree comparisons. We use this characterization to define a metric, in the sense of a true distance function, on tree shapes. The metric distinguishes trees from random models known to produce different tree shapes. It separates trees derived from tropical versus USA influenza A sequences, which reflect the differing epidemiology of tropical and seasonal flu. We describe several metrics based on the same core characterization, and illustrate how to extend the metric to incorporate trees' branch lengths or other features such as overall imbalance. Our approach allows us to construct addition and multiplication on trees, and to create a convex metric on tree shapes which formally allows computation of average tree shapes. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

Wildfire and forest disease interaction lead to greater loss of soil nutrients and carbon.

Science.gov (United States)

Cobb, Richard C; Meentemeyer, Ross K; Rizzo, David M

2016-09-01

Fire and forest disease have significant ecological impacts, but the interactions of these two disturbances are rarely studied. We measured soil C, N, Ca, P, and pH in forests of the Big Sur region of California impacted by the exotic pathogen Phytophthora ramorum, cause of sudden oak death, and the 2008 Basin wildfire complex. In Big Sur, overstory tree mortality following P. ramorum invasion has been extensive in redwood and mixed evergreen forests, where the pathogen kills true oaks and tanoak (Notholithocarpus densiflorus). Sampling was conducted across a full-factorial combination of disease/no disease and burned/unburned conditions in both forest types. Forest floor organic matter and associated nutrients were greater in unburned redwood compared to unburned mixed evergreen forests. Post-fire element pools were similar between forest types, but lower in burned-invaded compared to burned-uninvaded plots. We found evidence disease-generated fuels led to increased loss of forest floor C, N, Ca, and P. The same effects were associated with lower %C and higher PO4-P in the mineral soil. Fire-disease interactions were linear functions of pre-fire host mortality which was similar between the forest types. Our analysis suggests that these effects increased forest floor C loss by as much as 24.4 and 21.3 % in redwood and mixed evergreen forests, respectively, with similar maximum losses for the other forest floor elements. Accumulation of sudden oak death generated fuels has potential to increase fire-related loss of soil nutrients at the region-scale of this disease and similar patterns are likely in other forests, where fire and disease overlap.

Visualizing phylogenetic tree landscapes.

Science.gov (United States)

Wilgenbusch, James C; Huang, Wen; Gallivan, Kyle A

2017-02-02

Genomic-scale sequence alignments are increasingly used to infer phylogenies in order to better understand the processes and patterns of evolution. Different partitions within these new alignments (e.g., genes, codon positions, and structural features) often favor hundreds if not thousands of competing phylogenies. Summarizing and comparing phylogenies obtained from multi-source data sets using current consensus tree methods discards valuable information and can disguise potential methodological problems. Discovery of efficient and accurate dimensionality reduction methods used to display at once in 2- or 3- dimensions the relationship among these competing phylogenies will help practitioners diagnose the limits of current evolutionary models and potential problems with phylogenetic reconstruction methods when analyzing large multi-source data sets. We introduce several dimensionality reduction methods to visualize in 2- and 3-dimensions the relationship among competing phylogenies obtained from gene partitions found in three mid- to large-size mitochondrial genome alignments. We test the performance of these dimensionality reduction methods by applying several goodness-of-fit measures. The intrinsic dimensionality of each data set is also estimated to determine whether projections in 2- and 3-dimensions can be expected to reveal meaningful relationships among trees from different data partitions. Several new approaches to aid in the comparison of different phylogenetic landscapes are presented. Curvilinear Components Analysis (CCA) and a stochastic gradient decent (SGD) optimization method give the best representation of the original tree-to-tree distance matrix for each of the three- mitochondrial genome alignments and greatly outperformed the method currently used to visualize tree landscapes. The CCA + SGD method converged at least as fast as previously applied methods for visualizing tree landscapes. We demonstrate for all three mtDNA alignments that 3D

Human decision error (HUMDEE) trees

International Nuclear Information System (INIS)

Ostrom, L.T.

1993-01-01

Graphical presentations of human actions in incident and accident sequences have been used for many years. However, for the most part, human decision making has been underrepresented in these trees. This paper presents a method of incorporating the human decision process into graphical presentations of incident/accident sequences. This presentation is in the form of logic trees. These trees are called Human Decision Error Trees or HUMDEE for short. The primary benefit of HUMDEE trees is that they graphically illustrate what else the individuals involved in the event could have done to prevent either the initiation or continuation of the event. HUMDEE trees also present the alternate paths available at the operator decision points in the incident/accident sequence. This is different from the Technique for Human Error Rate Prediction (THERP) event trees. There are many uses of these trees. They can be used for incident/accident investigations to show what other courses of actions were available and for training operators. The trees also have a consequence component so that not only the decision can be explored, also the consequence of that decision

Tree felling: a necessary evil

CERN Multimedia

CERN Bulletin

2013-01-01

CERN started a campaign of tree felling in 2010 for safety reasons, and it will continue this year in various parts of the Meyrin site. As in previous years, the trees cut down in 2013 will be recycled and some will be replaced.   Diseased tree that had to be cut down on the Meyrin site. In association with the Geneva nature and countryside directorate (Direction générale de la nature et du paysage, DGNP), CERN commissioned the Geneva school of landscaping, engineering and architecture (Haute école du paysage, d’ingénierie et d’architecture, HEPIA) to compile an inventory of the trees on the Meyrin site. In total, 1285 trees (excluding poplars) were recorded. 75.5% of these trees were declared to be in a good state of health (i.e. 971 trees), 21.5% in a moderate state of health (276 trees) and 3% in a poor state of health (38 trees). As for the poplars, the 236 specimens recorded on the Meyrin site were judged to be too old, to...

Per tree estimates with n-tree distance sampling: an application to increment core data

Science.gov (United States)

Thomas B. Lynch; Robert F. Wittwer

2002-01-01

Per tree estimates using the n trees nearest a point can be obtained by using a ratio of per unit area estimates from n-tree distance sampling. This ratio was used to estimate average age by d.b.h. classes for cottonwood trees (Populus deltoides Bartr. ex Marsh.) on the Cimarron National Grassland. Increment...

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy.

Science.gov (United States)

Letunic, Ivica; Bork, Peer

2011-07-01

Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. In addition to classical tree viewer functions, iTOL offers many novel ways of annotating trees with various additional data. Current version introduces numerous new features and greatly expands the number of supported data set types. Trees can be interactively manipulated and edited. A free personal account system is available, providing management and sharing of trees in user defined workspaces and projects. Export to various bitmap and vector graphics formats is supported. Batch access interface is available for programmatic access or inclusion of interactive trees into other web services.

Maximum Gene-Support Tree

Directory of Open Access Journals (Sweden)

Yunfeng Shan

2008-01-01

Full Text Available Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced as well as plants that have the fossil-supported true phylogenetic trees available. In this study, we generated single gene trees of seven yeast species as well as single gene trees of nine baculovirus species using all the orthologous genes among the species compared. Homologous genes among seven known plants were used for validation of the finding. Four algorithms—maximum parsimony (MP, minimum evolution (ME, maximum likelihood (ML, and neighbor-joining (NJ—were used. Trees were reconstructed before and after weighting the DNA and protein sequence lengths among genes. Rarely a gene can always generate the “true tree” by all the four algorithms. However, the most frequent gene tree, termed “maximum gene-support tree” (MGS tree, or WMGS tree for the weighted one, in yeasts, baculoviruses, or plants was consistently found to be the “true tree” among the species. The results provide insights into the overall degree of divergence of orthologous genes of the genomes analyzed and suggest the following: 1 The true tree relationship among the species studied is still maintained by the largest group of orthologous genes; 2 There are usually more orthologous genes with higher similarities between genetically closer species than between genetically more distant ones; and 3 The maximum gene-support tree reflects the phylogenetic relationship among species in comparison.

Tree Rings: Timekeepers of the Past.

Science.gov (United States)

Phipps, R. L.; McGowan, J.

One of a series of general interest publications on science issues, this booklet describes the uses of tree rings in historical and biological recordkeeping. Separate sections cover the following topics: dating of tree rings, dating with tree rings, tree ring formation, tree ring identification, sample collections, tree ring cross dating, tree…

Flowering Trees

Indian Academy of Sciences (India)

Cassia siamia Lamk. (Siamese tree senna) of Caesalpiniaceae is a small or medium size handsome tree. Leaves are alternate, pinnately compound and glandular, upto 18 cm long with 8–12 pairs of leaflets. Inflorescence is axillary or terminal and branched. Flowering lasts for a long period from March to February. Fruit is ...

Flowering Trees

Indian Academy of Sciences (India)

Flowering Trees. Cerbera manghasL. (SEA MANGO) of Apocynaceae is a medium-sized evergreen coastal tree with milky latex. The bark is grey-brown, thick and ... Fruit is large. (5–10 cm long), oval containing two flattened seeds and resembles a mango, hence the name Mangas or. Manghas. Leaves and fruits contain ...

Talking Trees

Science.gov (United States)

Tolman, Marvin

2005-01-01

Students love outdoor activities and will love them even more when they build confidence in their tree identification and measurement skills. Through these activities, students will learn to identify the major characteristics of trees and discover how the pace--a nonstandard measuring unit--can be used to estimate not only distances but also the…

ELB-trees an efficient and lock-free B-tree derivative

DEFF Research Database (Denmark)

Bonnichsen, Lars Frydendal; Karlsson, Sven; Probst, Christian W.

2013-01-01

overhead. All lock-free data structures are based on simple atomic operations that, though supported by modern processors, are expensive in execution time. We present a lock-free data structure, ELB-trees, which under certain assumptions can be used as multimaps as well as priority queues. Specifically...... it cannot store duplicate key-value pairs, and it is not linearizable. Compared to existing data structures, ELB-trees require fewer atomic operations leading to improved performance. We measure the parallel performance of ELB-trees using a set of benchmarks and observe that ELB-trees are up to almost 30......As computer systems scale in the number of processors, scalable data structures with good parallel performance become increasingly important. Lock-free data structures promise such improved parallel performance at the expense of higher algorithmic complexity and higher sequential execution time...

A support vector machine based test for incongruence between sets of trees in tree space

Science.gov (United States)

2012-01-01

Background The increased use of multi-locus data sets for phylogenetic reconstruction has increased the need to determine whether a set of gene trees significantly deviate from the phylogenetic patterns of other genes. Such unusual gene trees may have been influenced by other evolutionary processes such as selection, gene duplication, or horizontal gene transfer. Results Motivated by this problem we propose a nonparametric goodness-of-fit test for two empirical distributions of gene trees, and we developed the software GeneOut to estimate a p-value for the test. Our approach maps trees into a multi-dimensional vector space and then applies support vector machines (SVMs) to measure the separation between two sets of pre-defined trees. We use a permutation test to assess the significance of the SVM separation. To demonstrate the performance of GeneOut, we applied it to the comparison of gene trees simulated within different species trees across a range of species tree depths. Applied directly to sets of simulated gene trees with large sample sizes, GeneOut was able to detect very small differences between two set of gene trees generated under different species trees. Our statistical test can also include tree reconstruction into its test framework through a variety of phylogenetic optimality criteria. When applied to DNA sequence data simulated from different sets of gene trees, results in the form of receiver operating characteristic (ROC) curves indicated that GeneOut performed well in the detection of differences between sets of trees with different distributions in a multi-dimensional space. Furthermore, it controlled false positive and false negative rates very well, indicating a high degree of accuracy. Conclusions The non-parametric nature of our statistical test provides fast and efficient analyses, and makes it an applicable test for any scenario where evolutionary or other factors can lead to trees with different multi-dimensional distributions. The

Atlas of United States Trees, Volume 2: Alaska Trees and Common Shrubs.

Science.gov (United States)

Viereck, Leslie A.; Little, Elbert L., Jr.

This volume is the second in a series of atlases describing the natural distribution or range of native tree species in the United States. The 82 species maps include 32 of trees in Alaska, 6 of shrubs rarely reaching tree size, and 44 more of common shrubs. More than 20 additional maps summarize environmental factors and furnish general…

Colourings of (k-r,k-trees

Directory of Open Access Journals (Sweden)

M. Borowiecki

2017-01-01

Full Text Available Trees are generalized to a special kind of higher dimensional complexes known as \\((j,k\\-trees ([L. W. Beineke, R. E. Pippert, On the structure of \\((m,n\\-trees, Proc. 8th S-E Conf. Combinatorics, Graph Theory and Computing, 1977, 75-80], and which are a natural extension of \\(k\\-trees for \\(j=k-1\\. The aim of this paper is to study\\((k-r,k\\-trees ([H. P. Patil, Studies on \\(k\\-trees and some related topics, PhD Thesis, University of Warsaw, Poland, 1984], which are a generalization of \\(k\\-trees (or usual trees when \\(k=1\\. We obtain the chromatic polynomial of \\((k-r,k\\-trees and show that any two \\((k-r,k\\-trees of the same order are chromatically equivalent. However, if \\(r\

The valuative tree

CERN Document Server

Favre, Charles

2004-01-01

This volume is devoted to a beautiful object, called the valuative tree and designed as a powerful tool for the study of singularities in two complex dimensions. Its intricate yet manageable structure can be analyzed by both algebraic and geometric means. Many types of singularities, including those of curves, ideals, and plurisubharmonic functions, can be encoded in terms of positive measures on the valuative tree. The construction of these measures uses a natural tree Laplace operator of independent interest.

A recursive algorithm for trees and forests

OpenAIRE

Guo, Song; Guo, Victor J. W.

2017-01-01

Trees or rooted trees have been generously studied in the literature. A forest is a set of trees or rooted trees. Here we give recurrence relations between the number of some kind of rooted forest with $k$ roots and that with $k+1$ roots on $\\{1,2,\\ldots,n\\}$. Classical formulas for counting various trees such as rooted trees, bipartite trees, tripartite trees, plane trees, $k$-ary plane trees, $k$-edge colored trees follow immediately from our recursive relations.

Understanding recruitment failure in tropical tree species: Insights from a tree ring study

NARCIS (Netherlands)

Vlam, M.; Baker, P.J.; Bunyavejchewin, S.; Mohren, G.M.J.; Zuidema, P.A.

2014-01-01

Many tropical tree species have population structures that exhibit strong recruitment failure. While the presence of adult trees indicates that appropriate regeneration conditions occurred in the past, it is often unclear why small individuals are absent. Knowing how, when and where these tree

Attack Trees with Sequential Conjunction

NARCIS (Netherlands)

Jhawar, Ravi; Kordy, Barbara; Mauw, Sjouke; Radomirović, Sasa; Trujillo-Rasua, Rolando

2015-01-01

We provide the first formal foundation of SAND attack trees which are a popular extension of the well-known attack trees. The SAND at- tack tree formalism increases the expressivity of attack trees by intro- ducing the sequential conjunctive operator SAND. This operator enables the modeling of

Tree Size Comparison of Some Important Street Trees Growing at ...

African Journals Online (AJOL)

PROF HORSFALL

More research is needed on these trees for healthy environment of city. The present ..... use and CO2 emissions from power plants. Environ. Poll. .... Anna. Bot., 65:567-574. Kozlowski, T.T., 1971. Growth and Development of. Trees. Vol. 1.

Flowering Trees

Indian Academy of Sciences (India)

medium-sized handsome tree with a straight bole that branches at the top. Leaves are once pinnate, with two to three pairs of leaflets. Young parts of the tree are velvety. Inflorescence is a branched raceme borne at the branch ends. Flowers are large, white, attractive, and fragrant. Corolla is funnel-shaped. Fruit is an ...

Flowering Trees

Indian Academy of Sciences (India)

Srimath

Grevillea robusta A. Cunn. ex R. Br. (Sil- ver Oak) of Proteaceae is a daintily lacy ornamental tree while young and growing into a mighty tree (45 m). Young shoots are silvery grey and the leaves are fern- like. Flowers are golden-yellow in one- sided racemes (10 cm). Fruit is a boat- shaped, woody follicle.

Mathematical foundations of event trees

International Nuclear Information System (INIS)

Papazoglou, Ioannis A.

1998-01-01

A mathematical foundation from first principles of event trees is presented. The main objective of this formulation is to offer a formal basis for developing automated computer assisted construction techniques for event trees. The mathematical theory of event trees is based on the correspondence between the paths of the tree and the elements of the outcome space of a joint event. The concept of a basic cylinder set is introduced to describe joint event outcomes conditional on specific outcomes of basic events or unconditional on the outcome of basic events. The concept of outcome space partition is used to describe the minimum amount of information intended to be preserved by the event tree representation. These concepts form the basis for an algorithm for systematic search for and generation of the most compact (reduced) form of an event tree consistent with the minimum amount of information the tree should preserve. This mathematical foundation allows for the development of techniques for automated generation of event trees corresponding to joint events which are formally described through other types of graphical models. Such a technique has been developed for complex systems described by functional blocks and it is reported elsewhere. On the quantification issue of event trees, a formal definition of a probability space corresponding to the event tree outcomes is provided. Finally, a short discussion is offered on the relationship of the presented mathematical theory with the more general use of event trees in reliability analysis of dynamic systems

Stand conditions and tree characteristics affect quality of longleaf pine for red-cockaded woodpecker cavity trees

Science.gov (United States)

W.G. Ross; D.L. Kulhavy; R.N. Conner

1997-01-01

We measured resin flow of longleaf (Pinus palustris Mill.) pines in red-cockaded woodpecker (Picoides borealis Vieillot) clusters in the Angelina National Forest in Texas, and the Apalachicola National Forest in Florida. Sample trees were categorized as active cavity trees, inactive cavity trees and control trees. Sample trees were further...

Making CSB + -Trees Processor Conscious

DEFF Research Database (Denmark)

Samuel, Michael; Pedersen, Anders Uhl; Bonnet, Philippe

2005-01-01

of the CSB+-tree. We argue that it is necessary to consider a larger group of parameters in order to adapt CSB+-tree to processor architectures as different as Pentium and Itanium. We identify this group of parameters and study how it impacts the performance of CSB+-tree on Itanium 2. Finally, we propose......Cache-conscious indexes, such as CSB+-tree, are sensitive to the underlying processor architecture. In this paper, we focus on how to adapt the CSB+-tree so that it performs well on a range of different processor architectures. Previous work has focused on the impact of node size on the performance...... a systematic method for adapting CSB+-tree to new platforms. This work is a first step towards integrating CSB+-tree in MySQL’s heap storage manager....

Tree architecture and life-history strategies across 200 co-occurring tropical tree species

NARCIS (Netherlands)

Iida, Y.; Kohyama, T.S.; Kubo, T.; Kassim, A.R.; Poorter, L.; Sterck, F.J.; Potts, M.D.

2011-01-01

1. Tree architecture is thought to allow species to partition horizontal and vertical light gradients in the forest canopy. Tree architecture is closely related to light capture, carbon gain and the efficiency with which trees reach the canopy. Previous studies that investigated how light gradients

Total well dominated trees

DEFF Research Database (Denmark)

Finbow, Arthur; Frendrup, Allan; Vestergaard, Preben D.

cardinality then G is a total well dominated graph. In this paper we study composition and decomposition of total well dominated trees. By a reversible process we prove that any total well dominated tree can both be reduced to and constructed from a family of three small trees....

Recursive algorithms for phylogenetic tree counting.

Science.gov (United States)

Gavryushkina, Alexandra; Welch, David; Drummond, Alexei J

2013-10-28

In Bayesian phylogenetic inference we are interested in distributions over a space of trees. The number of trees in a tree space is an important characteristic of the space and is useful for specifying prior distributions. When all samples come from the same time point and no prior information available on divergence times, the tree counting problem is easy. However, when fossil evidence is used in the inference to constrain the tree or data are sampled serially, new tree spaces arise and counting the number of trees is more difficult. We describe an algorithm that is polynomial in the number of sampled individuals for counting of resolutions of a constraint tree assuming that the number of constraints is fixed. We generalise this algorithm to counting resolutions of a fully ranked constraint tree. We describe a quadratic algorithm for counting the number of possible fully ranked trees on n sampled individuals. We introduce a new type of tree, called a fully ranked tree with sampled ancestors, and describe a cubic time algorithm for counting the number of such trees on n sampled individuals. These algorithms should be employed for Bayesian Markov chain Monte Carlo inference when fossil data are included or data are serially sampled.

New perspectives on the ecology of tree structure and tree communities through terrestrial laser scanning.

Science.gov (United States)

Malhi, Yadvinder; Jackson, Tobias; Patrick Bentley, Lisa; Lau, Alvaro; Shenkin, Alexander; Herold, Martin; Calders, Kim; Bartholomeus, Harm; Disney, Mathias I

2018-04-06

Terrestrial laser scanning (TLS) opens up the possibility of describing the three-dimensional structures of trees in natural environments with unprecedented detail and accuracy. It is already being extensively applied to describe how ecosystem biomass and structure vary between sites, but can also facilitate major advances in developing and testing mechanistic theories of tree form and forest structure, thereby enabling us to understand why trees and forests have the biomass and three-dimensional structure they do. Here we focus on the ecological challenges and benefits of understanding tree form, and highlight some advances related to capturing and describing tree shape that are becoming possible with the advent of TLS. We present examples of ongoing work that applies, or could potentially apply, new TLS measurements to better understand the constraints on optimization of tree form. Theories of resource distribution networks, such as metabolic scaling theory, can be tested and further refined. TLS can also provide new approaches to the scaling of woody surface area and crown area, and thereby better quantify the metabolism of trees. Finally, we demonstrate how we can develop a more mechanistic understanding of the effects of avoidance of wind risk on tree form and maximum size. Over the next few years, TLS promises to deliver both major empirical and conceptual advances in the quantitative understanding of trees and tree-dominated ecosystems, leading to advances in understanding the ecology of why trees and ecosystems look and grow the way they do.

Tree manipulation experiment

Science.gov (United States)

Nishina, K.; Takenaka, C.; Ishizuka, S.; Hashimoto, S.; Yagai, Y.

2012-12-01

Some forest operations such as thinning and harvesting management could cause changes in N cycling and N2O emission from soils, since thinning and harvesting managements are accompanied with changes in aboveground environments such as an increase of slash falling and solar radiation on the forest floor. However, a considerable uncertainty exists in effects of thinning and harvesting on N2O fluxes regarding changes in belowground environments by cutting trees. To focus on the effect of changes in belowground environments on the N2O emissions from soils, we conducted a tree manipulation experiment in Japanese cedar (Cryptomeria japonica) stand without soil compaction and slash falling near the chambers and measured N2O flux at 50 cm and 150 cm distances from the tree trunk (stump) before and after cutting. We targeted 5 trees for the manipulation and established the measurement chambers to the 4 directions around each targeted tree relative to upper slope (upper, left, right, lower positions). We evaluated the effect of logging on the emission by using hierarchical Bayesian model. HB model can evaluate the variability in observed data and their uncertainties in the estimation with various probability distributions. Moreover, the HB model can easily accommodate the non-linear relationship among the N2O emissions and the environmental factors, and explicitly take non-independent data (nested structure of data) for the estimation into account by using random effects in the model. Our results showed tree cutting stimulated N2O emission from soils, and also that the increase of N2O flux depended on the distance from the trunk (stump): the increase of N2O flux at 50 cm from the trunk (stump) was greater than that of 150 cm from the trunk. The posterior simulation of the HB model indicated that the stimulation of N2O emission by tree cut- ting could reach up to 200 cm in our experimental plot. By tree cutting, the estimated N2O emission at 0-40 cm from the trunk doubled

The Re-Think Tree.

Science.gov (United States)

Gear, Jim

1993-01-01

The Re-Think Tree is a simple framework to help individuals assess and improve their behaviors related to environmental issues. The branches of the tree in order of priority are refuse, reduce, re-use, and recycle. Roots of the tree include such things as public opinion, education, and watchdog groups. (KS)

Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood.

Science.gov (United States)

Wu, Yufeng

2012-03-01

Incomplete lineage sorting can cause incongruence between the phylogenetic history of genes (the gene tree) and that of the species (the species tree), which can complicate the inference of phylogenies. In this article, I present a new coalescent-based algorithm for species tree inference with maximum likelihood. I first describe an improved method for computing the probability of a gene tree topology given a species tree, which is much faster than an existing algorithm by Degnan and Salter (2005). Based on this method, I develop a practical algorithm that takes a set of gene tree topologies and infers species trees with maximum likelihood. This algorithm searches for the best species tree by starting from initial species trees and performing heuristic search to obtain better trees with higher likelihood. This algorithm, called STELLS (which stands for Species Tree InfErence with Likelihood for Lineage Sorting), has been implemented in a program that is downloadable from the author's web page. The simulation results show that the STELLS algorithm is more accurate than an existing maximum likelihood method for many datasets, especially when there is noise in gene trees. I also show that the STELLS algorithm is efficient and can be applied to real biological datasets. © 2011 The Author. Evolution© 2011 The Society for the Study of Evolution.

Coded Splitting Tree Protocols

DEFF Research Database (Denmark)

Sørensen, Jesper Hemming; Stefanovic, Cedomir; Popovski, Petar

2013-01-01

This paper presents a novel approach to multiple access control called coded splitting tree protocol. The approach builds on the known tree splitting protocols, code structure and successive interference cancellation (SIC). Several instances of the tree splitting protocol are initiated, each...... instance is terminated prematurely and subsequently iterated. The combined set of leaves from all the tree instances can then be viewed as a graph code, which is decodable using belief propagation. The main design problem is determining the order of splitting, which enables successful decoding as early...

Drawing Contour Trees in the Plane.

Science.gov (United States)

Heine, C; Schneider, D; Carr, Hamish; Scheuermann, G

2011-11-01

The contour tree compactly describes scalar field topology. From the viewpoint of graph drawing, it is a tree with attributes at vertices and optionally on edges. Standard tree drawing algorithms emphasize structural properties of the tree and neglect the attributes. Applying known techniques to convey this information proves hard and sometimes even impossible. We present several adaptions of popular graph drawing approaches to the problem of contour tree drawing and evaluate them. We identify five esthetic criteria for drawing contour trees and present a novel algorithm for drawing contour trees in the plane that satisfies four of these criteria. Our implementation is fast and effective for contour tree sizes usually used in interactive systems (around 100 branches) and also produces readable pictures for larger trees, as is shown for an 800 branch example.

Minnesota's Forest Trees. Revised.

Science.gov (United States)

Miles, William R.; Fuller, Bruce L.

This bulletin describes 46 of the more common trees found in Minnesota's forests and windbreaks. The bulletin contains two tree keys, a summer key and a winter key, to help the reader identify these trees. Besides the two keys, the bulletin includes an introduction, instructions for key use, illustrations of leaf characteristics and twig…

Covering tree with stars

DEFF Research Database (Denmark)

Baumbach, Jan; Guo, Jian-Ying; Ibragimov, Rashid

2013-01-01

We study the tree edit distance problem with edge deletions and edge insertions as edit operations. We reformulate a special case of this problem as Covering Tree with Stars (CTS): given a tree T and a set of stars, can we connect the stars in by adding edges between them such that the resulting ...

DIF Trees: Using Classification Trees to Detect Differential Item Functioning

Science.gov (United States)

Vaughn, Brandon K.; Wang, Qiu

2010-01-01

A nonparametric tree classification procedure is used to detect differential item functioning for items that are dichotomously scored. Classification trees are shown to be an alternative procedure to detect differential item functioning other than the use of traditional Mantel-Haenszel and logistic regression analysis. A nonparametric…

Picking a tree: habitat use by the tree agama, Acanthocercus ...

African Journals Online (AJOL)

We studied tree agama (Acanthocercus a. atricollis) habitat use in the Magaliesberg mountain range in northern South Africa using sightings of marked individuals, and in a few cases, radio-telemetry. Acanthocercus a. atricollis preferentially selected thorn trees (46%; Acacia karroo), followed by common sugarbush (10%; ...

Multi-level tree analysis of pulmonary artery/vein trees in non-contrast CT images

Science.gov (United States)

Gao, Zhiyun; Grout, Randall W.; Hoffman, Eric A.; Saha, Punam K.

2012-02-01

Diseases like pulmonary embolism and pulmonary hypertension are associated with vascular dystrophy. Identifying such pulmonary artery/vein (A/V) tree dystrophy in terms of quantitative measures via CT imaging significantly facilitates early detection of disease or a treatment monitoring process. A tree structure, consisting of nodes and connected arcs, linked to the volumetric representation allows multi-level geometric and volumetric analysis of A/V trees. Here, a new theory and method is presented to generate multi-level A/V tree representation of volumetric data and to compute quantitative measures of A/V tree geometry and topology at various tree hierarchies. The new method is primarily designed on arc skeleton computation followed by a tree construction based topologic and geometric analysis of the skeleton. The method starts with a volumetric A/V representation as input and generates its topologic and multi-level volumetric tree representations long with different multi-level morphometric measures. A new recursive merging and pruning algorithms are introduced to detect bad junctions and noisy branches often associated with digital geometric and topologic analysis. Also, a new notion of shortest axial path is introduced to improve the skeletal arc joining two junctions. The accuracy of the multi-level tree analysis algorithm has been evaluated using computer generated phantoms and pulmonary CT images of a pig vessel cast phantom while the reproducibility of method is evaluated using multi-user A/V separation of in vivo contrast-enhanced CT images of a pig lung at different respiratory volumes.

The national tree-list layer

Science.gov (United States)

Stacy A. Drury; Jason M. Herynk

2011-01-01

The National Tree-List Layer (NTLL) project used LANDFIRE map products to produce the first national tree-list map layer that represents tree populations at stand and regional levels. The NTLL was produced in a short time frame to address the needs of Fire and Aviation Management for a map layer that could be used as input for simulating fire-caused tree mortality...

Collateral damage: fire and Phytophthora ramorum interact to increase mortality in coast redwood

Science.gov (United States)

Margaret R. Metz; J. Morgan Varner; Kerri M. Frangioso; Ross K. Meentemeyer; David M. Rizzo

2013-01-01

Invading species can alter ecosystems by impacting the frequency, severity, and consequences of endemic disturbance regimes (Mack and D'Antonio 1998). Phytophthora ramorum, the causal agent of the emergent disease sudden oak death (SOD), is an invasive pathogen causing widespread tree mortality in coastal forests of California and Oregon. In...

Beyond Tree Throw: Wind, Water, Rock and the Mechanics of Tree-Driven Bedrock Physical Weathering

Science.gov (United States)

Marshall, J. A.; Anderson, R. S.; Dawson, T. E.; Dietrich, W. E.; Minear, J. T.

2017-12-01

Tree throw is often invoked as the dominant process in converting bedrock to soil and thus helping to build the Critical Zone (CZ). In addition, observations of tree roots lifting sidewalk slabs, occupying cracks, and prying slabs of rock from cliff faces have led to a general belief in the power of plant growth forces. These common observations have led to conceptual models with trees at the center of the soil genesis process. This is despite the observation that tree throw is rare in many forested settings, and a dearth of field measurements that quantify the magnitude of growth forces. While few trees blow down, every tree grows roots, inserting many tens of percent of its mass below ground. Yet we lack data quantifying the role of trees in both damaging bedrock and detaching it (and thus producing soil). By combing force measurements at the tree-bedrock interface with precipitation, solar radiation, wind speed, and wind-driven tree sway data we quantified the magnitude and frequency of tree-driven soil-production mechanisms from two contrasting climatic and lithologic regimes (Boulder and Eel Creek CZ Observatories). Preliminary data suggests that in settings with relatively thin soils, trees can damage and detach rock due to diurnal fluctuations, wind response and rainfall events. Surprisingly, our data suggests that forces from roots and trunks growing against bedrock are insufficient to pry rock apart or damage bedrock although much more work is needed in this area. The frequency, magnitude and style of wind-driven tree forces at the bedrock interface varies considerably from one to another species. This suggests that tree properties such as mass, elasticity, stiffness and branch structure determine whether trees respond to gusts big or small, move at the same frequency as large wind gusts, or are able to self-dampen near-ground sway response to extended wind forces. Our measurements of precipitation-driven and daily fluctuations in root pressures exerted on

Nonbinary Tree-Based Phylogenetic Networks.

Science.gov (United States)

Jetten, Laura; van Iersel, Leo

2018-01-01

Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with additional linking arcs, which can, for example, represent gene transfer events. Such phylogenetic networks are called tree-based. Here, we consider two possible generalizations of this concept to nonbinary networks, which we call tree-based and strictly-tree-based nonbinary phylogenetic networks. We give simple graph-theoretic characterizations of tree-based and strictly-tree-based nonbinary phylogenetic networks. Moreover, we show for each of these two classes that it can be decided in polynomial time whether a given network is contained in the class. Our approach also provides a new view on tree-based binary phylogenetic networks. Finally, we discuss two examples of nonbinary phylogenetic networks in biology and show how our results can be applied to them.

Submodular unsplittable flow on trees

DEFF Research Database (Denmark)

Adamaszek, Anna Maria; Chalermsook, Parinya; Ene, Alina

2016-01-01

We study the Unsplittable Flow problem (UFP) on trees with a submodular objective function. The input to this problem is a tree with edge capacities and a collection of tasks, each characterized by a source node, a sink node, and a demand. A subset of the tasks is feasible if the tasks can...... simultaneously send their demands from the source to the sink without violating the edge capacities. The goal is to select a feasible subset of the tasks that maximizes a submodular objective function. Our main result is an O(k log n)-approximation algorithm for Submodular UFP on trees where k denotes...... the pathwidth of the given tree. Since every tree has pathwidth O(log n), we obtain an O(log2 n) approximation for arbitrary trees. This is the first non-trivial approximation guarantee for the problem and it matches the best approximation known for UFP on trees with a linear objective function. Our main...

Tree Mortality Undercuts Ability of Tree-Planting Programs to Provide Benefits: Results of a Three-City Study

Directory of Open Access Journals (Sweden)

Sarah Widney

2016-03-01

Full Text Available Trees provide numerous benefits for urban residents, including reduced energy usage, improved air quality, stormwater management, carbon sequestration, and increased property values. Quantifying these benefits can help justify the costs of planting trees. In this paper, we use i-Tree Streets to quantify the benefits of street trees planted by nonprofits in three U.S. cities (Detroit, Michigan; Indianapolis, Indiana, and Philadelphia, Pennsylvania from 2009 to 2011. We also use both measured and modeled survival and growth rates to “grow” the tree populations 5 and 10 years into the future to project the future benefits of the trees under different survival and growth scenarios. The 4059 re-inventoried trees (2864 of which are living currently provide almost $40,000 (USD in estimated annual benefits ($9–$20/tree depending on the city, the majority (75% of which are increased property values. The trees can be expected to provide increasing annual benefits during the 10 years after planting if the annual survival rate is higher than the 93% annual survival measured during the establishment period. However, our projections show that with continued 93% or lower annual survival, the increase in annual benefits from tree growth will not be able to make up for the loss of benefits as trees die. This means that estimated total annual benefits from a cohort of planted trees will decrease between the 5-year projection and the 10-year projection. The results of this study indicate that without early intervention to ensure survival of planted street trees, tree mortality may be significantly undercutting the ability of tree-planting programs to provide benefits to neighborhood residents.

Coalescent methods for estimating phylogenetic trees.

Science.gov (United States)

Liu, Liang; Yu, Lili; Kubatko, Laura; Pearl, Dennis K; Edwards, Scott V

2009-10-01

We review recent models to estimate phylogenetic trees under the multispecies coalescent. Although the distinction between gene trees and species trees has come to the fore of phylogenetics, only recently have methods been developed that explicitly estimate species trees. Of the several factors that can cause gene tree heterogeneity and discordance with the species tree, deep coalescence due to random genetic drift in branches of the species tree has been modeled most thoroughly. Bayesian approaches to estimating species trees utilizes two likelihood functions, one of which has been widely used in traditional phylogenetics and involves the model of nucleotide substitution, and the second of which is less familiar to phylogeneticists and involves the probability distribution of gene trees given a species tree. Other recent parametric and nonparametric methods for estimating species trees involve parsimony criteria, summary statistics, supertree and consensus methods. Species tree approaches are an appropriate goal for systematics, appear to work well in some cases where concatenation can be misleading, and suggest that sampling many independent loci will be paramount. Such methods can also be challenging to implement because of the complexity of the models and computational time. In addition, further elaboration of the simplest of coalescent models will be required to incorporate commonly known issues such as deviation from the molecular clock, gene flow and other genetic forces.

Decision trees in epidemiological research.

Science.gov (United States)

Venkatasubramaniam, Ashwini; Wolfson, Julian; Mitchell, Nathan; Barnes, Timothy; JaKa, Meghan; French, Simone

2017-01-01

In many studies, it is of interest to identify population subgroups that are relatively homogeneous with respect to an outcome. The nature of these subgroups can provide insight into effect mechanisms and suggest targets for tailored interventions. However, identifying relevant subgroups can be challenging with standard statistical methods. We review the literature on decision trees, a family of techniques for partitioning the population, on the basis of covariates, into distinct subgroups who share similar values of an outcome variable. We compare two decision tree methods, the popular Classification and Regression tree (CART) technique and the newer Conditional Inference tree (CTree) technique, assessing their performance in a simulation study and using data from the Box Lunch Study, a randomized controlled trial of a portion size intervention. Both CART and CTree identify homogeneous population subgroups and offer improved prediction accuracy relative to regression-based approaches when subgroups are truly present in the data. An important distinction between CART and CTree is that the latter uses a formal statistical hypothesis testing framework in building decision trees, which simplifies the process of identifying and interpreting the final tree model. We also introduce a novel way to visualize the subgroups defined by decision trees. Our novel graphical visualization provides a more scientifically meaningful characterization of the subgroups identified by decision trees. Decision trees are a useful tool for identifying homogeneous subgroups defined by combinations of individual characteristics. While all decision tree techniques generate subgroups, we advocate the use of the newer CTree technique due to its simplicity and ease of interpretation.

SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees

OpenAIRE

Beccati, Alan; Gerken, Jan; Quast, Christian; Yilmaz, Pelin; Glöckner, Frank Oliver

2017-01-01

Background Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the taxonomic framework. Results The SILVA Tree Viewer is a web application designed for visualizing large phylogenetic trees without requiring the download of any software tool or data files. The SILVA T...

Estimation of Tree Cover in an Agricultural Parkland of Senegal Using Rule-Based Regression Tree Modeling

Directory of Open Access Journals (Sweden)

Stefanie M. Herrmann

2013-10-01

Full Text Available Field trees are an integral part of the farmed parkland landscape in West Africa and provide multiple benefits to the local environment and livelihoods. While field trees have received increasing interest in the context of strengthening resilience to climate variability and change, the actual extent of farmed parkland and spatial patterns of tree cover are largely unknown. We used the rule-based predictive modeling tool Cubist® to estimate field tree cover in the west-central agricultural region of Senegal. A collection of rules and associated multiple linear regression models was constructed from (1 a reference dataset of percent tree cover derived from very high spatial resolution data (2 m Orbview as the dependent variable, and (2 ten years of 10-day 250 m Moderate Resolution Imaging Spectrometer (MODIS Normalized Difference Vegetation Index (NDVI composites and derived phenological metrics as independent variables. Correlation coefficients between modeled and reference percent tree cover of 0.88 and 0.77 were achieved for training and validation data respectively, with absolute mean errors of 1.07 and 1.03 percent tree cover. The resulting map shows a west-east gradient from high tree cover in the peri-urban areas of horticulture and arboriculture to low tree cover in the more sparsely populated eastern part of the study area. A comparison of current (2000s tree cover along this gradient with historic cover as seen on Corona images reveals dynamics of change but also areas of remarkable stability of field tree cover since 1968. The proposed modeling approach can help to identify locations of high and low tree cover in dryland environments and guide ground studies and management interventions aimed at promoting the integration of field trees in agricultural systems.

Environmental tritium in trees

International Nuclear Information System (INIS)

Brown, R.M.

1979-01-01

The distribution of environmental tritium in the free water and organically bound hydrogen of trees growing in the vicinity of the Chalk River Nuclear Laboratories (CRNL) has been studied. The regional dispersal of HTO in the atmosphere has been observed by surveying the tritium content of leaf moisture. Measurement of the distribution of organically bound tritium in the wood of tree ring sequences has given information on past concentrations of HTO taken up by trees growing in the CRNL Liquid Waste Disposal Area. For samples at background environmental levels, cellulose separation and analysis was done. The pattern of bomb tritium in precipitation of 1955-68 was observed to be preserved in the organically bound tritium of a tree ring sequence. Reactor tritium was discernible in a tree growing at a distance of 10 km from CRNL. These techniques provide convenient means of monitoring dispersal of HTO from nuclear facilities. (author)

On the structure of path-like trees

OpenAIRE

Muntaner Batle, Francesc Antoni; Rius Font, Miquel

2007-01-01

We study the structure of path-like trees. In order to do this, we introduce a set of trees that we call expandable trees. In this paper we also generalize the concept of path-like trees and we call such generalization generalized path-like trees. As in the case of path-like trees, generalized path-like trees, have very nice labeling properties.

Arthropod but not bird predation in ethiopian homegardens is higher in tree-poor than in tree-rich landscapes.

Science.gov (United States)

Lemessa, Debissa; Hambäck, Peter A; Hylander, Kristoffer

2015-01-01

Bird and arthropod predation is often associated with natural pest control in agricultural landscapes, but the rates of predation may vary with the amount of tree cover or other environmental factors. We examined bird and arthropod predation in three tree-rich and three tree-poor landscapes across southwestern Ethiopia. Within each landscape we selected three tree-rich and three tree-poor homegardens in which we recorded the number of tree species and tree stems within 100 × 100 m surrounding the central house. To estimate predation rates, we attached plasticine caterpillars on leaves of two coffee and two avocado shrubs in each homegarden, and recorded the number of attacked caterpillars for 7-9 consecutive weeks. The overall mean daily predation rate was 1.45% for birds and 1.60% for arthropods. The rates of arthropod predation varied among landscapes and were higher in tree-poor landscapes. There was no such difference for birds. Within landscapes, predation rates from birds and arthropods did not vary between tree-rich and tree-poor homegardens in either tree-rich or tree-poor landscapes. The most surprising result was the lack of response by birds to tree cover at either spatial scale. Our results suggest that in tree-poor landscapes there are still enough non-crop habitats to support predatory arthropods and birds to deliver strong top-down effect on crop pests.

Arthropod but not bird predation in ethiopian homegardens is higher in tree-poor than in tree-rich landscapes.

Directory of Open Access Journals (Sweden)

Debissa Lemessa

Full Text Available Bird and arthropod predation is often associated with natural pest control in agricultural landscapes, but the rates of predation may vary with the amount of tree cover or other environmental factors. We examined bird and arthropod predation in three tree-rich and three tree-poor landscapes across southwestern Ethiopia. Within each landscape we selected three tree-rich and three tree-poor homegardens in which we recorded the number of tree species and tree stems within 100 × 100 m surrounding the central house. To estimate predation rates, we attached plasticine caterpillars on leaves of two coffee and two avocado shrubs in each homegarden, and recorded the number of attacked caterpillars for 7-9 consecutive weeks. The overall mean daily predation rate was 1.45% for birds and 1.60% for arthropods. The rates of arthropod predation varied among landscapes and were higher in tree-poor landscapes. There was no such difference for birds. Within landscapes, predation rates from birds and arthropods did not vary between tree-rich and tree-poor homegardens in either tree-rich or tree-poor landscapes. The most surprising result was the lack of response by birds to tree cover at either spatial scale. Our results suggest that in tree-poor landscapes there are still enough non-crop habitats to support predatory arthropods and birds to deliver strong top-down effect on crop pests.

Gene-Tree Reconciliation with MUL-Trees to Resolve Polyploidy Events.

Science.gov (United States)

Gregg, W C Thomas; Ather, S Hussain; Hahn, Matthew W

2017-11-01

Polyploidy can have a huge impact on the evolution of species, and it is a common occurrence, especially in plants. The two types of polyploids-autopolyploids and allopolyploids-differ in the level of divergence between the genes that are brought together in the new polyploid lineage. Because allopolyploids are formed via hybridization, the homoeologous copies of genes within them are at least as divergent as orthologs in the parental species that came together to form them. This means that common methods for estimating the parental lineages of allopolyploidy events are not accurate, and can lead to incorrect inferences about the number of gene duplications and losses. Here, we have adapted an algorithm for topology-based gene-tree reconciliation to work with multi-labeled trees (MUL-trees). By definition, MUL-trees have some tips with identical labels, which makes them a natural representation of the genomes of polyploids. Using this new reconciliation algorithm we can: accurately place allopolyploidy events on a phylogeny, identify the parental lineages that hybridized to form allopolyploids, distinguish between allo-, auto-, and (in most cases) no polyploidy, and correctly count the number of duplications and losses in a set of gene trees. We validate our method using gene trees simulated with and without polyploidy, and revisit the history of polyploidy in data from the clades including both baker's yeast and bread wheat. Our re-analysis of the yeast data confirms the allopolyploid origin and parental lineages previously identified for this group. The method presented here should find wide use in the growing number of genomes from species with a history of polyploidy. [Polyploidy; reconciliation; whole-genome duplication.]. © The Author(s) 2017. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Shade Trees Spatial Distribution and Its Effect on Grains and Beverage Quality of Shaded Coffee Trees

Directory of Open Access Journals (Sweden)

Francisco José da Silva Neto

2018-01-01

Full Text Available Shading coffee trees has gained importance, especially among smallholders, as an option to improve the products’ quality, therefore acquiring place at the specialty coffee market, where consumers are willing to give bonus for quality. This work aims to evaluate the influence of shade trees’ spatial distribution among coffee trees’ agronomic characteristics, yield, and beans and cup quality of shaded coffee trees. The experimental design consisted of completely randomized blocks with six repetitions and four treatments: coffee trees on shade trees planting rows, distant one meter from the trunk; coffee trees on shade trees planting row, distant six meters from the trunk; and coffee plants between the rows of shade trees, parallel to the previous treatments. The parameters analyzed were plant height, canopy diameter, plagiotropic branches’ length, yield, coffee fruits’ phenological stage, ripe cherries’ Brix degree, percentage of black, unripe, and insect damaged beans, bean size, and beverage quality. Shade trees quickened coffee fruits’ phenological stage of coffee trees nearest to them. This point also showed the best beverage quality, except for overripe fruits. The remaining parameters evaluated were not affected by shade trees’ spatial distribution.

Decision trees in epidemiological research

Directory of Open Access Journals (Sweden)

Ashwini Venkatasubramaniam

2017-09-01

Full Text Available Abstract Background In many studies, it is of interest to identify population subgroups that are relatively homogeneous with respect to an outcome. The nature of these subgroups can provide insight into effect mechanisms and suggest targets for tailored interventions. However, identifying relevant subgroups can be challenging with standard statistical methods. Main text We review the literature on decision trees, a family of techniques for partitioning the population, on the basis of covariates, into distinct subgroups who share similar values of an outcome variable. We compare two decision tree methods, the popular Classification and Regression tree (CART technique and the newer Conditional Inference tree (CTree technique, assessing their performance in a simulation study and using data from the Box Lunch Study, a randomized controlled trial of a portion size intervention. Both CART and CTree identify homogeneous population subgroups and offer improved prediction accuracy relative to regression-based approaches when subgroups are truly present in the data. An important distinction between CART and CTree is that the latter uses a formal statistical hypothesis testing framework in building decision trees, which simplifies the process of identifying and interpreting the final tree model. We also introduce a novel way to visualize the subgroups defined by decision trees. Our novel graphical visualization provides a more scientifically meaningful characterization of the subgroups identified by decision trees. Conclusions Decision trees are a useful tool for identifying homogeneous subgroups defined by combinations of individual characteristics. While all decision tree techniques generate subgroups, we advocate the use of the newer CTree technique due to its simplicity and ease of interpretation.

Human action analysis with randomized trees

CERN Document Server

Yu, Gang; Liu, Zicheng

2014-01-01

This book will provide a comprehensive overview on human action analysis with randomized trees. It will cover both the supervised random trees and the unsupervised random trees. When there are sufficient amount of labeled data available, supervised random trees provides a fast method for space-time interest point matching. When labeled data is minimal as in the case of example-based action search, unsupervised random trees is used to leverage the unlabelled data. We describe how the randomized trees can be used for action classification, action detection, action search, and action prediction.

Edge-Disjoint Fibonacci Trees in Hypercube

Directory of Open Access Journals (Sweden)

Indhumathi Raman

2014-01-01

Full Text Available The Fibonacci tree is a rooted binary tree whose number of vertices admit a recursive definition similar to the Fibonacci numbers. In this paper, we prove that a hypercube of dimension h admits two edge-disjoint Fibonacci trees of height h, two edge-disjoint Fibonacci trees of height h-2, two edge-disjoint Fibonacci trees of height h-4 and so on, as subgraphs. The result shows that an algorithm with Fibonacci trees as underlying data structure can be implemented concurrently on a hypercube network with no communication latency.

TreeCluster: Massively scalable transmission clustering using phylogenetic trees

OpenAIRE

Moshiri, Alexander

2018-01-01

Background: The ability to infer transmission clusters from molecular data is critical to designing and evaluating viral control strategies. Viral sequencing datasets are growing rapidly, but standard methods of transmission cluster inference do not scale well beyond thousands of sequences. Results: I present TreeCluster, a cross-platform tool that performs transmission cluster inference on a given phylogenetic tree orders of magnitude faster than existing inference methods and supports multi...

Value tree analysis

International Nuclear Information System (INIS)

Keeney, R.; Renn, O.; Winterfeldt, D. von; Kotte, U.

1985-01-01

What are the targets and criteria on which national energy policy should be based. What priorities should be set, and how can different social interests be matched. To answer these questions, a new instrument of decision theory is presented which has been applied with good results to controversial political issues in the USA. The new technique is known under the name of value tree analysis. Members of important West German organisations (BDI, VDI, RWE, the Catholic and Protestant Church, Deutscher Naturschutzring, and ecological research institutions) were asked about the goals of their organisations. These goals were then ordered systematically and arranged in a hierarchical tree structure. The value trees of different groups can be combined into a catalogue of social criteria of acceptability and policy assessment. The authors describe the philosophy and methodology of value tree analysis and give an outline of its application in the development of a socially acceptable energy policy. (orig.) [de

Adjustable chain trees for proteins

DEFF Research Database (Denmark)

Winter, Pawel; Fonseca, Rasmus

2012-01-01

A chain tree is a data structure for changing protein conformations. It enables very fast detection of clashes and free energy potential calculations. A modified version of chain trees that adjust themselves to the changing conformations of folding proteins is introduced. This results in much...... tighter bounding volume hierarchies and therefore fewer intersection checks. Computational results indicate that the efficiency of the adjustable chain trees is significantly improved compared to the traditional chain trees....

Introduction to fault tree analysis

International Nuclear Information System (INIS)

Barlow, R.E.; Lambert, H.E.

1975-01-01

An elementary, engineering oriented introduction to fault tree analysis is presented. The basic concepts, techniques and applications of fault tree analysis, FTA, are described. The two major steps of FTA are identified as (1) the construction of the fault tree and (2) its evaluation. The evaluation of the fault tree can be qualitative or quantitative depending upon the scope, extensiveness and use of the analysis. The advantages, limitations and usefulness of FTA are discussed

Steiner trees in industry

CERN Document Server

Du, Ding-Zhu

2001-01-01

This book is a collection of articles studying various Steiner tree prob­ lems with applications in industries, such as the design of electronic cir­ cuits, computer networking, telecommunication, and perfect phylogeny. The Steiner tree problem was initiated in the Euclidean plane. Given a set of points in the Euclidean plane, the shortest network interconnect­ ing the points in the set is called the Steiner minimum tree. The Steiner minimum tree may contain some vertices which are not the given points. Those vertices are called Steiner points while the given points are called terminals. The shortest network for three terminals was first studied by Fermat (1601-1665). Fermat proposed the problem of finding a point to minimize the total distance from it to three terminals in the Euclidean plane. The direct generalization is to find a point to minimize the total distance from it to n terminals, which is still called the Fermat problem today. The Steiner minimum tree problem is an indirect generalization. Sch...

Water, gravity and trees: Relationship of tree-ring widths and total water storage dynamics

Science.gov (United States)

Creutzfeldt, B.; Heinrich, I.; Merz, B.; Blume, T.; Güntner, A.

2012-04-01

Water stored in the subsurface as groundwater or soil moisture is the main fresh water source not only for drinking water and food production but also for the natural vegetation. In a changing environment water availability becomes a critical issue in many different regions. Long-term observations of the past are needed to improve the understanding of the hydrological system and the prediction of future developments. Tree ring data have repeatedly proved to be valuable sources for reconstructing long-term climate dynamics, e.g. temperature, precipitation and different hydrological variables. In water-limited environments, tree growth is primarily influenced by total water stored in the subsurface and hence, tree-ring records usually contain information about subsurface water storage. The challenge is to retrieve the information on total water storage from tree rings, because a training dataset of water stored in the sub-surface is required for calibration against the tree-ring series. However, measuring water stored in the subsurface is notoriously difficult. We here present high-precision temporal gravimeter measurements which allow for the depth-integrated quantification of total water storage dynamics at the field scale. In this study, we evaluate the relationship of total water storage change and tree ring growth also in the context of the complex interactions of other meteorological forcing factors. A tree-ring chronology was derived from a Norway spruce stand in the Bavarian Forest, Germany. Total water storage dynamics were measured directly by the superconducting gravimeter of the Geodetic Observatory Wettzell for a 9-years period. Time series were extended to 63-years period by a hydrological model using gravity data as the only calibration constrain. Finally, water storage changes were reconstructed based on the relationship between the hydrological model and the tree-ring chronology. Measurement results indicate that tree-ring growth is primarily

The longevity of broadleaf deciduous trees in Northern Hemisphere temperate forests: insights from tree-ring series

Directory of Open Access Journals (Sweden)

Alfredo eDi Filippo

2015-05-01

Full Text Available Understanding the factors controlling the expression of longevity in trees is still an outstanding challenge for tree biologists and forest ecologists. We gathered tree-ring data and literature for broadleaf deciduous (BD temperate trees growing in closed-canopy old-growth forests in the Northern Hemisphere to explore the role of geographic patterns, climate variability, and growth rates on longevity. Our pan-continental analysis, covering 32 species from 12 genera, showed that 300-400 years can be considered a baseline threshold for maximum tree lifespan in many temperate deciduous forests. Maximum age varies greatly in relation to environmental features, even within the same species. Tree longevity is generally promoted by reduced growth rates across large genetic differences and environmental gradients. We argue that slower growth rates, and the associated smaller size, provide trees with an advantage against biotic and abiotic disturbance agents, supporting the idea that size, not age, is the main constraint to tree longevity. The oldest trees were living most of their life in subordinate canopy conditions and/or within primary forests in cool temperate environments and outside major storm tracks. Very old trees are thus characterized by slow growth and often live in forests with harsh site conditions and infrequent disturbance events that kill much of the trees. Temperature inversely controls the expression of longevity in mesophilous species (Fagus spp., but its role in Quercus spp. is more complex and warrants further research in disturbance ecology. Biological, ecological and historical drivers must be considered to understand the constraints imposed to longevity within different forest landscapes.

Up in the tree--the overlooked richness of bryophytes and lichens in tree crowns.

Science.gov (United States)

Boch, Steffen; Müller, Jörg; Prati, Daniel; Blaser, Stefan; Fischer, Markus

2013-01-01

Assessing diversity is among the major tasks in ecology and conservation science. In ecological and conservation studies, epiphytic cryptogams are usually sampled up to accessible heights in forests. Thus, their diversity, especially of canopy specialists, likely is underestimated. If the proportion of those species differs among forest types, plot-based diversity assessments are biased and may result in misleading conservation recommendations. We sampled bryophytes and lichens in 30 forest plots of 20 m × 20 m in three German regions, considering all substrates, and including epiphytic litter fall. First, the sampling of epiphytic species was restricted to the lower 2 m of trees and shrubs. Then, on one representative tree per plot, we additionally recorded epiphytic species in the crown, using tree climbing techniques. Per tree, on average 54% of lichen and 20% of bryophyte species were overlooked if the crown was not been included. After sampling all substrates per plot, including the bark of all shrubs and trees, still 38% of the lichen and 4% of the bryophyte species were overlooked if the tree crown of the sampled tree was not included. The number of overlooked lichen species varied strongly among regions. Furthermore, the number of overlooked bryophyte and lichen species per plot was higher in European beech than in coniferous stands and increased with increasing diameter at breast height of the sampled tree. Thus, our results indicate a bias of comparative studies which might have led to misleading conservation recommendations of plot-based diversity assessments.

Modelling tree biomasses in Finland

Energy Technology Data Exchange (ETDEWEB)

Repola, J.

2013-06-01

Biomass equations for above- and below-ground tree components of Scots pine (Pinus sylvestris L), Norway spruce (Picea abies [L.] Karst) and birch (Betula pendula Roth and Betula pubescens Ehrh.) were compiled using empirical material from a total of 102 stands. These stands (44 Scots pine, 34 Norway spruce and 24 birch stands) were located mainly on mineral soil sites representing a large part of Finland. The biomass models were based on data measured from 1648 sample trees, comprising 908 pine, 613 spruce and 127 birch trees. Biomass equations were derived for the total above-ground biomass and for the individual tree components: stem wood, stem bark, living and dead branches, needles, stump, and roots, as dependent variables. Three multivariate models with different numbers of independent variables for above-ground biomass and one for below-ground biomass were constructed. Variables that are normally measured in forest inventories were used as independent variables. The simplest model formulations, multivariate models (1) were mainly based on tree diameter and height as independent variables. In more elaborated multivariate models, (2) and (3), additional commonly measured tree variables such as age, crown length, bark thickness and radial growth rate were added. Tree biomass modelling includes consecutive phases, which cause unreliability in the prediction of biomass. First, biomasses of sample trees should be determined reliably to decrease the statistical errors caused by sub-sampling. In this study, methods to improve the accuracy of stem biomass estimates of the sample trees were developed. In addition, the reliability of the method applied to estimate sample-tree crown biomass was tested, and no systematic error was detected. Second, the whole information content of data should be utilized in order to achieve reliable parameter estimates and applicable and flexible model structure. In the modelling approach, the basic assumption was that the biomasses of

Geodesic atlas-based labeling of anatomical trees

DEFF Research Database (Denmark)

Feragen, Aasa; Petersen, Jens; Owen, Megan

2015-01-01

We present a fast and robust atlas-based algorithm for labeling airway trees, using geodesic distances in a geometric tree-space. Possible branch label configurations for an unlabeled airway tree are evaluated using distances to a training set of labeled airway trees. In tree-space, airway tree t...... equally complete airway trees, and comparable in performance to that of experts in pulmonary medicine, emphasizing the suitability of the labeling algorithm for clinical use....

Current and potential tree locations in tree line ecotone of Changbai Mountains, Northeast China: the controlling effects of topography.

Science.gov (United States)

Zong, Shengwei; Wu, Zhengfang; Xu, Jiawei; Li, Ming; Gao, Xiaofeng; He, Hongshi; Du, Haibo; Wang, Lei

2014-01-01

Tree line ecotone in the Changbai Mountains has undergone large changes in the past decades. Tree locations show variations on the four sides of the mountains, especially on the northern and western sides, which has not been fully explained. Previous studies attributed such variations to the variations in temperature. However, in this study, we hypothesized that topographic controls were responsible for causing the variations in the tree locations in tree line ecotone of the Changbai Mountains. To test the hypothesis, we used IKONOS images and WorldView-1 image to identify the tree locations and developed a logistic regression model using topographical variables to identify the dominant controls of the tree locations. The results showed that aspect, wetness, and slope were dominant controls for tree locations on western side of the mountains, whereas altitude, SPI, and aspect were the dominant factors on northern side. The upmost altitude a tree can currently reach was 2140 m asl on the northern side and 2060 m asl on western side. The model predicted results showed that habitats above the current tree line on the both sides were available for trees. Tree recruitments under the current tree line may take advantage of the available habitats at higher elevations based on the current tree location. Our research confirmed the controlling effects of topography on the tree locations in the tree line ecotone of Changbai Mountains and suggested that it was essential to assess the tree response to topography in the research of tree line ecotone.

Moose?tree interactions: rebrowsing is common across tree species

OpenAIRE

Mathisen, Karen Marie; Milner, Jos M.; Skarpe, Christina

2017-01-01

Background Plant strategies to resist herbivory include tolerance and avoidance. Tolerance strategies, such as rapid regrowth which increases the palatability of new shoots, can lead to positive feedback loops between plants and herbivores. An example of such a positive feedback occurs when moose (Alces alces) browse trees in boreal forests. We described the degree of change in tree morphology that accumulated over time in response to repeated browsing by moose, using an index of accumulated ...

Mitered fractal trees: constructions and properties

NARCIS (Netherlands)

Verhoeff, T.; Verhoeff, K.; Bosch, R.; McKenna, D.; Sarhangi, R.

2012-01-01

Tree-like structures, that is, branching structures without cycles, are attractive for artful expression. Especially interesting are fractal trees, where each subtree is a scaled and possibly otherwise transformed version of the entire tree. Such trees can be rendered in 3D by using beams with a

Genetic transformation of forest trees

African Journals Online (AJOL)

Admin

In this review, the recent progress on genetic transformation of forest trees were discussed. Its described also, different applications of genetic engineering for improving forest trees or understanding the mechanisms governing genes expression in woody plants. Key words: Genetic transformation, transgenic forest trees, ...

How eco-evolutionary principles can guide tree breeding and tree biotechnology for enhanced productivity.

Science.gov (United States)

Franklin, Oskar; Palmroth, Sari; Näsholm, Torgny

2014-11-01

Tree breeding and biotechnology can enhance forest productivity and help alleviate the rising pressure on forests from climate change and human exploitation. While many physiological processes and genes are targeted in search of genetically improved tree productivity, an overarching principle to guide this search is missing. Here, we propose a method to identify the traits that can be modified to enhance productivity, based on the differences between trees shaped by natural selection and 'improved' trees with traits optimized for productivity. We developed a tractable model of plant growth and survival to explore such potential modifications under a range of environmental conditions, from non-water limited to severely drought-limited sites. We show how key traits are controlled by a trade-off between productivity and survival, and that productivity can be increased at the expense of long-term survival by reducing isohydric behavior (stomatal regulation of leaf water potential) and allocation to defense against pests compared with native trees. In contrast, at dry sites occupied by naturally drought-resistant trees, the model suggests a better strategy may be to select trees with slightly lower wood density than the native trees and to augment isohydric behavior and allocation to defense. Thus, which traits to modify, and in which direction, depend on the original tree species or genotype, the growth environment and wood-quality versus volume production preferences. In contrast to this need for customization of drought and pest resistances, consistent large gains in productivity for all genotypes can be obtained if root traits can be altered to reduce competition for water and nutrients. Our approach illustrates the potential of using eco-evolutionary theory and modeling to guide plant breeding and genetic technology in selecting target traits in the quest for higher forest productivity. © The Author 2014. Published by Oxford University Press. All rights reserved

The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees.

Science.gov (United States)

Soria-Carrasco, Víctor; Talavera, Gerard; Igea, Javier; Castresana, Jose

2007-11-01

We introduce a new phylogenetic comparison method that measures overall differences in the relative branch length and topology of two phylogenetic trees. To do this, the algorithm first scales one of the trees to have a global divergence as similar as possible to the other tree. Then, the branch length distance, which takes differences in topology and branch lengths into account, is applied to the two trees. We thus obtain the minimum branch length distance or K tree score. Two trees with very different relative branch lengths get a high K score whereas two trees that follow a similar among-lineage rate variation get a low score, regardless of the overall rates in both trees. There are several applications of the K tree score, two of which are explained here in more detail. First, this score allows the evaluation of the performance of phylogenetic algorithms, not only with respect to their topological accuracy, but also with respect to the reproduction of a given branch length variation. In a second example, we show how the K score allows the selection of orthologous genes by choosing those that better follow the overall shape of a given reference tree. http://molevol.ibmb.csic.es/Ktreedist.html

Up in the tree--the overlooked richness of bryophytes and lichens in tree crowns.

Directory of Open Access Journals (Sweden)

Steffen Boch

Full Text Available Assessing diversity is among the major tasks in ecology and conservation science. In ecological and conservation studies, epiphytic cryptogams are usually sampled up to accessible heights in forests. Thus, their diversity, especially of canopy specialists, likely is underestimated. If the proportion of those species differs among forest types, plot-based diversity assessments are biased and may result in misleading conservation recommendations. We sampled bryophytes and lichens in 30 forest plots of 20 m × 20 m in three German regions, considering all substrates, and including epiphytic litter fall. First, the sampling of epiphytic species was restricted to the lower 2 m of trees and shrubs. Then, on one representative tree per plot, we additionally recorded epiphytic species in the crown, using tree climbing techniques. Per tree, on average 54% of lichen and 20% of bryophyte species were overlooked if the crown was not been included. After sampling all substrates per plot, including the bark of all shrubs and trees, still 38% of the lichen and 4% of the bryophyte species were overlooked if the tree crown of the sampled tree was not included. The number of overlooked lichen species varied strongly among regions. Furthermore, the number of overlooked bryophyte and lichen species per plot was higher in European beech than in coniferous stands and increased with increasing diameter at breast height of the sampled tree. Thus, our results indicate a bias of comparative studies which might have led to misleading conservation recommendations of plot-based diversity assessments.

Tree Notation: an antifragile program notation

OpenAIRE

Yunits, Breck

2017-01-01

This paper presents Tree Notation, a new simple, universal syntax. Language designers can invent new programming languages, called Tree Languages, on top of Tree Notation. Tree Languages have a number of advantages over traditional programming languages. We include a Visual Abstract to succinctly display the problem and discovery. Then we describe the problem--the BNF to abstract syntax tree (AST) parse step--and introduce the novel solution we discovered: a new family of 2D programming langu...

Tree growth visualization

Science.gov (United States)

L. Linsen; B.J. Karis; E.G. McPherson; B. Hamann

2005-01-01

In computer graphics, models describing the fractal branching structure of trees typically exploit the modularity of tree structures. The models are based on local production rules, which are applied iteratively and simultaneously to create a complex branching system. The objective is to generate three-dimensional scenes of often many realistic- looking and non-...

Individual tree control

Science.gov (United States)

Harvey A. Holt

1989-01-01

Controlling individual unwanted trees in forest stands is a readily accepted method for improving the value of future harvests. The practice is especially important in mixed hardwood forests where species differ considerably in value and within species individual trees differ in quality. Individual stem control is a mechanical or chemical weeding operation that...

Using tree diversity to compare phylogenetic heuristics.

Science.gov (United States)

Sul, Seung-Jin; Matthews, Suzanne; Williams, Tiffani L

2009-04-29

Evolutionary trees are family trees that represent the relationships between a group of organisms. Phylogenetic heuristics are used to search stochastically for the best-scoring trees in tree space. Given that better tree scores are believed to be better approximations of the true phylogeny, traditional evaluation techniques have used tree scores to determine the heuristics that find the best scores in the fastest time. We develop new techniques to evaluate phylogenetic heuristics based on both tree scores and topologies to compare Pauprat and Rec-I-DCM3, two popular Maximum Parsimony search algorithms. Our results show that although Pauprat and Rec-I-DCM3 find the trees with the same best scores, topologically these trees are quite different. Furthermore, the Rec-I-DCM3 trees cluster distinctly from the Pauprat trees. In addition to our heatmap visualizations of using parsimony scores and the Robinson-Foulds distance to compare best-scoring trees found by the two heuristics, we also develop entropy-based methods to show the diversity of the trees found. Overall, Pauprat identifies more diverse trees than Rec-I-DCM3. Overall, our work shows that there is value to comparing heuristics beyond the parsimony scores that they find. Pauprat is a slower heuristic than Rec-I-DCM3. However, our work shows that there is tremendous value in using Pauprat to reconstruct trees-especially since it finds identical scoring but topologically distinct trees. Hence, instead of discounting Pauprat, effort should go in improving its implementation. Ultimately, improved performance measures lead to better phylogenetic heuristics and will result in better approximations of the true evolutionary history of the organisms of interest.

Integrating cyber attacks within fault trees

International Nuclear Information System (INIS)

Nai Fovino, Igor; Masera, Marcelo; De Cian, Alessio

2009-01-01

In this paper, a new method for quantitative security risk assessment of complex systems is presented, combining fault-tree analysis, traditionally used in reliability analysis, with the recently introduced Attack-tree analysis, proposed for the study of malicious attack patterns. The combined use of fault trees and attack trees helps the analyst to effectively face the security challenges posed by the introduction of modern ICT technologies in the control systems of critical infrastructures. The proposed approach allows considering the interaction of malicious deliberate acts with random failures. Formal definitions of fault tree and attack tree are provided and a mathematical model for the calculation of system fault probabilities is presented.

Integrating cyber attacks within fault trees

Energy Technology Data Exchange (ETDEWEB)

Nai Fovino, Igor [Joint Research Centre - EC, Institute for the Protection and Security of the Citizen, Ispra, VA (Italy)], E-mail: igor.nai@jrc.it; Masera, Marcelo [Joint Research Centre - EC, Institute for the Protection and Security of the Citizen, Ispra, VA (Italy); De Cian, Alessio [Department of Electrical Engineering, University di Genova, Genoa (Italy)

2009-09-15

In this paper, a new method for quantitative security risk assessment of complex systems is presented, combining fault-tree analysis, traditionally used in reliability analysis, with the recently introduced Attack-tree analysis, proposed for the study of malicious attack patterns. The combined use of fault trees and attack trees helps the analyst to effectively face the security challenges posed by the introduction of modern ICT technologies in the control systems of critical infrastructures. The proposed approach allows considering the interaction of malicious deliberate acts with random failures. Formal definitions of fault tree and attack tree are provided and a mathematical model for the calculation of system fault probabilities is presented.

Tree and shrub expansion over the past 34 years at the tree-line near Abisko, Sweden.

Science.gov (United States)

Rundqvist, Sara; Hedenås, Henrik; Sandström, Anneli; Emanuelsson, Urban; Eriksson, Håkan; Jonasson, Christer; Callaghan, Terry V

2011-09-01

Shrubs and trees are expected to expand in the sub-Arctic due to global warming. Our study was conducted in Abisko, sub-arctic Sweden. We recorded the change in coverage of shrub and tree species over a 32- to 34-year period, in three 50 x 50 m plots; in the alpine-tree-line ecotone. The cover of shrubs and trees (tree stems (> or =3.5 cm) were noted and positions determined. There has been a substantial increase of cover of shrubs and trees, particularly dwarf birch (Betula nana), and mountain birch (Betula pubescens ssp. czerepanovii), and an establishment of aspen (Populus tremula). The other species willows (Salix spp.), juniper (Juniperus communis), and rowan (Sorbus aucuparia) revealed inconsistent changes among the plots. Although this study was unable to identify the causes for the change in shrubs and small trees, they are consistent with anticipated changes due to climate change and reduced herbivory.

DLRS: gene tree evolution in light of a species tree.

Science.gov (United States)

Sjöstrand, Joel; Sennblad, Bengt; Arvestad, Lars; Lagergren, Jens

2012-11-15

PrIME-DLRS (or colloquially: 'Delirious') is a phylogenetic software tool to simultaneously infer and reconcile a gene tree given a species tree. It accounts for duplication and loss events, a relaxed molecular clock and is intended for the study of homologous gene families, for example in a comparative genomics setting involving multiple species. PrIME-DLRS uses a Bayesian MCMC framework, where the input is a known species tree with divergence times and a multiple sequence alignment, and the output is a posterior distribution over gene trees and model parameters. PrIME-DLRS is available for Java SE 6+ under the New BSD License, and JAR files and source code can be downloaded from http://code.google.com/p/jprime/. There is also a slightly older C++ version available as a binary package for Ubuntu, with download instructions at http://prime.sbc.su.se. The C++ source code is available upon request. joel.sjostrand@scilifelab.se or jens.lagergren@scilifelab.se. PrIME-DLRS is based on a sound probabilistic model (Åkerborg et al., 2009) and has been thoroughly validated on synthetic and biological datasets (Supplementary Material online).

Tree Species Richness Promotes Invertebrate Herbivory on Congeneric Native and Exotic Tree Saplings in a Young Diversity Experiment.

Directory of Open Access Journals (Sweden)

Annika Wein

Full Text Available Tree diversity in forests is an important driver of ecological processes including herbivory. Empirical evidence suggests both negative and positive effects of tree diversity on herbivory, which can be, respectively, attributed to associational resistance or associational susceptibility. Tree diversity experiments allow testing for associational effects, but evidence regarding which pattern predominates is mixed. Furthermore, it is unknown if herbivory on tree species of native vs. exotic origin is influenced by changing tree diversity in a similar way, or if exotic tree species escape natural enemies, resulting in lower damage that is unrelated to tree diversity. To address these questions, we established a young tree diversity experiment in temperate southwestern Germany that uses high planting density (49 trees per plot; plot size 13 m2. The species pool consists of six congeneric species pairs of European and North American origin (12 species in total planted in monocultures and mixtures (1, 2, 4, 6 species. We assessed leaf damage by leaf-chewing insects on more than 5,000 saplings of six broadleaved tree species. Plot-level tree species richness increased leaf damage, which more than doubled from monocultures to six-species mixtures, strongly supporting associational susceptibility. However, leaf damage among congeneric native and exotic species pairs was similar. There were marked differences in patterns of leaf damage across tree genera, and only the genera likely having a predominately generalist herbivore community showed associational susceptibility, irrespective of the geographical origin of a tree species. In conclusion, an increase in tree species richness in young temperate forests may result in associational susceptibility to feeding by generalist herbivores.

Effects of tree-to-tree variations on sap flux-based transpiration estimates in a forested watershed

Science.gov (United States)

Kume, Tomonori; Tsuruta, Kenji; Komatsu, Hikaru; Kumagai, Tomo'omi; Higashi, Naoko; Shinohara, Yoshinori; Otsuki, Kyoichi

2010-05-01

To estimate forest stand-scale water use, we assessed how sample sizes affect confidence of stand-scale transpiration (E) estimates calculated from sap flux (Fd) and sapwood area (AS_tree) measurements of individual trees. In a Japanese cypress plantation, we measured Fd and AS_tree in all trees (n = 58) within a 20 × 20 m study plot, which was divided into four 10 × 10 subplots. We calculated E from stand AS_tree (AS_stand) and mean stand Fd (JS) values. Using Monte Carlo analyses, we examined potential errors associated with sample sizes in E, AS_stand, and JS by using the original AS_tree and Fd data sets. Consequently, we defined optimal sample sizes of 10 and 15 for AS_stand and JS estimates, respectively, in the 20 × 20 m plot. Sample sizes greater than the optimal sample sizes did not decrease potential errors. The optimal sample sizes for JS changed according to plot size (e.g., 10 × 10 m and 10 × 20 m), while the optimal sample sizes for AS_stand did not. As well, the optimal sample sizes for JS did not change in different vapor pressure deficit conditions. In terms of E estimates, these results suggest that the tree-to-tree variations in Fd vary among different plots, and that plot size to capture tree-to-tree variations in Fd is an important factor. This study also discusses planning balanced sampling designs to extrapolate stand-scale estimates to catchment-scale estimates.

Tests with VHR images for the identification of olive trees and other fruit trees in the European Union

Science.gov (United States)

Masson, Josiane; Soille, Pierre; Mueller, Rick

2004-10-01

In the context of the Common Agricultural Policy (CAP) there is a strong interest of the European Commission for counting and individually locating fruit trees. An automatic counting algorithm developed by the JRC (OLICOUNT) was used in the past for olive trees only, on 1m black and white orthophotos but with limits in case of young trees or irregular groves. This study investigates the improvement of fruit tree identification using VHR images on a large set of data in three test sites, one in Creta (Greece; one in the south-east of France with a majority of olive trees and associated fruit trees, and the last one in Florida on citrus trees. OLICOUNT was compared with two other automatic tree counting, applications, one using the CRISP software on citrus trees and the other completely automatic based on regional minima (morphological image analysis). Additional investigation was undertaken to refine the methods. This paper describes the automatic methods and presents the results derived from the tests.

The Hopi Fruit Tree Book.

Science.gov (United States)

Nyhuis, Jane

Referring as often as possible to traditional Hopi practices and to materials readily available on the reservation, the illustrated booklet provides information on the care and maintenance of young fruit trees. An introduction to fruit trees explains the special characteristics of new trees, e.g., grafting, planting pits, and watering. The…

Rectilinear Full Steiner Tree Generation

DEFF Research Database (Denmark)

Zachariasen, Martin

1999-01-01

The fastest exact algorithm (in practice) for the rectilinear Steiner tree problem in the plane uses a two-phase scheme: First, a small but sufficient set of full Steiner trees (FSTs) is generated and then a Steiner minimum tree is constructed from this set by using simple backtrack search, dynamic...

Reconciliation with non-binary species trees.

Science.gov (United States)

Vernot, Benjamin; Stolzer, Maureen; Goldman, Aiton; Durand, Dannie

2008-10-01

Reconciliation extracts information from the topological incongruence between gene and species trees to infer duplications and losses in the history of a gene family. The inferred duplication-loss histories provide valuable information for a broad range of biological applications, including ortholog identification, estimating gene duplication times, and rooting and correcting gene trees. While reconciliation for binary trees is a tractable and well studied problem, there are no algorithms for reconciliation with non-binary species trees. Yet a striking proportion of species trees are non-binary. For example, 64% of branch points in the NCBI taxonomy have three or more children. When applied to non-binary species trees, current algorithms overestimate the number of duplications because they cannot distinguish between duplication and incomplete lineage sorting. We present the first algorithms for reconciling binary gene trees with non-binary species trees under a duplication-loss parsimony model. Our algorithms utilize an efficient mapping from gene to species trees to infer the minimum number of duplications in O(|V(G) | x (k(S) + h(S))) time, where |V(G)| is the number of nodes in the gene tree, h(S) is the height of the species tree and k(S) is the size of its largest polytomy. We present a dynamic programming algorithm which also minimizes the total number of losses. Although this algorithm is exponential in the size of the largest polytomy, it performs well in practice for polytomies with outdegree of 12 or less. We also present a heuristic which estimates the minimal number of losses in polynomial time. In empirical tests, this algorithm finds an optimal loss history 99% of the time. Our algorithms have been implemented in NOTUNG, a robust, production quality, tree-fitting program, which provides a graphical user interface for exploratory analysis and also supports automated, high-throughput analysis of large data sets.

Heterogeneous Compression of Large Collections of Evolutionary Trees.

Science.gov (United States)

Matthews, Suzanne J

2015-01-01

Compressing heterogeneous collections of trees is an open problem in computational phylogenetics. In a heterogeneous tree collection, each tree can contain a unique set of taxa. An ideal compression method would allow for the efficient archival of large tree collections and enable scientists to identify common evolutionary relationships over disparate analyses. In this paper, we extend TreeZip to compress heterogeneous collections of trees. TreeZip is the most efficient algorithm for compressing homogeneous tree collections. To the best of our knowledge, no other domain-based compression algorithm exists for large heterogeneous tree collections or enable their rapid analysis. Our experimental results indicate that TreeZip averages 89.03 percent (72.69 percent) space savings on unweighted (weighted) collections of trees when the level of heterogeneity in a collection is moderate. The organization of the TRZ file allows for efficient computations over heterogeneous data. For example, consensus trees can be computed in mere seconds. Lastly, combining the TreeZip compressed (TRZ) file with general-purpose compression yields average space savings of 97.34 percent (81.43 percent) on unweighted (weighted) collections of trees. Our results lead us to believe that TreeZip will prove invaluable in the efficient archival of tree collections, and enables scientists to develop novel methods for relating heterogeneous collections of trees.

Fault tree graphics

International Nuclear Information System (INIS)

Bass, L.; Wynholds, H.W.; Porterfield, W.R.

1975-01-01

Described is an operational system that enables the user, through an intelligent graphics terminal, to construct, modify, analyze, and store fault trees. With this system, complex engineering designs can be analyzed. This paper discusses the system and its capabilities. Included is a brief discussion of fault tree analysis, which represents an aspect of reliability and safety modeling

Environmental Fate of Emamectin Benzoate After Tree Micro Injection of Horse Chestnut Trees

OpenAIRE

Burkhard, Rene; Binz, Heinz; Roux, Christian A; Brunner, Matthias; Ruesch, Othmar; Wyss, Peter

2014-01-01

Emamectin benzoate, an insecticide derived from the avermectin family of natural products, has a unique translocation behavior in trees when applied by tree micro injection (TMI), which can result in protection from insect pests (foliar and borers) for several years. Active ingredient imported into leaves was measured at the end of season in the fallen leaves of treated horse chestnut (Aesculus hippocastanum) trees. The dissipation of emamectin benzoate in these leaves seems to be biphasic an...

Factors that influence Christmas tree sales

Science.gov (United States)

Thomas H. Pendleton; Lawrence D. Garrett

1970-01-01

An analysis of the metropolitan Christmas tree market in Winston-Salem, N. C., shows that to sell more trees, Christmas tree retailers should locate their lots on heavily traveled streets in business areas, have adequate parking facilities, advertise, and have attractive displays of trees. Retailers who follow these practices can expect to receive higher prices for...

The View from the Trees: Nocturnal Bull Ants, Myrmecia midas, Use the Surrounding Panorama While Descending from Trees.

Science.gov (United States)

Freas, Cody A; Wystrach, Antione; Narendra, Ajay; Cheng, Ken

2018-01-01

Solitary foraging ants commonly use visual cues from their environment for navigation. Foragers are known to store visual scenes from the surrounding panorama for later guidance to known resources and to return successfully back to the nest. Several ant species travel not only on the ground, but also climb trees to locate resources. The navigational information that guides animals back home during their descent, while their body is perpendicular to the ground, is largely unknown. Here, we investigate in a nocturnal ant, Myrmecia midas , whether foragers travelling down a tree use visual information to return home. These ants establish nests at the base of a tree on which they forage and in addition, they also forage on nearby trees. We collected foragers and placed them on the trunk of the nest tree or a foraging tree in multiple compass directions. Regardless of the displacement location, upon release ants immediately moved to the side of the trunk facing the nest during their descent. When ants were released on non-foraging trees near the nest, displaced foragers again travelled around the tree to the side facing the nest. All the displaced foragers reached the correct side of the tree well before reaching the ground. However, when the terrestrial cues around the tree were blocked, foragers were unable to orient correctly, suggesting that the surrounding panorama is critical to successful orientation on the tree. Through analysis of panoramic pictures, we show that views acquired at the base of the foraging tree nest can provide reliable nest-ward orientation up to 1.75 m above the ground. We discuss, how animals descending from trees compare their current scene to a memorised scene and report on the similarities in visually guided behaviour while navigating on the ground and descending from trees.

The View from the Trees: Nocturnal Bull Ants, Myrmecia midas, Use the Surrounding Panorama While Descending from Trees

Directory of Open Access Journals (Sweden)

Cody A. Freas

2018-01-01

Full Text Available Solitary foraging ants commonly use visual cues from their environment for navigation. Foragers are known to store visual scenes from the surrounding panorama for later guidance to known resources and to return successfully back to the nest. Several ant species travel not only on the ground, but also climb trees to locate resources. The navigational information that guides animals back home during their descent, while their body is perpendicular to the ground, is largely unknown. Here, we investigate in a nocturnal ant, Myrmecia midas, whether foragers travelling down a tree use visual information to return home. These ants establish nests at the base of a tree on which they forage and in addition, they also forage on nearby trees. We collected foragers and placed them on the trunk of the nest tree or a foraging tree in multiple compass directions. Regardless of the displacement location, upon release ants immediately moved to the side of the trunk facing the nest during their descent. When ants were released on non-foraging trees near the nest, displaced foragers again travelled around the tree to the side facing the nest. All the displaced foragers reached the correct side of the tree well before reaching the ground. However, when the terrestrial cues around the tree were blocked, foragers were unable to orient correctly, suggesting that the surrounding panorama is critical to successful orientation on the tree. Through analysis of panoramic pictures, we show that views acquired at the base of the foraging tree nest can provide reliable nest-ward orientation up to 1.75 m above the ground. We discuss, how animals descending from trees compare their current scene to a memorised scene and report on the similarities in visually guided behaviour while navigating on the ground and descending from trees.

Encoding phylogenetic trees in terms of weighted quartets.

Science.gov (United States)

Grünewald, Stefan; Huber, Katharina T; Moulton, Vincent; Semple, Charles

2008-04-01

One of the main problems in phylogenetics is to develop systematic methods for constructing evolutionary or phylogenetic trees. For a set of species X, an edge-weighted phylogenetic X-tree or phylogenetic tree is a (graph theoretical) tree with leaf set X and no degree 2 vertices, together with a map assigning a non-negative length to each edge of the tree. Within phylogenetics, several methods have been proposed for constructing such trees that work by trying to piece together quartet trees on X, i.e. phylogenetic trees each having four leaves in X. Hence, it is of interest to characterise when a collection of quartet trees corresponds to a (unique) phylogenetic tree. Recently, Dress and Erdös provided such a characterisation for binary phylogenetic trees, that is, phylogenetic trees all of whose internal vertices have degree 3. Here we provide a new characterisation for arbitrary phylogenetic trees.

Microwave sensing of tree trunks

Science.gov (United States)

Jezova, Jana; Mertens, Laurence; Lambot, Sebastien

2015-04-01

The main subject of this research is the observation of the inner part of living tree trunks using ground-penetrating radar (GPR). Trees are everyday part of human life and therefore it is important to pay attention to the tree conditions. The most obvious consequence of the poor tree condition is dead or injury caused by falling tree. The trunk internal structure is divided into three main parts: heartwood, sapwood and bark, which make this medium highly anisotropic and heterogeneous. Furthermore, the properties of the wood are not only specie-dependent but also depend on genetic and on environmental conditions. In urban areas the main problem for the stability of the trees relies in the apparition of decays provoked by fungi, insect or birds. This results in cavities or decreasing of the support capacity of the tree. GPR has proved itself to be a very powerful electromagnetic tool for non-destructive detection of buried objects. Since the beginning of the 20th century it has been used in several different areas (archaeology, landmine detection, civil engineering, ...). GPR uses the principle of the scattering of the electromagnetic waves that are radiated from a transmitting antenna. Then the waves propagate through the medium and are reflected from the object and then they are received by a receiving antenna. The velocity of the scattered signal is determined primarily by the permittivity of the material. The optimal functionality of the GPR was investigated using the numerical simulation tool gprMax2D. This tool is based on a Finite-Difference Time-Domain (FDTD) numerical model. Subsequently, the GPR functionality was tested using the laboratory model of a decayed tree trunk. Afterwards, the results and lessons learnt in the simplified tests will be used in the processing of the real data and will help to achieve deeper understanding of them. The laboratory model of the tree trunk was made by plastic or carton pipes and filled by sand. Space inside the model

Effects of stock use and backpackers on water quality in wilderness in Sequoia and Kings Canyon National Parks, USA

Science.gov (United States)

Clow, David W.; Forrester, Harrison; Miller, Benjamin; Roop, Heidi; Sickman, James O.; Ryu, Hodon; Santo Domingo, Jorge

2013-01-01

During 2010-2011, a study was conducted in Sequoia and Kings Canyon National Parks (SEKI) to evaluate the influence of pack animals (stock) and backpackers on water quality in wilderness lakes and streams. The study had three main components: (1) a synoptic survey of water quality in wilderness areas of the parks, (2) paired water-quality sampling above and below several areas with differing types and amounts of visitor use, and (3) intensive monitoring at six sites to document temporal variations in water quality. Data from the synoptic water-quality survey indicated that wilderness lakes and streams are dilute and have low nutrient and Escherichia coli (E. coli) concentrations. The synoptic survey sites were categorized as minimal use, backpacker use, or mixed use (stock and backpackers), depending on the most prevalent type of use upstream from the sampling locations. Sites with mixed use tended to have higher concentrations of most constituents (including E.coli) than those categorized as minimal-use (p≤0.05); concentrations at backpacker-use sites were intermediate. Data from paired-site sampling indicated that E.coli, total coliform, and particulate phosphorus concentrations were greater in streams downstream from mixed-use areas than upstream from those areas (p≤0.05). Paired-site data also indicated few statistically significant differences in nutrient, E. coli, or total coliform concentrations in streams upstream and downstream from backpacker-use areas. The intensive-monitoring data indicated that nutrient and E. coli concentrations normally were low, except during storms, when notable increases in concentrations of E.coli, nutrients, dissolved organic carbon, and turbidity occurred. In summary, results from this study indicate that water quality in SEKI wilderness generally is good, except during storms; and visitor use appears to have a small, but statistically significant influence on stream water quality.

TREE2FASTA: a flexible Perl script for batch extraction of FASTA sequences from exploratory phylogenetic trees.

Science.gov (United States)

Sauvage, Thomas; Plouviez, Sophie; Schmidt, William E; Fredericq, Suzanne

2018-03-05

The body of DNA sequence data lacking taxonomically informative sequence headers is rapidly growing in user and public databases (e.g. sequences lacking identification and contaminants). In the context of systematics studies, sorting such sequence data for taxonomic curation and/or molecular diversity characterization (e.g. crypticism) often requires the building of exploratory phylogenetic trees with reference taxa. The subsequent step of segregating DNA sequences of interest based on observed topological relationships can represent a challenging task, especially for large datasets. We have written TREE2FASTA, a Perl script that enables and expedites the sorting of FASTA-formatted sequence data from exploratory phylogenetic trees. TREE2FASTA takes advantage of the interactive, rapid point-and-click color selection and/or annotations of tree leaves in the popular Java tree-viewer FigTree to segregate groups of FASTA sequences of interest to separate files. TREE2FASTA allows for both simple and nested segregation designs to facilitate the simultaneous preparation of multiple data sets that may overlap in sequence content.

Public Reactions to New Street Tree Planting

Directory of Open Access Journals (Sweden)

Ruth A. Rae

2010-01-01

Full Text Available MillionTreesNYC, which has the goal of planting one million trees in New York City by 2017, is intended to make New York City a greener, more sustainable city and is part of the Mayor’s comprehensive long term strategic plan, PlaNYC. Through planting a tree at every suitable sidewalk location in the city, the City of New York is transforming blocks and communities, and providing a variety of environmental, social and aesthetic benefits. This article examines the large scale municipal planting of new street trees and the reaction by some of the pubic to this planting.Trees offer benefits to the city overall, but the public may not understand these benefits or the street tree planting process. Between 2007 and 2009, the Department of Parks & Recreation planted 53,235 new street trees, and received 4,108 items of correspondence from the public. The majority of this correspondence consisted of public comments about the City’s new street tree planting policies and processes including placement objections, maintenance concerns, reports of resultant damage from tree planting operations, requests for new street trees and reports of tree conditions.This study describes the operational policies that guide New York City's municipal street tree planting, and results of content and spatial analysis of the correspondence. Qualitative analysis of the correspondence revealed the public perceptions and concerns related to the MillionTreesNYC program. Spatial analysis explored the relationship between the planting locations of new street trees and the locations of the citizen correspondence.Public reactions to this large scale municipal planting are related to the dual public and private nature of the sidewalk, issues of territoriality, responsibility, aesthetics and place attachment. Correspondence volume was associated with the scale of the new street tree block planting program, and the effectiveness of NYC’s 311 Customer Service Center. The discussion

Generic physical protection logic trees

International Nuclear Information System (INIS)

Paulus, W.K.

1981-10-01

Generic physical protection logic trees, designed for application to nuclear facilities and materials, are presented together with a method of qualitative evaluation of the trees for design and analysis of physical protection systems. One or more defense zones are defined where adversaries interact with the physical protection system. Logic trees that are needed to describe the possible scenarios within a defense zone are selected. Elements of a postulated or existing physical protection system are tagged to the primary events of the logic tree. The likelihood of adversary success in overcoming these elements is evaluated on a binary, yes/no basis. The effect of these evaluations is propagated through the logic of each tree to determine whether the adversary is likely to accomplish the end event of the tree. The physical protection system must be highly likely to overcome the adversary before he accomplishes his objective. The evaluation must be conducted for all significant states of the site. Deficiencies uncovered become inputs to redesign and further analysis, closing the loop on the design/analysis cycle

Generic physical protection logic trees

Energy Technology Data Exchange (ETDEWEB)

Paulus, W.K.

1981-10-01

Generic physical protection logic trees, designed for application to nuclear facilities and materials, are presented together with a method of qualitative evaluation of the trees for design and analysis of physical protection systems. One or more defense zones are defined where adversaries interact with the physical protection system. Logic trees that are needed to describe the possible scenarios within a defense zone are selected. Elements of a postulated or existing physical protection system are tagged to the primary events of the logic tree. The likelihood of adversary success in overcoming these elements is evaluated on a binary, yes/no basis. The effect of these evaluations is propagated through the logic of each tree to determine whether the adversary is likely to accomplish the end event of the tree. The physical protection system must be highly likely to overcome the adversary before he accomplishes his objective. The evaluation must be conducted for all significant states of the site. Deficiencies uncovered become inputs to redesign and further analysis, closing the loop on the design/analysis cycle.

Tree-Based Unrooted Phylogenetic Networks.

Science.gov (United States)

Francis, A; Huber, K T; Moulton, V

2018-02-01

Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An unrooted phylogenetic network on a non-empty, finite set X of taxa, or network, is a connected, simple graph in which every vertex has degree 1 or 3 and whose leaf set is X. It is called a phylogenetic tree if the underlying graph is a tree. In this paper we consider properties of tree-based networks, that is, networks that can be constructed by adding edges into a phylogenetic tree. We show that although they have some properties in common with their rooted analogues which have recently drawn much attention in the literature, they have some striking differences in terms of both their structural and computational properties. We expect that our results could eventually have applications to, for example, detecting horizontal gene transfer or hybridization which are important factors in the evolution of many organisms.

Improved prediction of hardwood tree biomass derived from wood density estimates and form factors for whole trees

Science.gov (United States)

David W. MacFarlane; Neil R. Ver Planck

2012-01-01

Data from hardwood trees in Michigan were analyzed to investigate how differences in whole-tree form and wood density between trees of different stem diameter relate to residual error in standard-type biomass equations. The results suggested that whole-tree wood density, measured at breast height, explained a significant proportion of residual error in standard-type...

Wood density variation and tree ring distinctness in Gmelina arborea trees by x-ray densitometry

Directory of Open Access Journals (Sweden)

Roger Moya

2009-03-01

Full Text Available Due to its relationship with other properties, wood density is the main wood quality parameter. Modern, accuratemethods such as X-ray densitometry - are applied to determine the spatial distribution of density in wood sections and to evaluatewood quality. The objectives of this study were to determinate the influence of growing conditions on wood density variation andtree ring demarcation of gmelina trees from fast growing plantations in Costa Rica. The wood density was determined by X-raydensitometry method. Wood samples were cut from gmelina trees and were exposed to low X-rays. The radiographic films weredeveloped and scanned using a 256 gray scale with 1000 dpi resolution and the wood density was determined by CRAD and CERDsoftware. The results showed tree-ring boundaries were distinctly delimited in trees growing in site with rainfall lower than 2510 mm/year. It was demonstrated that tree age, climatic conditions and management of plantation affects wood density and its variability. Thespecific effect of variables on wood density was quantified by for multiple regression method. It was determined that tree yearexplained 25.8% of the total variation of density and 19.9% were caused by climatic condition where the tree growing. Wood densitywas less affected by the intensity of forest management with 5.9% of total variation.

Autumn frost hardiness in Norway spruce plus tree progeny and trees of the local and transferred provenances in central Sweden.

Science.gov (United States)

Hannerz, Mats; Westin, Johan

2005-09-01

Reforestation with provenances from locations remote from the planting site (transferred provenances) or the progeny of trees of local provenances selected for superior form and vigor (plus trees) offer alternative means to increase yield over that obtained by the use of seed from unselected trees of the local provenance. Under Swedish conditions, Norway spruce (Picea abies (L.) Karst.) of certain transferred provenances generally has an advantage in productivity relative to the local provenance comparable to that of progeny of plus trees. The aim of this study was to explore the extent to which productivity gains achieved by provenance transfer or the use of plus tree progeny are associated with reductions in autumn frost hardiness, relative to that of trees of the local provenance. In a field trial with 19-year-old trees in central Sweden, bud hardiness was tested on four occasions during the autumn of 2002. Trees of the local provenance were compared with trees of a south Swedish provenance originating 3 degrees of latitude to the south, a Belarusian provenance and the progeny of plus trees of local origin. The Belarusian provenance was the least hardy and the local provenance the most hardy, with plus tree progeny and the south Swedish provenance being intermediate in hardiness. Both the Belarusian provenance and the plus tree progeny were significantly taller than trees of the other populations. Within provenances, tree height was negatively correlated with autumn frost hardiness. Among the plus tree progeny, however, no such correlation between tree height and autumn frost hardiness was found. It is concluded that although the gain in productivity achieved by provenance transfer from Belarus was comparable to that achieved by using the progeny of plus trees of the local provenance, the use of trees of the Belarus provenance involved an increased risk of autumn frost damage because of later hardening.

Inferences from growing trees backwards

Science.gov (United States)

David W. Green; Kent A. McDonald

1997-01-01

The objective of this paper is to illustrate how longitudinal stress wave techniques can be useful in tracking the future quality of a growing tree. Monitoring the quality of selected trees in a plantation forest could provide early input to decisions on the effectiveness of management practices, or future utilization options, for trees in a plantation. There will...

The stopping rules for winsorized tree

Science.gov (United States)

Ch'ng, Chee Keong; Mahat, Nor Idayu

2017-11-01

Winsorized tree is a modified tree-based classifier that is able to investigate and to handle all outliers in all nodes along the process of constructing the tree. It overcomes the tedious process of constructing a classical tree where the splitting of branches and pruning go concurrently so that the constructed tree would not grow bushy. This mechanism is controlled by the proposed algorithm. In winsorized tree, data are screened for identifying outlier. If outlier is detected, the value is neutralized using winsorize approach. Both outlier identification and value neutralization are executed recursively in every node until predetermined stopping criterion is met. The aim of this paper is to search for significant stopping criterion to stop the tree from further splitting before overfitting. The result obtained from the conducted experiment on pima indian dataset proved that the node could produce the final successor nodes (leaves) when it has achieved the range of 70% in information gain.

Meta-learning in decision tree induction

CERN Document Server

Grąbczewski, Krzysztof

2014-01-01

The book focuses on different variants of decision tree induction but also describes  the meta-learning approach in general which is applicable to other types of machine learning algorithms. The book discusses different variants of decision tree induction and represents a useful source of information to readers wishing to review some of the techniques used in decision tree learning, as well as different ensemble methods that involve decision trees. It is shown that the knowledge of different components used within decision tree learning needs to be systematized to enable the system to generate and evaluate different variants of machine learning algorithms with the aim of identifying the top-most performers or potentially the best one. A unified view of decision tree learning enables to emulate different decision tree algorithms simply by setting certain parameters. As meta-learning requires running many different processes with the aim of obtaining performance results, a detailed description of the experimen...

Generic Ising trees

DEFF Research Database (Denmark)

Durhuus, Bergfinnur Jøgvan; Napolitano, George Maria

2012-01-01

The Ising model on a class of infinite random trees is defined as a thermodynamiclimit of finite systems. A detailed description of the corresponding distribution of infinite spin configurations is given. As an application, we study the magnetization properties of such systems and prove that they......The Ising model on a class of infinite random trees is defined as a thermodynamiclimit of finite systems. A detailed description of the corresponding distribution of infinite spin configurations is given. As an application, we study the magnetization properties of such systems and prove...... that they exhibit no spontaneous magnetization. Furthermore, the values of the Hausdorff and spectral dimensions of the underlying trees are calculated and found to be, respectively,¯dh =2 and¯ds = 4/3....

Phylogenetic trees and Euclidean embeddings.

Science.gov (United States)

Layer, Mark; Rhodes, John A

2017-01-01

It was recently observed by de Vienne et al. (Syst Biol 60(6):826-832, 2011) that a simple square root transformation of distances between taxa on a phylogenetic tree allowed for an embedding of the taxa into Euclidean space. While the justification for this was based on a diffusion model of continuous character evolution along the tree, here we give a direct and elementary explanation for it that provides substantial additional insight. We use this embedding to reinterpret the differences between the NJ and BIONJ tree building algorithms, providing one illustration of how this embedding reflects tree structures in data.

Tritium concentrations in tree ring cellulose

International Nuclear Information System (INIS)

Kaji, Toshio; Momoshima, Noriyuki; Takashima, Yoshimasa.

1989-01-01

Measurements of tritium (tissue bound tritium; TBT) concentration in tree rings are presented and discussed. Such measurement is expected to provide a useful means of estimating the tritium level in the environment in the past. The concentration of tritium bound in the tissue (TBT) in a tree ring considered to reflect the environmental tritium level in the area at the time of the formation of the ring, while the concentration of tritium in the free water in the tissue represents the current environmental tritium level. First, tritium concentration in tree ring cellulose sampled from a cedar tree grown in a typical environment in Fukuoka Prefecture is compared with the tritium concentration in precipitation in Tokyo. Results show that the year-to-year variations in the tritium concentration in the tree rings agree well with those in precipitation. The maximum concentration, which occurred in 1963, is attibuted to atmospheric nuclear testing which was performed frequently during the 1961 - 1963 period. Measurement is also made of the tritium concentration in tree ring cellulose sampled from a pine tree grown near the Isotope Center of Kyushu University (Fukuoka). Results indicate that the background level is higher probably due to the release of tritium from the facilities around the pine tree. Thus, measurement of tritium in tree ring cellulose clearly shows the year-to-year variation in the tritium concentration in the atmosphere. (N.K.)

Totally optimal decision trees for Boolean functions

KAUST Repository

Chikalov, Igor

2016-07-28

We study decision trees which are totally optimal relative to different sets of complexity parameters for Boolean functions. A totally optimal tree is an optimal tree relative to each parameter from the set simultaneously. We consider the parameters characterizing both time (in the worst- and average-case) and space complexity of decision trees, i.e., depth, total path length (average depth), and number of nodes. We have created tools based on extensions of dynamic programming to study totally optimal trees. These tools are applicable to both exact and approximate decision trees, and allow us to make multi-stage optimization of decision trees relative to different parameters and to count the number of optimal trees. Based on the experimental results we have formulated the following hypotheses (and subsequently proved): for almost all Boolean functions there exist totally optimal decision trees (i) relative to the depth and number of nodes, and (ii) relative to the depth and average depth.

Trees for future forests

DEFF Research Database (Denmark)

Lobo, Albin

Climate change creates new challenges in forest management. The increase in temperature may in the long run be beneficial for the forests in the northern latitudes, but the high rate at which climate change is predicted to proceed will make adaptation difficult because trees are long living sessile...... organisms. The aim of the present thesis is therefore to explore genetic resilience and phenotypic plasticity mechanisms that allows trees to adapt and evolve with changing climates. The thesis focus on the abiotic factors associated with climate change, especially raised temperatures and lack...... age of these tree species and the uncertainty around the pace and effect of climate, it remains an open question if the native populations can respond fast enough. Phenotypic plasticity through epigenetic regulation of spring phenology is found to be present in a tree species which might act...

A Durable Flash Memory Search Tree

OpenAIRE

Clay III, James; Wortman, Kevin

2012-01-01

We consider the task of optimizing the B-tree data structure, used extensively in operating systems and databases, for sustainable usage on multi-level flash memory. Empirical evidence shows that this new flash memory tree, or FM Tree, extends the operational lifespan of each block of flash memory by a factor of roughly 27 to 70 times, while still supporting logarithmic-time search tree operations.

Are There Infinite Irrigation Trees?

Science.gov (United States)

Bernot, M.; Caselles, V.; Morel, J. M.

2006-08-01

In many natural or artificial flow systems, a fluid flow network succeeds in irrigating every point of a volume from a source. Examples are the blood vessels, the bronchial tree and many irrigation and draining systems. Such systems have raised recently a lot of interest and some attempts have been made to formalize their description, as a finite tree of tubes, and their scaling laws [25], [26]. In contrast, several mathematical models [5], [22], [10], propose an idealization of these irrigation trees, where a countable set of tubes irrigates any point of a volume with positive Lebesgue measure. There is no geometric obstruction to this infinitesimal model and general existence and structure theorems have been proved. As we show, there may instead be an energetic obstruction. Under Poiseuille law R(s) = s -2 for the resistance of tubes with section s, the dissipated power of a volume irrigating tree cannot be finite. In other terms, infinite irrigation trees seem to be impossible from the fluid mechanics viewpoint. This also implies that the usual principle analysis performed for the biological models needs not to impose a minimal size for the tubes of an irrigating tree; the existence of the minimal size can be proven from the only two obvious conditions for such irrigation trees, namely the Kirchhoff and Poiseuille laws.

Trees and highway safety.

Science.gov (United States)

2011-03-01

To minimize the severity of run-off-road collisions of vehicles with trees, departments of transportation (DOTs) : commonly establish clear zones for trees and other fixed objects. Caltrans clear zone on freeways is 30 feet : minimum (40 feet pref...

Influence of sample composition on aerosol organic and black carbon determinations

Energy Technology Data Exchange (ETDEWEB)

Novakov, T.; Corrigan, C.E.

1995-07-01

In this paper we present results on characterization of filter-collected redwood (Sequoia sempevirens)-needle and eucalyptus smoke particles by thermal, optical, and solvent extraction methods. Our results demonstrate that organic and black carbon concentrations determined by thermal and optical methods are not only method dependent, but also critically influenced by the overall chemical composition of the samples. These conclusions are supported by the following: (1) the organic fraction of biomass smoke particles analyzed includes a component, ranging in concentration from about 6-20% of total carbon or from 16-30% of organic carbon, that is relatively non-volatile and has a combustion temperature close to that of black carbon; (2) presence of K or Na in biomass smoke samples lowers the combustion temperatures of this organic component and of black carbon, making their combustion properties indistinguishable; (3) about 20% of total organic material is nonvolatile when heated to 550{degrees}C in an inert atmosphere. Consequently, thermal methods that rely on a specific temperature to separate organic from black carbon may either underestimate or overestimate the black and organic carbon concentrations, depending on the amounts of Na and K and on the composition and concentration of organic material present in a sample. These analytical uncertainties and, under some conditions, absorption by organic material may contribute to the variability of empirically derived proportionality between light transmission through filter deposits and black carbon concentrations.

Influence of sample composition on aerosol organic and black carbon determinations

International Nuclear Information System (INIS)

Novakov, T.; Corrigan, C.E.

1995-07-01

In this paper we present results on characterization of filter-collected redwood (Sequoia sempevirens)-needle and eucalyptus smoke particles by thermal, optical, and solvent extraction methods. Our results demonstrate that organic and black carbon concentrations determined by thermal and optical methods are not only method dependent, but also critically influenced by the overall chemical composition of the samples. These conclusions are supported by the following: (1) the organic fraction of biomass smoke particles analyzed includes a component, ranging in concentration from about 6-20% of total carbon or from 16-30% of organic carbon, that is relatively non-volatile and has a combustion temperature close to that of black carbon; (2) presence of K or Na in biomass smoke samples lowers the combustion temperatures of this organic component and of black carbon, making their combustion properties indistinguishable; (3) about 20% of total organic material is nonvolatile when heated to 550 degrees C in an inert atmosphere. Consequently, thermal methods that rely on a specific temperature to separate organic from black carbon may either underestimate or overestimate the black and organic carbon concentrations, depending on the amounts of Na and K and on the composition and concentration of organic material present in a sample. These analytical uncertainties and, under some conditions, absorption by organic material may contribute to the variability of empirically derived proportionality between light transmission through filter deposits and black carbon concentrations

Estimation of Tree Lists from Airborne Laser Scanning Using Tree Model Clustering and k-MSN Imputation

Directory of Open Access Journals (Sweden)

Jörgen Wallerman

2013-04-01

Full Text Available Individual tree crowns may be delineated from airborne laser scanning (ALS data by segmentation of surface models or by 3D analysis. Segmentation of surface models benefits from using a priori knowledge about the proportions of tree crowns, which has not yet been utilized for 3D analysis to any great extent. In this study, an existing surface segmentation method was used as a basis for a new tree model 3D clustering method applied to ALS returns in 104 circular field plots with 12 m radius in pine-dominated boreal forest (64°14'N, 19°50'E. For each cluster below the tallest canopy layer, a parabolic surface was fitted to model a tree crown. The tree model clustering identified more trees than segmentation of the surface model, especially smaller trees below the tallest canopy layer. Stem attributes were estimated with k-Most Similar Neighbours (k-MSN imputation of the clusters based on field-measured trees. The accuracy at plot level from the k-MSN imputation (stem density root mean square error or RMSE 32.7%; stem volume RMSE 28.3% was similar to the corresponding results from the surface model (stem density RMSE 33.6%; stem volume RMSE 26.1% with leave-one-out cross-validation for one field plot at a time. Three-dimensional analysis of ALS data should also be evaluated in multi-layered forests since it identified a larger number of small trees below the tallest canopy layer.

Tree-Substrate Water Relations and Root Development in Tree Plantations Used for Mine Tailings Reclamation.

Science.gov (United States)

Guittonny-Larchevêque, Marie; Bussière, Bruno; Pednault, Carl

2016-05-01

Tree water uptake relies on well-developed root systems. However, mine wastes can restrict root growth, in particular metalliferous mill tailings, which consist of the finely crushed ore that remains after valuable metals are removed. Thus, water stress could limit plantation success in reclaimed mine lands. This study evaluates the effect of substrates varying in quality (topsoil, overburden, compost and tailings mixture, and tailings alone) and quantity (50- or 20-cm-thick topsoil layer vs. 1-m plantation holes) on root development and water stress exposure of trees planted in low-sulfide mine tailings under boreal conditions. A field experiment was conducted over 2 yr with two tree species: basket willow ( L.) and hybrid poplar ( Moench × A. Henry). Trees developed roots in the tailings underlying the soil treatments despite tailings' low macroporosity. However, almost no root development occurred in tailings underlying a compost and tailings mixture. Because root development and associated water uptake was not limited to the soil, soil volume influenced neither short-term (water potential and instantaneous transpiration) nor long-term (δC) water stress exposure in trees. However, trees were larger and had greater total leaf area when grown in thicker topsoil. Despite a volumetric water content that always remained above permanent wilting point in the tailings colonized by tree roots, measured foliar water potentials at midday were lower than drought thresholds reported for both tested tree species. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Up in the Tree – The Overlooked Richness of Bryophytes and Lichens in Tree Crowns

Science.gov (United States)

Boch, Steffen; Müller, Jörg; Prati, Daniel; Blaser, Stefan; Fischer, Markus

2013-01-01

Assessing diversity is among the major tasks in ecology and conservation science. In ecological and conservation studies, epiphytic cryptogams are usually sampled up to accessible heights in forests. Thus, their diversity, especially of canopy specialists, likely is underestimated. If the proportion of those species differs among forest types, plot-based diversity assessments are biased and may result in misleading conservation recommendations. We sampled bryophytes and lichens in 30 forest plots of 20 m × 20 m in three German regions, considering all substrates, and including epiphytic litter fall. First, the sampling of epiphytic species was restricted to the lower 2 m of trees and shrubs. Then, on one representative tree per plot, we additionally recorded epiphytic species in the crown, using tree climbing techniques. Per tree, on average 54% of lichen and 20% of bryophyte species were overlooked if the crown was not been included. After sampling all substrates per plot, including the bark of all shrubs and trees, still 38% of the lichen and 4% of the bryophyte species were overlooked if the tree crown of the sampled tree was not included. The number of overlooked lichen species varied strongly among regions. Furthermore, the number of overlooked bryophyte and lichen species per plot was higher in European beech than in coniferous stands and increased with increasing diameter at breast height of the sampled tree. Thus, our results indicate a bias of comparative studies which might have led to misleading conservation recommendations of plot-based diversity assessments. PMID:24358373

VC-dimension of univariate decision trees.

Science.gov (United States)

Yildiz, Olcay Taner

2015-02-01

In this paper, we give and prove the lower bounds of the Vapnik-Chervonenkis (VC)-dimension of the univariate decision tree hypothesis class. The VC-dimension of the univariate decision tree depends on the VC-dimension values of its subtrees and the number of inputs. Via a search algorithm that calculates the VC-dimension of univariate decision trees exhaustively, we show that our VC-dimension bounds are tight for simple trees. To verify that the VC-dimension bounds are useful, we also use them to get VC-generalization bounds for complexity control using structural risk minimization in decision trees, i.e., pruning. Our simulation results show that structural risk minimization pruning using the VC-dimension bounds finds trees that are more accurate as those pruned using cross validation.

Tree growth and competition in an old-growth Picea abies forest of boreal Sweden: influence of tree spatial patterning

Science.gov (United States)

Fraver, Shawn; D'Amato, Anthony W.; Bradford, John B.; Jonsson, Bengt Gunnar; Jönsson, Mari; Esseen, Per-Anders

2013-01-01

Question: What factors best characterize tree competitive environments in this structurally diverse old-growth forest, and do these factors vary spatially within and among stands? Location: Old-growth Picea abies forest of boreal Sweden. Methods: Using long-term, mapped permanent plot data augmented with dendrochronological analyses, we evaluated the effect of neighbourhood competition on focal tree growth by means of standard competition indices, each modified to include various metrics of trees size, neighbour mortality weighting (for neighbours that died during the inventory period), and within-neighbourhood tree clustering. Candidate models were evaluated using mixed-model linear regression analyses, with mean basal area increment as the response variable. We then analysed stand-level spatial patterns of competition indices and growth rates (via kriging) to determine if the relationship between these patterns could further elucidate factors influencing tree growth. Results: Inter-tree competition clearly affected growth rates, with crown volume being the size metric most strongly influencing the neighbourhood competitive environment. Including neighbour tree mortality weightings in models only slightly improved descriptions of competitive interactions. Although the within-neighbourhood clustering index did not improve model predictions, competition intensity was influenced by the underlying stand-level tree spatial arrangement: stand-level clustering locally intensified competition and reduced tree growth, whereas in the absence of such clustering, inter-tree competition played a lesser role in constraining tree growth. Conclusions: Our findings demonstrate that competition continues to influence forest processes and structures in an old-growth system that has not experienced major disturbances for at least two centuries. The finding that the underlying tree spatial pattern influenced the competitive environment suggests caution in interpreting traditional tree

Phylogenetic tree reconstruction accuracy and model fit when proportions of variable sites change across the tree.

Science.gov (United States)

Shavit Grievink, Liat; Penny, David; Hendy, Michael D; Holland, Barbara R

2010-05-01

Commonly used phylogenetic models assume a homogeneous process through time in all parts of the tree. However, it is known that these models can be too simplistic as they do not account for nonhomogeneous lineage-specific properties. In particular, it is now widely recognized that as constraints on sequences evolve, the proportion and positions of variable sites can vary between lineages causing heterotachy. The extent to which this model misspecification affects tree reconstruction is still unknown. Here, we evaluate the effect of changes in the proportions and positions of variable sites on model fit and tree estimation. We consider 5 current models of nucleotide sequence evolution in a Bayesian Markov chain Monte Carlo framework as well as maximum parsimony (MP). We show that for a tree with 4 lineages where 2 nonsister taxa undergo a change in the proportion of variable sites tree reconstruction under the best-fitting model, which is chosen using a relative test, often results in the wrong tree. In this case, we found that an absolute test of model fit is a better predictor of tree estimation accuracy. We also found further evidence that MP is not immune to heterotachy. In addition, we show that increased sampling of taxa that have undergone a change in proportion and positions of variable sites is critical for accurate tree reconstruction.

Which trees should be removed in thinning?

Directory of Open Access Journals (Sweden)

Timo Pukkala

2015-12-01

Full Text Available Background: In economically optimal management, trees that are removed in a thinning treatment should be selected on the basis of their value, relative value increment and the effect of removal on the growth of remaining trees. Large valuable trees with decreased value increment should be removed, especially when they overtop smaller trees. Methods: This study optimized the tree selection rule in the thinning treatments of continuous cover management when the aim is to maximize the profitability of forest management. The weights of three criteria (stem value, relative value increment and effect of removal on the competition of remaining trees were optimized together with thinning intervals. Results and conclusions: The results confirmed the hypothesis that optimal thinning involves removing predominantly large trees. Increasing stumpage value, decreasing relative value increment, and increasing competitive influence increased the likelihood that removal is optimal decision. However, if the spatial distribution of trees is irregular, it is optimal to leave large trees in sparse places and remove somewhat smaller trees from dense places. However, the benefit of optimal thinning, as compared to diameter limit cutting is not usually large in pure one-species stands. On the contrary, removing the smallest trees from the stand may lead to significant (30–40 % reductions in the net present value of harvest incomes. Keywords: Continuous cover forestry, Tree selection, High thinning, Optimal management, Spatial distribution, Spatial growth model

Folding and unfolding phylogenetic trees and networks.

Science.gov (United States)

Huber, Katharina T; Moulton, Vincent; Steel, Mike; Wu, Taoyang

2016-12-01

Phylogenetic networks are rooted, labelled directed acyclic graphswhich are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any phylogenetic network N can be "unfolded" to obtain a MUL-tree U(N) and, conversely, a MUL-tree T can in certain circumstances be "folded" to obtain aphylogenetic network F(T) that exhibits T. In this paper, we study properties of the operations U and F in more detail. In particular, we introduce the class of stable networks, phylogenetic networks N for which F(U(N)) is isomorphic to N, characterise such networks, and show that they are related to the well-known class of tree-sibling networks. We also explore how the concept of displaying a tree in a network N can be related to displaying the tree in the MUL-tree U(N). To do this, we develop aphylogenetic analogue of graph fibrations. This allows us to view U(N) as the analogue of the universal cover of a digraph, and to establish a close connection between displaying trees in U(N) and reconciling phylogenetic trees with networks.

Estimating phylogenetic trees from genome-scale data.

Science.gov (United States)

Liu, Liang; Xi, Zhenxiang; Wu, Shaoyuan; Davis, Charles C; Edwards, Scott V

2015-12-01

The heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. Phylogenetic methods known as "species tree" methods have been proposed to directly address one important source of gene tree heterogeneity, namely the incomplete lineage sorting that occurs when evolving lineages radiate rapidly, resulting in a diversity of gene trees from a single underlying species tree. Here we review theory and empirical examples that help clarify conflicts between species tree and concatenation methods, and misconceptions in the literature about the performance of species tree methods. Considering concatenation as a special case of the multispecies coalescent model helps explain differences in the behavior of the two methods on phylogenomic data sets. Recent work suggests that species tree methods are more robust than concatenation approaches to some of the classic challenges of phylogenetic analysis, including rapidly evolving sites in DNA sequences and long-branch attraction. We show that approaches, such as binning, designed to augment the signal in species tree analyses can distort the distribution of gene trees and are inconsistent. Computationally efficient species tree methods incorporating biological realism are a key to phylogenetic analysis of whole-genome data. © 2015 New York Academy of Sciences.

Fuzzy tree automata and syntactic pattern recognition.

Science.gov (United States)

Lee, E T

1982-04-01

An approach of representing patterns by trees and processing these trees by fuzzy tree automata is described. Fuzzy tree automata are defined and investigated. The results include that the class of fuzzy root-to-frontier recognizable ¿-trees is closed under intersection, union, and complementation. Thus, the class of fuzzy root-to-frontier recognizable ¿-trees forms a Boolean algebra. Fuzzy tree automata are applied to processing fuzzy tree representation of patterns based on syntactic pattern recognition. The grade of acceptance is defined and investigated. Quantitative measures of ``approximate isosceles triangle,'' ``approximate elongated isosceles triangle,'' ``approximate rectangle,'' and ``approximate cross'' are defined and used in the illustrative examples of this approach. By using these quantitative measures, a house, a house with high roof, and a church are also presented as illustrative examples. In addition, three fuzzy tree automata are constructed which have the capability of processing the fuzzy tree representations of ``fuzzy houses,'' ``houses with high roofs,'' and ``fuzzy churches,'' respectively. The results may have useful applications in pattern recognition, image processing, artificial intelligence, pattern database design and processing, image science, and pictorial information systems.

Environmental fate of emamectin benzoate after tree micro injection of horse chestnut trees.

Science.gov (United States)

Burkhard, Rene; Binz, Heinz; Roux, Christian A; Brunner, Matthias; Ruesch, Othmar; Wyss, Peter

2015-02-01

Emamectin benzoate, an insecticide derived from the avermectin family of natural products, has a unique translocation behavior in trees when applied by tree micro injection (TMI), which can result in protection from insect pests (foliar and borers) for several years. Active ingredient imported into leaves was measured at the end of season in the fallen leaves of treated horse chestnut (Aesculus hippocastanum) trees. The dissipation of emamectin benzoate in these leaves seems to be biphasic and depends on the decomposition of the leaf. In compost piles, where decomposition of leaves was fastest, a cumulative emamectin benzoate degradation half-life time of 20 d was measured. In leaves immersed in water, where decomposition was much slower, the degradation half-life time was 94 d, and in leaves left on the ground in contact with soil, where decomposition was slowest, the degradation half-life time was 212 d. The biphasic decline and the correlation with leaf decomposition might be attributed to an extensive sorption of emamectin benzoate residues to leaf macromolecules. This may also explain why earthworms ingesting leaves from injected trees take up very little emamectin benzoate and excrete it with the feces. Furthermore, no emamectin benzoate was found in water containing decomposing leaves from injected trees. It is concluded, that emamectin benzoate present in abscised leaves from horse chestnut trees injected with the insecticide is not available to nontarget organisms present in soil or water bodies. Published 2014 SETAC.

The transposition distance for phylogenetic trees

OpenAIRE

Rossello, Francesc; Valiente, Gabriel

2006-01-01

The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in bioinformatics. The transposition distance for fully resolved phylogenetic trees is a recent addition to the extensive collection of available metrics for comparing phylogenetic trees. In this paper, we generalize the transposition distance from fully resolved to arbi...

ETE: a python Environment for Tree Exploration.

Science.gov (United States)

Huerta-Cepas, Jaime; Dopazo, Joaquín; Gabaldón, Toni

2010-01-13

Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale. Here we present the Environment for Tree Exploration (ETE), a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations. ETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org.

ETE: a python Environment for Tree Exploration

Directory of Open Access Journals (Sweden)

Gabaldón Toni

2010-01-01

Full Text Available Abstract Background Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale. Results Here we present the Environment for Tree Exploration (ETE, a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations. Conclusions ETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org.

Effects of liana load, tree diameter and distances between conspecifics on seed production in tropical timber trees

DEFF Research Database (Denmark)

Nabe-Nielsen, Jacob; Kollmann, Johannes Christian; Peña-Claros, Marielos

2009-01-01

Seed production in tropical timber trees is limited by abiotic resources, pollination and pre-dispersal seed predation. Resource availability is influenced by the number of competing trees and by lianas that often reach high densities in disturbed parts of tropical forests. The distance between...... conspecific trees affects pollination efficiency and seed predation intensity, and may therefore indirectly affect the long-term sustainability of selective logging. Here we investigate how reproductive status and the number of seeds dispersed per tree are affected by liana load, distance to the nearest...... and positively with tree diameter. In C. ianeirensis the most liana-infested trees dispersed fewer seeds. In T. oblonga the intensity of pre-dispersal seed predation decreased with distance to the nearest conspecifics. There was no evidence that seed viability or seed production decreased with distance...

The Efficacy of Consensus Tree Methods for Summarizing Phylogenetic Relationships from a Posterior Sample of Trees Estimated from Morphological Data.

Science.gov (United States)

O'Reilly, Joseph E; Donoghue, Philip C J

2018-03-01

Consensus trees are required to summarize trees obtained through MCMC sampling of a posterior distribution, providing an overview of the distribution of estimated parameters such as topology, branch lengths, and divergence times. Numerous consensus tree construction methods are available, each presenting a different interpretation of the tree sample. The rise of morphological clock and sampled-ancestor methods of divergence time estimation, in which times and topology are coestimated, has increased the popularity of the maximum clade credibility (MCC) consensus tree method. The MCC method assumes that the sampled, fully resolved topology with the highest clade credibility is an adequate summary of the most probable clades, with parameter estimates from compatible sampled trees used to obtain the marginal distributions of parameters such as clade ages and branch lengths. Using both simulated and empirical data, we demonstrate that MCC trees, and trees constructed using the similar maximum a posteriori (MAP) method, often include poorly supported and incorrect clades when summarizing diffuse posterior samples of trees. We demonstrate that the paucity of information in morphological data sets contributes to the inability of MCC and MAP trees to accurately summarise of the posterior distribution. Conversely, majority-rule consensus (MRC) trees represent a lower proportion of incorrect nodes when summarizing the same posterior samples of trees. Thus, we advocate the use of MRC trees, in place of MCC or MAP trees, in attempts to summarize the results of Bayesian phylogenetic analyses of morphological data.

Distance labeling schemes for trees

DEFF Research Database (Denmark)

Alstrup, Stephen; Gørtz, Inge Li; Bistrup Halvorsen, Esben

2016-01-01

We consider distance labeling schemes for trees: given a tree with n nodes, label the nodes with binary strings such that, given the labels of any two nodes, one can determine, by looking only at the labels, the distance in the tree between the two nodes. A lower bound by Gavoille et al. [Gavoille...... variants such as, for example, small distances in trees [Alstrup et al., SODA, 2003]. We improve the known upper and lower bounds of exact distance labeling by showing that 1/4 log2(n) bits are needed and that 1/2 log2(n) bits are sufficient. We also give (1 + ε)-stretch labeling schemes using Theta...

Long-term monitoring of Sacramento Shade program trees: tree survival, growth and energy-saving performance

Science.gov (United States)

Yekang Ko; Jun-Hak Lee; E. Gregory McPherson; Lara A. Roman

2015-01-01

Long-term survival and growth of urban forests are critical to achieve the targeted benefits of urban tree planting programs, such as building energy savings from tree shade. However, little is known about how trees perform in the long-term, especially in residential areas. Given this gap in the literature, we monitored 22-years of post-planting survival, growth, and...

Nodal distances for rooted phylogenetic trees.

Science.gov (United States)

Cardona, Gabriel; Llabrés, Mercè; Rosselló, Francesc; Valiente, Gabriel

2010-08-01

Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths between pairs of taxa, have been present in the systematics literature since the early seventies. For rooted phylogenetic trees, however, these vectors can only separate non-weighted binary trees, and therefore these dissimilarity measures are metrics only on this class of rooted phylogenetic trees. In this paper we overcome this problem, by splitting in a suitable way each path length between two taxa into two lengths. We prove that the resulting splitted path lengths matrices single out arbitrary rooted phylogenetic trees with nested taxa and arcs weighted in the set of positive real numbers. This allows the definition of metrics on this general class of rooted phylogenetic trees by comparing these matrices through metrics in spaces M(n)(R) of real-valued n x n matrices. We conclude this paper by establishing some basic facts about the metrics for non-weighted phylogenetic trees defined in this way using L(p) metrics on M(n)(R), with p [epsilon] R(>0).

Atmospheric carbon reduction by urban trees

International Nuclear Information System (INIS)

Nowak, D.J.

1993-01-01

Trees, because they sequester atmospheric carbon through their growth process and conserve energy in urban areas, have been suggested as one means to combat increasing levels of atmospheric carbon. Analysis of the urban forest in Oakland, California (21% tree cover), reveals a tree carbon storage level of 11·0 metric tons/hectare. Trees in the area of the 1991 fire in Oakland stored approximately 14,500 metric tons of carbon, 10% of the total amount stored by Oakland's urban forest. National urban forest carbon storage in the United States (28% tree cover) is estimated at between 350 and 750 million metric tons. Establishment of 10 million urban trees annually over the next 10 years is estimated to sequester and offset the production of 363 million metric tons of carbon over the next 50 years-less than 1% of the estimated carbon emissions in the United States over the same time period. Advantages and limitations of managing urban trees to reduce atmospheric carbon are discussed. 36 refs., 2 figs., 3 tabs

Navigation and Tree Mapping in Orchards

DEFF Research Database (Denmark)

Jæger-Hansen, Claes Lund; Griepentrog, Hans W.; Andersen, Jens Christian

In this paper an algorithm for estimating tree positions is presented. The sensors used for the algorithm is GNSS and LIDAR, and data is collected in an orchard with grapefruit trees while driving along the rows. The positions of the trees are estimated using ellipse fitting on point clouds....... The average accuracy for the center point estimation is 0.2 m in the along track direction and 0.35 m in the across track direction. The goal of the tree mapping algorithm is create a database of individual trees, and be the basis for creation of a graph map that can be used for mission planning...

Computer aided construction of fault tree

International Nuclear Information System (INIS)

Kovacs, Z.

1982-01-01

Computer code CAT for the automatic construction of the fault tree is briefly described. Code CAT makes possible simple modelling of components using decision tables, it accelerates the fault tree construction process, constructs fault trees of different complexity, and is capable of harmonized co-operation with programs PREPandKITT 1,2 for fault tree analysis. The efficiency of program CAT and thus the accuracy and completeness of fault trees constructed significantly depends on the compilation and sophistication of decision tables. Currently, program CAT is used in co-operation with programs PREPandKITT 1,2 in reliability analyses of nuclear power plant systems. (B.S.)

Shapes of tree representations of spin-glass landscapes

International Nuclear Information System (INIS)

Hordijk, Wim; Fontanari, Jose F; Stadler, Peter F

2003-01-01

Much of the information about the multi-valley structure of disordered spin systems can be convened in a simple tree structure - a barrier tree - the leaves and internal nodes of which represent, respectively, the local minima and the lowest energy saddles connecting those minima. Here we apply several statistics used in the study of phylogenetic trees to barrier trees that result from the energy landscapes of p-spin models. These statistics give information about the shape of these barrier trees, in particular about balance and symmetry. We then ask if they can be used to classify different types of landscapes, compare them with results obtained from random trees, and investigate the structure of subtrees of the barrier trees. We conclude that at least one of the used statistics is capable of distinguishing different types of landscapes, that the barrier trees from p-spin energy landscapes are quite different from random trees, and that subtrees of barrier trees do not reflect the overall tree structure, but their structure is correlated with their 'depth' in the tree

Computing Refined Buneman Trees in Cubic Time

DEFF Research Database (Denmark)

Brodal, G.S.; Fagerberg, R.; Östlin, A.

2003-01-01

Reconstructing the evolutionary tree for a set of n species based on pairwise distances between the species is a fundamental problem in bioinformatics. Neighbor joining is a popular distance based tree reconstruction method. It always proposes fully resolved binary trees despite missing evidence...... in the underlying distance data. Distance based methods based on the theory of Buneman trees and refined Buneman trees avoid this problem by only proposing evolutionary trees whose edges satisfy a number of constraints. These trees might not be fully resolved but there is strong combinatorial evidence for each...... proposed edge. The currently best algorithm for computing the refined Buneman tree from a given distance measure has a running time of O(n 5) and a space consumption of O(n 4). In this paper, we present an algorithm with running time O(n 3) and space consumption O(n 2). The improved complexity of our...

Tree-centered spot firing - a technique for prescribed burning beneath standing trees.

Science.gov (United States)

C. Phillip Weatherspoon; George A. Almond; Carl N. Skinner

1989-01-01

Prescribed burning beneath standing trees normally requires efforts to protect residual trees from excessive fire damage. Damage to both crowns and boles is strongly influenced by flame length, a fire characteristic functionally related to fireline intensity (Albini 1976). In a good prescribed burn, therefore, the prescription specifies desired or maximum flame lengths...

Dissimilarity-based classification of anatomical tree structures

DEFF Research Database (Denmark)

Sørensen, Lauge; Lo, Pechin Chien Pau; Dirksen, Asger

2011-01-01

A novel method for classification of abnormality in anatomical tree structures is presented. A tree is classified based on direct comparisons with other trees in a dissimilarity-based classification scheme. The pair-wise dissimilarity measure between two trees is based on a linear assignment betw...

Dissimilarity-based classification of anatomical tree structures

DEFF Research Database (Denmark)

Sørensen, Lauge Emil Borch Laurs; Lo, Pechin Chien Pau; Dirksen, Asger

2011-01-01

A novel method for classification of abnormality in anatomical tree structures is presented. A tree is classified based on direct comparisons with other trees in a dissimilarity-based classification scheme. The pair-wise dissimilarity measure between two trees is based on a linear assignment...

Application of Goal Tree-Success Tree model as the knowledge-base of operator advisory systems

International Nuclear Information System (INIS)

Kim, I.S.; Modarres, M.

1987-01-01

The most important portion of an expert system development is the articulation of knowledge by the expert and its satisfactory formulation in a suitable knowledge representation scheme for mechanization by a computer. A 'deep knowledge' approach called Goal Tree-Success Tree model is devised to represent complex dynamic domain knowledge. This approach can hierarchically model the underlying principles of a given process domain (for example nuclear power plant operations domain). The Goal Tree-Success Tree can then be used to represent the knowledge-base and provide means of selecting an efficient search routine in the inference engine of an expert system. A prototype expert system has been developed to demonstrate the method. This expert system models the operation of a typical system used in the pressurized water reactors. The expert system is modeled for real-time operations if an interface between plant parameters and the expert system is established. The real-time operation provides an ability to quickly remedy minor disturbances that can quickly lead to a system malfunction or trip. A description of both the Goal Tree-Success Tree model and the prototype expert system is presented. (orig.)

Species trees for the tree swallows (Genus Tachycineta): an alternative phylogenetic hypothesis to the mitochondrial gene tree.

Science.gov (United States)

Dor, Roi; Carling, Matthew D; Lovette, Irby J; Sheldon, Frederick H; Winkler, David W

2012-10-01

The New World swallow genus Tachycineta comprises nine species that collectively have a wide geographic distribution and remarkable variation both within- and among-species in ecologically important traits. Existing phylogenetic hypotheses for Tachycineta are based on mitochondrial DNA sequences, thus they provide estimates of a single gene tree. In this study we sequenced multiple individuals from each species at 16 nuclear intron loci. We used gene concatenated approaches (Bayesian and maximum likelihood) as well as coalescent-based species tree inference to reconstruct phylogenetic relationships of the genus. We examined the concordance and conflict between the nuclear and mitochondrial trees and between concatenated and coalescent-based inferences. Our results provide an alternative phylogenetic hypothesis to the existing mitochondrial DNA estimate of phylogeny. This new hypothesis provides a more accurate framework in which to explore trait evolution and examine the evolution of the mitochondrial genome in this group. Copyright © 2012 Elsevier Inc. All rights reserved.

The dynamics of strangling among forest trees.

Science.gov (United States)

Okamoto, Kenichi W

2015-11-07

Strangler trees germinate and grow on other trees, eventually enveloping and potentially even girdling their hosts. This allows them to mitigate fitness costs otherwise incurred by germinating and competing with other trees on the forest floor, as well as minimize risks associated with host tree-fall. If stranglers can themselves host other strangler trees, they may not even seem to need non-stranglers to persist. Yet despite their high fitness potential, strangler trees neither dominate the communities in which they occur nor is the strategy particularly common outside of figs (genus Ficus). Here we analyze how dynamic interactions between strangling and non-strangling trees can shape the adaptive landscape for strangling mutants and mutant trees that have lost the ability to strangle. We find a threshold which strangler germination rates must exceed for selection to favor the evolution of strangling, regardless of how effectively hemiepiphytic stranglers may subsequently replace their hosts. This condition describes the magnitude of the phenotypic displacement in the ability to germinate on other trees necessary for invasion by a mutant tree that could potentially strangle its host following establishment as an epiphyte. We show how the relative abilities of strangling and non-strangling trees to occupy empty sites can govern whether strangling is an evolutionarily stable strategy, and obtain the conditions for strangler coexistence with non-stranglers. We then elucidate when the evolution of strangling can disrupt stable coexistence between commensal epiphytic ancestors and their non-strangling host trees. This allows us to highlight parallels between the invasion fitness of strangler trees arising from commensalist ancestors, and cases where strangling can arise in concert with the evolution of hemiepiphytism among free-standing ancestors. Finally, we discuss how our results can inform the evolutionary ecology of antagonistic interactions more generally

Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics.

Science.gov (United States)

Vaniya, Arpana; Fiehn, Oliver

2015-06-01

Identification of unknown metabolites is the bottleneck in advancing metabolomics, leaving interpretation of metabolomics results ambiguous. The chemical diversity of metabolism is vast, making structure identification arduous and time consuming. Currently, comprehensive analysis of mass spectra in metabolomics is limited to library matching, but tandem mass spectral libraries are small compared to the large number of compounds found in the biosphere, including xenobiotics. Resolving this bottleneck requires richer data acquisition and better computational tools. Multi-stage mass spectrometry (MSn) trees show promise to aid in this regard. Fragmentation trees explore the fragmentation process, generate fragmentation rules and aid in sub-structure identification, while mass spectral trees delineate the dependencies in multi-stage MS of collision-induced dissociations. This review covers advancements over the past 10 years as a tool for metabolite identification, including algorithms, software and databases used to build and to implement fragmentation trees and mass spectral annotations.

Evaluating potential overlap between pack stock and Sierra Nevada bighorn sheep (Ovis canadensis sierrae) in Sequoia and Kings Canyon National Parks, California

Science.gov (United States)

Klinger, Robert C.; Few, Alexandra P.; Knox, Kathleen A.; Hatfield, Brian E.; Clark, Jonathan; German, David W.; Stephenson, Thomas R.

2015-01-01

Pack stock (horses, mules, burros, llamas, and goats) are frequently assumed to have negative effects on public lands, but there is a general lack of data to be able to quantify the degree to which this is actually the case. Sequoia and Kings Canyon National Parks have received complaints that pack stock may affect Sierra Nevada bighorn sheep (Ovis canadensis sierrae; SNBS), a federally endangered subspecies that occurs in largely disjunct herds in the Sierra Nevada Range of California. The potential effects are thought to be displacement of SNBS from meadows on their summer range (altered habitat use) or, more indirectly, through changes in SNBS habitat or forage quality. Our goals were to conduct an association analysis to quantify the degree of potential spatial overlap in meadow use between SNBS and pack stock and to compare differences in vegetation community composition, structure, and diversity among meadows with different levels of use by bighorn sheep and pack stock. For the association analysis, we used two approaches: (1) we quantified the proportion of meadows that were within the herd home ranges of bighorn sheep and were potentially open to pack stock, and, (2) we used Monte Carlo simulations and use-availability analyses to compare the proportion of meadows used by bighorn sheep relative to the proportional occurrence or area of meadows available to bighorn sheep that were used by pack stock. To evaluate potential effects of pack stock on meadow plant communities and SNBS forage, we sampled vegetation in 2011 and 2012 at 100 plots to generate data that allowed us to compare:

Utilizing Remote Sensing Information to Improve Post-fire Rainfall-runoff Predictions after the 2010 Bull Fire in the Sequoia National Forest, CA

Science.gov (United States)

Kinoshita, A. M.; Hale, B.; Hogue, T. S.

2012-12-01

Post-fire management decisions are guided by rainfall-runoff predictions, which ultimately influence downstream treatment and mitigation costs. The current study investigates evolving rainfall-runoff partitioning at the watershed scale over a two-year period after the 2010 Bull Fire which occurred in the southern Sequoia National Forest in California. Stage height was measured at five-minute intervals using pressure transducers, tipping buckets were installed for rainfall duration and intensity, and channel cross-sections were measured approximately every two months to detail sediment deposition or scour. We also utilize remotely sensed vegetation data to evaluate vegetation recovery in the studied watersheds and the corresponding relationship to storm runoff. Normalized Difference Vegetation Index (NDVI), a measure of vegetation greenness, is evaluated for its potential use as a key recovery indicator. Preliminary results focus on alterations in annual and seasonal precipitation and discharge relationships using in-situ data and Landsat NDVI values for the period of study. NDVI values are consistent with a comprehensive burn, with an acute decrease observed in the initial post-fire period. However, vegetation recovery is highly variable in the studied systems and influenced by shorter-term biomass pulses (grasses) while longer-term recovery of other species (chaparral and pine) is ongoing. Runoff ratios are elevated during early storms and show some recovery in the later part of the study period. The ability to accurately and confidently predict post-fire runoff and longer-term recovery is critical for monitoring values-at-risk, reducing mitigation costs, and improving warnings to downstream public communities.

An efficient and extensible approach for compressing phylogenetic trees.

Science.gov (United States)

Matthews, Suzanne J; Williams, Tiffani L

2011-10-18

Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. Our previous work showed that TreeZip is a promising approach for compressing phylogenetic trees. In this paper, we extend our TreeZip algorithm by handling trees with weighted branches. Furthermore, by using the compressed TreeZip file as input, we have designed an extensible decompressor that can extract subcollections of trees, compute majority and strict consensus trees, and merge tree collections using set operations such as union, intersection, and set difference. On unweighted phylogenetic trees, TreeZip is able to compress Newick files in excess of 98%. On weighted phylogenetic trees, TreeZip is able to compress a Newick file by at least 73%. TreeZip can be combined with 7zip with little overhead, allowing space savings in excess of 99% (unweighted) and 92%(weighted). Unlike TreeZip, 7zip is not immune to branch rotations, and performs worse as the level of variability in the Newick string representation increases. Finally, since the TreeZip compressed text (TRZ) file contains all the semantic information in a collection of trees, we can easily filter and decompress a subset of trees of interest (such as the set of unique trees), or build the resulting consensus tree in a matter of seconds. We also show the ease of which set operations can be performed on TRZ files, at speeds quicker than those performed on Newick or 7zip compressed Newick files, and without loss of space savings. TreeZip is an efficient approach for compressing large collections of phylogenetic trees. The semantic and compact nature of the TRZ file allow it to be operated upon directly and quickly, without a need to decompress the original Newick file. We believe that TreeZip will be vital for compressing and archiving trees in the biological community.

Animals and trees: food for thought

Energy Technology Data Exchange (ETDEWEB)

Openshaw, K.

1979-01-01

In many areas of Africa, combining tree-growing with animal rearing is advantageous, as the trees provide shade, animal fodder and timber for fuel and building, while grazing animals reduce the fire hazard from ground vegetation and improve soil fertility through droppings. Acacia albida, Prosopis cineraria, P. chilensis, leucaena leucocephala and Ailanthus excelsa are discussed as promising fodder trees, and an appendix is included with notes on 21 other trees for fodder or the production of medicines.

Regolith properties under trees and the biomechanical effects caused by tree root systems as recognized by electrical resistivity tomography (ERT)

Science.gov (United States)

Pawlik, Łukasz; Kasprzak, Marek

2018-01-01

Following previous findings regarding the influence of vascular plants (mainly trees) on weathering, soil production and hillslope stability, in this study, we attempted to test a hypothesis regarding significant impacts of tree root systems on soil and regolith properties. Different types of impacts from tree root system (direct and indirect) are commonly gathered under the key term of "biomechanical effects". To add to the discussion of the biomechanical effects of trees, we used a non-invasive geophysical method, electrical resistivity tomography (ERT), to investigate the profiles of four different configurations at three study sites within the Polish section of the Outer Western Carpathians. At each site, one long profile (up to 189 m) of a large section of a hillslope and three short profiles (up to 19.5 m), that is, microsites occupied by trees or their remnants, were made. Short profiles included the tree root zone of a healthy large tree, the tree stump of a decaying tree and the pit-and-mound topography formed after a tree uprooting. The resistivity of regolith and bedrock presented on the long profiles and in comparison with the short profiles through the microsites it can be seen how tree roots impact soil and regolith properties and add to the complexity of the whole soil/regolith profile. Trees change soil and regolith properties directly through root channels and moisture migration and indirectly through the uprooting of trees and the formation of pit-and-mound topography. Within tree stump microsites, the impact of tree root systems, evaluated by a resistivity model, was smaller compared to microsites with living trees or those with pit-and-mound topography but was still visible even several decades after the trees were windbroken or cut down. The ERT method is highly useful for quick evaluation of the impact of tree root systems on soils and regolith. This method, in contrast to traditional soil analyses, offers a continuous dataset for the entire

Mean-field lattice trees

NARCIS (Netherlands)

Borgs, C.; Chayes, J.T.; Hofstad, van der R.W.; Slade, G.

1999-01-01

We introduce a mean-field model of lattice trees based on embeddings into d of abstract trees having a critical Poisson offspring distribution. This model provides a combinatorial interpretation for the self-consistent mean-field model introduced previously by Derbez and Slade [9], and provides an

The space of ultrametric phylogenetic trees.

Science.gov (United States)

Gavryushkin, Alex; Drummond, Alexei J

2016-08-21

The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data. Hence the question of statistical consistency of such methods is equivalent to the consistency of the summary of the sample. More generally, statistical consistency is ensured by the tree space used to analyse the sample. In this paper, we consider two standard parameterisations of phylogenetic time-trees used in evolutionary models: inter-coalescent interval lengths and absolute times of divergence events. For each of these parameterisations we introduce a natural metric space on ultrametric phylogenetic trees. We compare the introduced spaces with existing models of tree space and formulate several formal requirements that a metric space on phylogenetic trees must possess in order to be a satisfactory space for statistical analysis, and justify them. We show that only a few known constructions of the space of phylogenetic trees satisfy these requirements. However, our results suggest that these basic requirements are not enough to distinguish between the two metric spaces we introduce and that the choice between metric spaces requires additional properties to be considered. Particularly, that the summary tree minimising the square distance to the trees from the sample might be different for different parameterisations. This suggests that further fundamental insight is needed into the problem of statistical consistency of phylogenetic inference methods. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Differences in xylogenesis between dominant and suppressed trees.

Science.gov (United States)

Liu, Shushan; Li, Xiaoxia; Rossi, Sergio; Wang, Lily; Li, Wei; Liang, Eryuan; Leavitt, Steven W

2018-05-01

Most dendroecological studies focus on dominant trees, but little is known about the growing season of trees belonging to different size classes and their sensitivity to biotic factors. The objective of this study was to compare the dynamics of xylem formation between dominant and suppressed trees of Abies fabri of similar age growing in the Gongga Mountains, southeastern Tibetan Plateau, and to identify the association between xylem growth and climate. The timing and duration of xylogenesis in histological sections were investigated weekly during the 2013-2015 growing seasons. Our investigation found that timing and duration of xylogenesis varied with canopy position and its associated tree size. Xylogenesis started 6-14 days earlier, and ended 5-11 days later in dominant trees than in suppressed trees, resulting in a significantly longer growing season. Dominant trees also exhibited higher temperature sensitivity of tracheid production rate than suppressed trees. The observed differences in xylogenesis among trees suggested that competition affects tree growth by reducing the growing period in suppressed trees. Representative climate-growth relationships should involve trees of all size classes when evaluating the effects of the environment on forest dynamics. © 2018 Botanical Society of America.

Track treeing mechanism and its application

International Nuclear Information System (INIS)

Li Boyang

1993-01-01

Based on electrostriction and fracture mechanics, experiment observation and data-processing, two models (restriction among tree tracks and induction of tree track onto stress concentrated spots) and factors (restriction and induction) are proposed; The existence of four types of plastic zone (spot-block pz, single crack isolate pz, transition from isolate to block pz and crack-block pz) and two types of annex (plastic zone and crack zone) are pointed out. The development regularities of Gp (diameter of plastic zone), G(diameter of tree track), S(tree track density) and total areal of tree track (SG 2 ) in two basic experiments (H=H+dH, H=Hc H-field strength) are described by using four basic formulae. (author)

Values for rooted-tree and sink-tree digraphs games and sharing a river

NARCIS (Netherlands)

Khmelnitskaya, Anna Borisovna

We introduce values for rooted-tree and sink-tree digraph games axiomatically and provide their explicit formula representation. These values may be considered as natural extensions of the lower equivalent and upper equivalent solutions for line-graph games studied in Brink, Laan, and Vasil'ev

TreeQ-VISTA: An Interactive Tree Visualization Tool withFunctional Annotation Query Capabilities

Energy Technology Data Exchange (ETDEWEB)

Gu, Shengyin; Anderson, Iain; Kunin, Victor; Cipriano, Michael; Minovitsky, Simon; Weber, Gunther; Amenta, Nina; Hamann, Bernd; Dubchak,Inna

2007-05-07

Summary: We describe a general multiplatform exploratorytool called TreeQ-Vista, designed for presenting functional annotationsin a phylogenetic context. Traits, such as phenotypic and genomicproperties, are interactively queried from a relational database with auser-friendly interface which provides a set of tools for users with orwithout SQL knowledge. The query results are projected onto aphylogenetic tree and can be displayed in multiple color groups. A richset of browsing, grouping and query tools are provided to facilitatetrait exploration, comparison and analysis.Availability: The program,detailed tutorial and examples are available online athttp://genome-test.lbl.gov/vista/TreeQVista.

Maintenance of carbohydrate transport in tall trees

DEFF Research Database (Denmark)

Savage, Jessica A.; Beecher, Sierra D.; Clerx, Laura

2017-01-01

Trees present a critical challenge to long-distance transport because as a tree grows in height and the transport pathway increases in length, the hydraulic resistance of the vascular tissue should increase. This has led many to question whether trees can rely on a passive transport mechanism to ...... that reduce transport resistance. As a result, the key to the long-standing mystery of how trees maintain phloem transport as they increase in size lies in the structure of the phloem and its ability to change hydraulic properties with plant height.......Trees present a critical challenge to long-distance transport because as a tree grows in height and the transport pathway increases in length, the hydraulic resistance of the vascular tissue should increase. This has led many to question whether trees can rely on a passive transport mechanism...... in the leaves of a tall tree in situ. Across nine deciduous species, we find that hydraulic resistance in the phloem scales inversely with plant height because of a shift in sieve element structure along the length of individual trees. This scaling relationship seems robust across multiple species despite large...

Objective consensus from decision trees.

Science.gov (United States)

Putora, Paul Martin; Panje, Cedric M; Papachristofilou, Alexandros; Dal Pra, Alan; Hundsberger, Thomas; Plasswilm, Ludwig

2014-12-05

Consensus-based approaches provide an alternative to evidence-based decision making, especially in situations where high-level evidence is limited. Our aim was to demonstrate a novel source of information, objective consensus based on recommendations in decision tree format from multiple sources. Based on nine sample recommendations in decision tree format a representative analysis was performed. The most common (mode) recommendations for each eventuality (each permutation of parameters) were determined. The same procedure was applied to real clinical recommendations for primary radiotherapy for prostate cancer. Data was collected from 16 radiation oncology centres, converted into decision tree format and analyzed in order to determine the objective consensus. Based on information from multiple sources in decision tree format, treatment recommendations can be assessed for every parameter combination. An objective consensus can be determined by means of mode recommendations without compromise or confrontation among the parties. In the clinical example involving prostate cancer therapy, three parameters were used with two cut-off values each (Gleason score, PSA, T-stage) resulting in a total of 27 possible combinations per decision tree. Despite significant variations among the recommendations, a mode recommendation could be found for specific combinations of parameters. Recommendations represented as decision trees can serve as a basis for objective consensus among multiple parties.

Longest common extensions in trees

DEFF Research Database (Denmark)

Bille, Philip; Gawrychowski, Pawel; Gørtz, Inge Li

2016-01-01

to trees and suggest a few applications of LCE in trees to tries and XML databases. Given a labeled and rooted tree T of size n, the goal is to preprocess T into a compact data structure that support the following LCE queries between subpaths and subtrees in T. Let v1, v2, w1, and w2 be nodes of T...... such that w1 and w2 are descendants of v1 and v2 respectively. - LCEPP(v1, w1, v2, w2): (path-path LCE) return the longest common prefix of the paths v1 ~→ w1 and v2 ~→ w2. - LCEPT(v1, w1, v2): (path-tree LCE) return maximal path-path LCE of the path v1 ~→ w1 and any path from v2 to a descendant leaf. - LCETT......(v1, v2): (tree-tree LCE) return a maximal path-path LCE of any pair of paths from v1 and v2 to descendant leaves. We present the first non-trivial bounds for supporting these queries. For LCEPP queries, we present a linear-space solution with O(log* n) query time. For LCEPT queries, we present...

Longest Common Extensions in Trees

DEFF Research Database (Denmark)

Bille, Philip; Gawrychowski, Pawel; Gørtz, Inge Li

2015-01-01

to trees and suggest a few applications of LCE in trees to tries and XML databases. Given a labeled and rooted tree T of size n, the goal is to preprocess T into a compact data structure that support the following LCE queries between subpaths and subtrees in T. Let v1, v2, w1, and w2 be nodes of T...... such that w1 and w2 are descendants of v1 and v2 respectively. - LCEPP(v1, w1, v2, w2): (path-path LCE) return the longest common prefix of the paths v1 ~→ w1 and v2 ~→ w2. - LCEPT(v1, w1, v2): (path-tree LCE) return maximal path-path LCE of the path v1 ~→ w1 and any path from v2 to a descendant leaf. - LCETT......(v1, v2): (tree-tree LCE) return a maximal path-path LCE of any pair of paths from v1 and v2 to descendant leaves. We present the first non-trivial bounds for supporting these queries. For LCEPP queries, we present a linear-space solution with O(log* n) query time. For LCEPT queries, we present...

Objective consensus from decision trees

International Nuclear Information System (INIS)

Putora, Paul Martin; Panje, Cedric M; Papachristofilou, Alexandros; Pra, Alan Dal; Hundsberger, Thomas; Plasswilm, Ludwig

2014-01-01

Consensus-based approaches provide an alternative to evidence-based decision making, especially in situations where high-level evidence is limited. Our aim was to demonstrate a novel source of information, objective consensus based on recommendations in decision tree format from multiple sources. Based on nine sample recommendations in decision tree format a representative analysis was performed. The most common (mode) recommendations for each eventuality (each permutation of parameters) were determined. The same procedure was applied to real clinical recommendations for primary radiotherapy for prostate cancer. Data was collected from 16 radiation oncology centres, converted into decision tree format and analyzed in order to determine the objective consensus. Based on information from multiple sources in decision tree format, treatment recommendations can be assessed for every parameter combination. An objective consensus can be determined by means of mode recommendations without compromise or confrontation among the parties. In the clinical example involving prostate cancer therapy, three parameters were used with two cut-off values each (Gleason score, PSA, T-stage) resulting in a total of 27 possible combinations per decision tree. Despite significant variations among the recommendations, a mode recommendation could be found for specific combinations of parameters. Recommendations represented as decision trees can serve as a basis for objective consensus among multiple parties

Sub-pixel estimation of tree cover and bare surface densities using regression tree analysis

Directory of Open Access Journals (Sweden)

Carlos Augusto Zangrando Toneli

2011-09-01

Full Text Available Sub-pixel analysis is capable of generating continuous fields, which represent the spatial variability of certain thematic classes. The aim of this work was to develop numerical models to represent the variability of tree cover and bare surfaces within the study area. This research was conducted in the riparian buffer within a watershed of the São Francisco River in the North of Minas Gerais, Brazil. IKONOS and Landsat TM imagery were used with the GUIDE algorithm to construct the models. The results were two index images derived with regression trees for the entire study area, one representing tree cover and the other representing bare surface. The use of non-parametric and non-linear regression tree models presented satisfactory results to characterize wetland, deciduous and savanna patterns of forest formation.

Reconciliation of Gene and Species Trees

Directory of Open Access Journals (Sweden)

L. Y. Rusin

2014-01-01

Full Text Available The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating horizontal gene transfers, binarization and reconciliation of polytomous trees, and construction of species trees and scenarios. The review does not intend to cover the vast diversity of literature published on these subjects. Instead, the authors strived to overview the problem of the evolutionary scenario as a central concept in many areas of evolutionary research. The second part provides detailed mathematical proofs for the solutions of two problems: (i inferring a gene evolution along a species tree accounting for various types of evolutionary events and (ii trees reconciliation into a single species tree when only gene duplications and losses are allowed. All proposed algorithms have a cubic time complexity and are mathematically proved to find exact solutions. Solving algorithms for problem (ii can be naturally extended to incorporate horizontal transfers, other evolutionary events, and time scales on the species tree.

Recruiting Conventional Tree Architecture Models into State-of-the-Art LiDAR Mapping for Investigating Tree Growth Habits in Structure.

Science.gov (United States)

Lin, Yi; Jiang, Miao; Pellikka, Petri; Heiskanen, Janne

2018-01-01

Mensuration of tree growth habits is of considerable importance for understanding forest ecosystem processes and forest biophysical responses to climate changes. However, the complexity of tree crown morphology that is typically formed after many years of growth tends to render it a non-trivial task, even for the state-of-the-art 3D forest mapping technology-light detection and ranging (LiDAR). Fortunately, botanists have deduced the large structural diversity of tree forms into only a limited number of tree architecture models, which can present a-priori knowledge about tree structure, growth, and other attributes for different species. This study attempted to recruit Hallé architecture models (HAMs) into LiDAR mapping to investigate tree growth habits in structure. First, following the HAM-characterized tree structure organization rules, we run the kernel procedure of tree species classification based on the LiDAR-collected point clouds using a support vector machine classifier in the leave-one-out-for-cross-validation mode. Then, the HAM corresponding to each of the classified tree species was identified based on expert knowledge, assisted by the comparison of the LiDAR-derived feature parameters. Next, the tree growth habits in structure for each of the tree species were derived from the determined HAM. In the case of four tree species growing in the boreal environment, the tests indicated that the classification accuracy reached 85.0%, and their growth habits could be derived by qualitative and quantitative means. Overall, the strategy of recruiting conventional HAMs into LiDAR mapping for investigating tree growth habits in structure was validated, thereby paving a new way for efficiently reflecting tree growth habits and projecting forest structure dynamics.

Sampling the quality of hardwood trees

Science.gov (United States)

Adrian M. Gilbert

1959-01-01

Anyone acquainted with the conversion of hardwood trees into wood products knows that timber has a wide range in quality. Some trees will yield better products than others. So, in addition to rate of growth and size, tree values are affected by the quality of products yielded.

Nonbinary tree-based phylogenetic networks

OpenAIRE

Jetten, Laura; van Iersel, Leo

2016-01-01

Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic base-tree with additional linking arcs, which can for example represent gene transfer events. Such phylogenetic networks are called tree-based. Here, we consider two possible generalizations of this concept to nonbinary networks, which we call tree-based and st...

Speeding Up Neighbour-Joining Tree Construction

DEFF Research Database (Denmark)

Brodal, Gerth Stølting; Fagerberg, Rolf; Mailund, Thomas

A widely used method for constructing phylogenetic trees is the neighbour-joining method of Saitou and Nei. We develope heuristics for speeding up the neighbour-joining method which generate the same phylogenetic trees as the original method. All heuristics are based on using a quad-tree to guide...... the search for the next pair of nodes to join, but di#er in the information stored in quad-tree nodes, the way the search is performed, and in the way the quad-tree is updated after a join. We empirically evaluate the performance of the heuristics on distance matrices obtained from the Pfam collection...... of alignments, and compare the running time with that of the QuickTree tool, a well-known and widely used implementation of the standard neighbour-joining method. The results show that the presented heuristics can give a significant speed-up over the standard neighbour-joining method, already for medium sized...

An efficient and extensible approach for compressing phylogenetic trees

KAUST Repository

Matthews, Suzanne J

2011-01-01

Background: Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. Our previous work showed that TreeZip is a promising approach for compressing phylogenetic trees. In this paper, we extend our TreeZip algorithm by handling trees with weighted branches. Furthermore, by using the compressed TreeZip file as input, we have designed an extensible decompressor that can extract subcollections of trees, compute majority and strict consensus trees, and merge tree collections using set operations such as union, intersection, and set difference.Results: On unweighted phylogenetic trees, TreeZip is able to compress Newick files in excess of 98%. On weighted phylogenetic trees, TreeZip is able to compress a Newick file by at least 73%. TreeZip can be combined with 7zip with little overhead, allowing space savings in excess of 99% (unweighted) and 92%(weighted). Unlike TreeZip, 7zip is not immune to branch rotations, and performs worse as the level of variability in the Newick string representation increases. Finally, since the TreeZip compressed text (TRZ) file contains all the semantic information in a collection of trees, we can easily filter and decompress a subset of trees of interest (such as the set of unique trees), or build the resulting consensus tree in a matter of seconds. We also show the ease of which set operations can be performed on TRZ files, at speeds quicker than those performed on Newick or 7zip compressed Newick files, and without loss of space savings.Conclusions: TreeZip is an efficient approach for compressing large collections of phylogenetic trees. The semantic and compact nature of the TRZ file allow it to be operated upon directly and quickly, without a need to decompress the original Newick file. We believe that TreeZip will be vital for compressing and archiving trees in the biological community. © 2011 Matthews and Williams; licensee BioMed Central Ltd.

Can live tree size-density relationships provide a mechanism for predicting down and dead tree resources?

Science.gov (United States)

Christopher Woodall; James Westfall

2009-01-01

Live tree size-density relationships in forests have long provided a framework for understanding stand dynamics. There has been little examination of the relationship between the size-density attributes of live and standing/down dead trees (e.g., number and mean tree size per unit area, such information could help in large-scale efforts to estimate dead wood resources...

Object-based methods for individual tree identification and tree species classification from high-spatial resolution imagery

Science.gov (United States)

Wang, Le

2003-10-01

Modern forest management poses an increasing need for detailed knowledge of forest information at different spatial scales. At the forest level, the information for tree species assemblage is desired whereas at or below the stand level, individual tree related information is preferred. Remote Sensing provides an effective tool to extract the above information at multiple spatial scales in the continuous time domain. To date, the increasing volume and readily availability of high-spatial-resolution data have lead to a much wider application of remotely sensed products. Nevertheless, to make effective use of the improving spatial resolution, conventional pixel-based classification methods are far from satisfactory. Correspondingly, developing object-based methods becomes a central challenge for researchers in the field of Remote Sensing. This thesis focuses on the development of methods for accurate individual tree identification and tree species classification. We develop a method in which individual tree crown boundaries and treetop locations are derived under a unified framework. We apply a two-stage approach with edge detection followed by marker-controlled watershed segmentation. Treetops are modeled from radiometry and geometry aspects. Specifically, treetops are assumed to be represented by local radiation maxima and to be located near the center of the tree-crown. As a result, a marker image was created from the derived treetop to guide a watershed segmentation to further differentiate overlapping trees and to produce a segmented image comprised of individual tree crowns. The image segmentation method developed achieves a promising result for a 256 x 256 CASI image. Then further effort is made to extend our methods to the multiscales which are constructed from a wavelet decomposition. A scale consistency and geometric consistency are designed to examine the gradients along the scale-space for the purpose of separating true crown boundary from unwanted

A bicriterion Steiner tree problem on graph

Directory of Open Access Journals (Sweden)

Vujošević Mirko B.

2003-01-01

Full Text Available This paper presents a formulation of bicriterion Steiner tree problem which is stated as a task of finding a Steiner tree with maximal capacity and minimal length. It is considered as a lexicographic multicriteria problem. This means that the bottleneck Steiner tree problem is solved first. After that, the next optimization problem is stated as a classical minimums Steiner tree problem under the constraint on capacity of the tree. The paper also presents some computational experiments with the multicriteria problem.

The impact of tree age on biomass growth and carbon accumulation capacity: A retrospective analysis using tree ring data of three tropical tree species grown in natural forests of Suriname.

Science.gov (United States)

Köhl, Michael; Neupane, Prem R; Lotfiomran, Neda

2017-01-01

The world's forests play a pivotal role in the mitigation of global climate change. By photosynthesis they remove CO2 from the atmosphere and store carbon in their biomass. While old trees are generally acknowledged for a long carbon residence time, there is no consensus on their contribution to carbon accumulation due to a lack of long-term individual tree data. Tree ring analyses, which use anatomical differences in the annual formation of wood for dating growth zones, are a retrospective approach that provides growth patterns of individual trees over their entire lifetime. We developed time series of diameter growth and related annual carbon accumulation for 61 trees of the species Cedrela odorata L. (Meliacea), Hymenaea courbaril L. (Fabacea) and Goupia glabra Aubl. (Goupiacea). The trees grew in unmanaged tropical wet-forests of Suriname and reached ages from 84 to 255 years. Most of the trees show positive trends of diameter growth and carbon accumulation over time. For some trees we observed fluctuating growth-periods of lower growth alternate with periods of increased growth. In the last quarter of their lifetime trees accumulate on average between 39 percent (C. odorata) and 50 percent (G. glabra) of their final carbon stock. This suggests that old-growth trees in tropical forests do not only contribute to carbon stocks by long carbon resistance times, but maintain high rates of carbon accumulation at later stages of their life time.

The gravity apple tree

International Nuclear Information System (INIS)

Aldama, Mariana Espinosa

2015-01-01

The gravity apple tree is a genealogical tree of the gravitation theories developed during the past century. The graphic representation is full of information such as guides in heuristic principles, names of main proponents, dates and references for original articles (See under Supplementary Data for the graphic representation). This visual presentation and its particular classification allows a quick synthetic view for a plurality of theories, many of them well validated in the Solar System domain. Its diachronic structure organizes information in a shape of a tree following similarities through a formal concept analysis. It can be used for educational purposes or as a tool for philosophical discussion. (paper)

Trees as templates for tropical litter arthropod diversity.

Science.gov (United States)

Donoso, David A; Johnston, Mary K; Kaspari, Michael

2010-09-01

Increased tree species diversity in the tropics is associated with even greater herbivore diversity, but few tests of tree effects on litter arthropod diversity exist. We studied whether tree species influence patchiness in diversity and abundance of three common soil arthropod taxa (ants, gamasid mites, and oribatid mites) in a Panama forest. The tree specialization hypothesis proposes that tree-driven habitat heterogeneity maintains litter arthropod diversity. We tested whether tree species differed in resource quality and quantity of their leaf litter and whether more heterogeneous litter supports more arthropod species. Alternatively, the abundance-extinction hypothesis states that arthropod diversity increases with arthropod abundance, which in turn tracks resource quantity (e.g., litter depth). We found little support for the hypothesis that tropical trees are templates for litter arthropod diversity. Ten tree species differed in litter depth, chemistry, and structural variability. However, the extent of specialization of invertebrates on particular tree taxa was low and the more heterogeneous litter between trees failed to support higher arthropod diversity. Furthermore, arthropod diversity did not track abundance or litter depth. The lack of association between tree species and litter arthropods suggests that factors other than tree species diversity may better explain the high arthropod diversity in tropical forests.

Tree biology and dendrochemistry

Science.gov (United States)

Kevin T. Smith; Walter C. Shortle

1996-01-01

Dendrochemistry, the interpretation of elemental analysis of dated tree rings, can provide a temporal record of environmental change. Using the dendrochemical record requires an understanding of tree biology. In this review, we pose four questions concerning assumptions that underlie recent dendrochemical research: 1) Does the chemical composition of the wood directly...

Tree biomass in the Swiss landscape: nationwide modelling for improved accounting for forest and non-forest trees.

Science.gov (United States)

Price, B; Gomez, A; Mathys, L; Gardi, O; Schellenberger, A; Ginzler, C; Thürig, E

2017-03-01

Trees outside forest (TOF) can perform a variety of social, economic and ecological functions including carbon sequestration. However, detailed quantification of tree biomass is usually limited to forest areas. Taking advantage of structural information available from stereo aerial imagery and airborne laser scanning (ALS), this research models tree biomass using national forest inventory data and linear least-square regression and applies the model both inside and outside of forest to create a nationwide model for tree biomass (above ground and below ground). Validation of the tree biomass model against TOF data within settlement areas shows relatively low model performance (R 2 of 0.44) but still a considerable improvement on current biomass estimates used for greenhouse gas inventory and carbon accounting. We demonstrate an efficient and easily implementable approach to modelling tree biomass across a large heterogeneous nationwide area. The model offers significant opportunity for improved estimates on land use combination categories (CC) where tree biomass has either not been included or only roughly estimated until now. The ALS biomass model also offers the advantage of providing greater spatial resolution and greater within CC spatial variability compared to the current nationwide estimates.

A whole-tree chamber system for examining tree-level physiological responses of field-grown trees to environmental variation and climate change.

Science.gov (United States)

Medhurst, Jane; Parsby, Jan; Linder, Sune; Wallin, Göran; Ceschia, Eric; Slaney, Michelle

2006-09-01

A whole-tree chamber (WTC) system was installed at Flakaliden in northern Sweden to examine the long-term physiological responses of field-grown 40-year-old Norway spruce trees [Picea abies (L.) Karst.] to climate change. The WTCs were designed as large cuvettes to allow the net tree-level CO(2) and water fluxes to be measured on a continuous basis. A total of 12 WTCs were used to impose combinations of atmospheric carbon dioxide concentration, [CO(2)], and air temperature treatments. The air inside the ambient and elevated [CO(2)] WTCs was maintained at 365 and 700 micromol mol(-1), respectively. The air temperature inside the ambient temperature WTCs tracked air temperature outside the WTCs. Elevated temperatures were altered on a monthly time-step and ranged between +2.8 and +5.6 degrees C above ambient temperature. The system allowed continuous, long-term measurement of whole-tree photosynthesis, night-time respiration and transpiration. The performance of the WTCs was assessed using winter and spring data sets. The ability of the WTC system to measure tree-level physiological responses is demonstrated. All WTCs displayed a high level of control over tracking of air temperatures. The set target of 365 micromol mol(-1) in the ambient [CO(2)] chambers was too low to be maintained during winter because of tree dormancy and the high natural increase in [CO(2)] over winter at high latitudes such as the Flakaliden site. Accurate control over [CO(2)] in the ambient [CO(2)] chambers was restored during the spring and the system maintained the elevated [CO(2)] target of 700 micromol mol(-1) for both measurement periods. Air water vapour deficit (VPD) was accurately tracked in ambient temperature WTCs. However, as water vapour pressure in all 12 WTCs was maintained at the level of non-chambered (reference) air, VPD of elevated temperature WTCs was increased.

Molecular basis of angiosperm tree architecture.

Science.gov (United States)

Hollender, Courtney A; Dardick, Chris

2015-04-01

The architecture of trees greatly impacts the productivity of orchards and forestry plantations. Amassing greater knowledge on the molecular genetics that underlie tree form can benefit these industries, as well as contribute to basic knowledge of plant developmental biology. This review describes the fundamental components of branch architecture, a prominent aspect of tree structure, as well as genetic and hormonal influences inferred from studies in model plant systems and from trees with non-standard architectures. The bulk of the molecular and genetic data described here is from studies of fruit trees and poplar, as these species have been the primary subjects of investigation in this field of science. No claim to original US Government works. New Phytologist © 2014 New Phytologist Trust.

snpTree - a web-server to identify and construct SNP trees from whole genome sequence data

DEFF Research Database (Denmark)

Leekitcharoenphon, Pimlapas; Kaas, Rolf Sommer; Thomsen, Martin Christen Frølund

2012-01-01

identify SNPs and construct phylogenetic trees from WGS as well as from assembled genomes or contigs. WGS data in fastq format are aligned to reference genomes by BWA while contigs in fasta format are processed by Nucmer. SNPs are concatenated based on position on reference genome and a tree is constructed...... to differentiate and classify isolates. One of the successfully and broadly used methods is analysis of single nucletide polymorphisms (SNPs). Currently, there are different tools and methods to identify SNPs including various options and cut-off values. Furthermore, all current methods require bioinformatic...... skills. Thus, we lack a standard and simple automatic tool to determine SNPs and construct phylogenetic tree from WGS data. Results Here we introduce snpTree, a server for online-automatic SNPs analysis. This tool is composed of different SNPs analysis suites, perl and python scripts. snpTree can...

Recruiting Conventional Tree Architecture Models into State-of-the-Art LiDAR Mapping for Investigating Tree Growth Habits in Structure

Directory of Open Access Journals (Sweden)

Yi Lin

2018-02-01

Full Text Available Mensuration of tree growth habits is of considerable importance for understanding forest ecosystem processes and forest biophysical responses to climate changes. However, the complexity of tree crown morphology that is typically formed after many years of growth tends to render it a non-trivial task, even for the state-of-the-art 3D forest mapping technology—light detection and ranging (LiDAR. Fortunately, botanists have deduced the large structural diversity of tree forms into only a limited number of tree architecture models, which can present a-priori knowledge about tree structure, growth, and other attributes for different species. This study attempted to recruit Hallé architecture models (HAMs into LiDAR mapping to investigate tree growth habits in structure. First, following the HAM-characterized tree structure organization rules, we run the kernel procedure of tree species classification based on the LiDAR-collected point clouds using a support vector machine classifier in the leave-one-out-for-cross-validation mode. Then, the HAM corresponding to each of the classified tree species was identified based on expert knowledge, assisted by the comparison of the LiDAR-derived feature parameters. Next, the tree growth habits in structure for each of the tree species were derived from the determined HAM. In the case of four tree species growing in the boreal environment, the tests indicated that the classification accuracy reached 85.0%, and their growth habits could be derived by qualitative and quantitative means. Overall, the strategy of recruiting conventional HAMs into LiDAR mapping for investigating tree growth habits in structure was validated, thereby paving a new way for efficiently reflecting tree growth habits and projecting forest structure dynamics.

The Tree of Industrial Life

DEFF Research Database (Denmark)

Andersen, Esben Sloth

2002-01-01

The purpose of this paper is to bring forth an interaction between evolutionary economics and industrial systematics. The suggested solution is to reconstruct the "family tree" of the industries. Such a tree is based on similarities, but it may also reflect the evolutionary history in industries....... For this purpose the paper shows how matrices of input-output coefficients can be transformed into binary characteristics matrices and to distance matrices, and it also discusses the possible evolutionary meaning of this translation. Then these derived matrices are used as inputs to algorithms for the heuristic...... finding of optimal industrial trees. The results are presented as taxonomic trees that can easily be compared with the hierarchical structure of existing systems of industrial classification....

Decision tree modeling using R.

Science.gov (United States)

Zhang, Zhongheng

2016-08-01

In machine learning field, decision tree learner is powerful and easy to interpret. It employs recursive binary partitioning algorithm that splits the sample in partitioning variable with the strongest association with the response variable. The process continues until some stopping criteria are met. In the example I focus on conditional inference tree, which incorporates tree-structured regression models into conditional inference procedures. While growing a single tree is subject to small changes in the training data, random forests procedure is introduced to address this problem. The sources of diversity for random forests come from the random sampling and restricted set of input variables to be selected. Finally, I introduce R functions to perform model based recursive partitioning. This method incorporates recursive partitioning into conventional parametric model building.

Whole-tree water transport scales with sapwood capacitance in tropical forest canopy trees.

Science.gov (United States)

F.C. Meinzer; S.A. James; G. Goldstein; D. Woodruff

2003-01-01

The present study examines the manner in which several whole-tree water transport properties scale with species specific variation in sapwood water storage capacity. The hypothesis that constraints on relationships between sapwood capacitance and other water relations characteristics lead to predictable scaling relationships between intrinsic capacitance and whole-tree...

GuiaTreeKey, a multi-access electronic key to identify tree genera in French Guiana

OpenAIRE

Brousseau, Louise; Baraloto, Christopher

2016-01-01

The tropical rainforest of Amazonia is one of the most species-rich ecosystems on earth, with an estimated 16000 tree species. Due to this high diversity, botanical identification of trees in the Amazon is difficult, even to genus, often requiring the assistance of parataxonomists or taxonomic specialists. Advances in informatics tools offer a promising opportunity to develop user-friendly electronic keys to improve Amazonian tree identification. Here, we introduce an original mult...

Effects of nurse trees, spacing, and tree species on biomass production in mixed forest plantations

DEFF Research Database (Denmark)

Nord-Larsen, Thomas; Meilby, Henrik

2016-01-01

Growing concern about increasing concentrations of greenhouse gases in the atmosphere, and resulting global climate change, has spurred a growing demand for renewable energy. In this study, we hypothesized that a nurse tree crop may provide additional early yields of biomass for fuel, while...... was in most cases reduced due to competition. However, provided timely thinning of nurse trees, the qualitative development of the trees will allow for long-term timber production....

Modeling Caribbean tree stem diameters from tree height and crown width measurements

Science.gov (United States)

Thomas Brandeis; KaDonna Randolph; Mike Strub

2009-01-01

Regression models to predict diameter at breast height (DBH) as a function of tree height and maximum crown radius were developed for Caribbean forests based on data collected by the U.S. Forest Service in the Commonwealth of Puerto Rico and Territory of the U.S. Virgin Islands. The model predicting DBH from tree height fit reasonably well (R2 = 0.7110), with...

Field guide to red tree vole nests

Science.gov (United States)

Damon B. Lesmeister; James K. Swingle

2017-01-01

Surveys for red tree vole (Arborimus longicaudus) nests require tree climbing because the species is a highly specialized arboreal rodent that live in the tree canopy of coniferous forests in western Oregon and northwestern California. Tree voles are associated with old coniferous forest (≥80 years old) that are structurally complex, but are often...

Growing Greener Cities: A Tree-Planting Handbook.

Science.gov (United States)

Moll, Gary; Young, Stanley

This step-by-step guide, developed by the Global ReLeaf organization, presents tree-planting advice and simple steps to organizing a successful community tree-planting and tree-care program. The text is divided into three parts. Part 1 introduces trees and discusses the role they play as components of the living urban environment. Distinctions are…

Type extension trees

DEFF Research Database (Denmark)

Jaeger, Manfred

2006-01-01

We introduce type extension trees as a formal representation language for complex combinatorial features of relational data. Based on a very simple syntax this language provides a unified framework for expressing features as diverse as embedded subgraphs on the one hand, and marginal counts...... of attribute values on the other. We show by various examples how many existing relational data mining techniques can be expressed as the problem of constructing a type extension tree and a discriminant function....

The tree BVOC index

Science.gov (United States)

J.R. Simpson; E.G. McPherson

2011-01-01

Urban trees can produce a number of benefits, among them improved air quality. Biogenic volatile organic compounds (BVOCs) emitted by some species are ozone precursors. Modifying future tree planting to favor lower-emitting species can reduce these emissions and aid air management districts in meeting federally mandated emissions reductions for these compounds. Changes...

Structural Equation Model Trees

Science.gov (United States)

Brandmaier, Andreas M.; von Oertzen, Timo; McArdle, John J.; Lindenberger, Ulman

2013-01-01

In the behavioral and social sciences, structural equation models (SEMs) have become widely accepted as a modeling tool for the relation between latent and observed variables. SEMs can be seen as a unification of several multivariate analysis techniques. SEM Trees combine the strengths of SEMs and the decision tree paradigm by building tree…

Automated Generation of Attack Trees

DEFF Research Database (Denmark)

Vigo, Roberto; Nielson, Flemming; Nielson, Hanne Riis

2014-01-01

Attack trees are widely used to represent threat scenarios in a succinct and intuitive manner, suitable for conveying security information to non-experts. The manual construction of such objects relies on the creativity and experience of specialists, and therefore it is error-prone and impractica......Attack trees are widely used to represent threat scenarios in a succinct and intuitive manner, suitable for conveying security information to non-experts. The manual construction of such objects relies on the creativity and experience of specialists, and therefore it is error......-prone and impracticable for large systems. Nonetheless, the automated generation of attack trees has only been explored in connection to computer networks and levering rich models, whose analysis typically leads to an exponential blow-up of the state space. We propose a static analysis approach where attack trees...... are automatically inferred from a process algebraic specification in a syntax-directed fashion, encompassing a great many application domains and avoiding incurring systematically an exponential explosion. Moreover, we show how the standard propositional denotation of an attack tree can be used to phrase...

Computer-aided Fault Tree Analysis

International Nuclear Information System (INIS)

Willie, R.R.

1978-08-01

A computer-oriented methodology for deriving minimal cut and path set families associated with arbitrary fault trees is discussed first. Then the use of the Fault Tree Analysis Program (FTAP), an extensive FORTRAN computer package that implements the methodology is described. An input fault tree to FTAP may specify the system state as any logical function of subsystem or component state variables or complements of these variables. When fault tree logical relations involve complements of state variables, the analyst may instruct FTAP to produce a family of prime implicants, a generalization of the minimal cut set concept. FTAP can also identify certain subsystems associated with the tree as system modules and provide a collection of minimal cut set families that essentially expresses the state of the system as a function of these module state variables. Another FTAP feature allows a subfamily to be obtained when the family of minimal cut sets or prime implicants is too large to be found in its entirety; this subfamily consists only of sets that are interesting to the analyst in a special sense

Analyzing and synthesizing phylogenies using tree alignment graphs.

Directory of Open Access Journals (Sweden)

Stephen A Smith

Full Text Available Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG. The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees, we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to

Analyzing and synthesizing phylogenies using tree alignment graphs.

Science.gov (United States)

Smith, Stephen A; Brown, Joseph W; Hinchliff, Cody E

2013-01-01

Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe.

Variability of the tree-rings structure of Gmelin’s larch at northern tree line (peninsula of Taymyr

Directory of Open Access Journals (Sweden)

V. V. Fakhrutdinova

2017-04-01

Full Text Available The study of tree-ring cell structure changes as the result of tree adaptation to varying environmental conditions becomes increasingly important to predict future vegetation shifts under projected climate changes. The estimate of intrapopulation annual variability of wood anatomy characteristics is particularly informative. It helps to divide the contribution of different ecological factors to total features dispersion. In this work, a comparative analysis of individual and climatic variability of tree ring structure characteristics of Gmelin’s larch Larix gmelinii (Rupr. growth within northernmost forest was carried out. The trees from forest-tundra boundary has greater radial growth intensity, forms the bigger conductive zone in rings with wider mean lumen area in comparison with trees from closed forest. This result can be explained by adaptive features and height ecological xylem plasticity of larch. The tree rings structure of larch from boundary with tundra is determined by largely current weather conditions. Is because these ones evince high adaptive plasticity on the level of xylem structure. The xylem reflects joint changes of climate factors and local ecological conditions. The trees from closed forest are characterized by larger individual variability. The local conditions in oldest forest (for example, bad hydrothermal soil conditions inhibit the radial growth and sensitivity to environmental factors. In this case, the trees on individual level are tended to save the normal functioning of water-transport system. The significant differences in ratio individual to climate variability of tree ring structure characteristics can be caused by the different in the level of ecological habitat heterogeneity or the different in the level genetic within-population heterogeneity.

Cafts: computer aided fault tree analysis

International Nuclear Information System (INIS)

Poucet, A.

1985-01-01

The fault tree technique has become a standard tool for the analysis of safety and reliability of complex system. In spite of the costs, which may be high for a complete and detailed analysis of a complex plant, the fault tree technique is popular and its benefits are fully recognized. Due to this applications of these codes have mostly been restricted to simple academic examples and rarely concern complex, real world systems. In this paper an interactive approach to fault tree construction is presented. The aim is not to replace the analyst, but to offer him an intelligent tool which can assist him in modeling complex systems. Using the CAFTS-method, the analyst interactively constructs a fault tree in two phases: (1) In a first phase he generates an overall failure logic structure of the system; the macrofault tree. In this phase, CAFTS features an expert system approach to assist the analyst. It makes use of a knowledge base containing generic rules on the behavior of subsystems and components; (2) In a second phase the macrofault tree is further refined and transformed in a fully detailed and quantified fault tree. In this phase a library of plant-specific component failure models is used

Human reliability analysis using event trees

International Nuclear Information System (INIS)

Heslinga, G.

1983-01-01

The shut-down procedure of a technologically complex installation as a nuclear power plant consists of a lot of human actions, some of which have to be performed several times. The procedure is regarded as a chain of modules of specific actions, some of which are analyzed separately. The analysis is carried out by making a Human Reliability Analysis event tree (HRA event tree) of each action, breaking down each action into small elementary steps. The application of event trees in human reliability analysis implies more difficulties than in the case of technical systems where event trees were mainly used until now. The most important reason is that the operator is able to recover a wrong performance; memory influences play a significant role. In this study these difficulties are dealt with theoretically. The following conclusions can be drawn: (1) in principle event trees may be used in human reliability analysis; (2) although in practice the operator will recover his fault partly, theoretically this can be described as starting the whole event tree again; (3) compact formulas have been derived, by which the probability of reaching a specific failure consequence on passing through the HRA event tree after several times of recovery is to be calculated. (orig.)

On the book thickness of $k$-trees

OpenAIRE

Dujmović, Vida; Wood, David R.

2009-01-01

Graphs and Algorithms; International audience; Every k-tree has book thickness at most k + 1, and this bound is best possible for all k \\textgreater= 3. Vandenbussche et al. [SIAM J. Discrete Math., 2009] proved that every k-tree that has a smooth degree-3 tree decomposition with width k has book thickness at most k. We prove this result is best possible for k \\textgreater= 4, by constructing a k-tree with book thickness k + 1 that has a smooth degree-4 tree decomposition with width k. This s...

Border trees of complex networks

International Nuclear Information System (INIS)

Villas Boas, Paulino R; Rodrigues, Francisco A; Travieso, Gonzalo; Fontoura Costa, Luciano da

2008-01-01

The comprehensive characterization of the structure of complex networks is essential to understand the dynamical processes which guide their evolution. The discovery of the scale-free distribution and the small-world properties of real networks were fundamental to stimulate more realistic models and to understand important dynamical processes related to network growth. However, the properties of the network borders (nodes with degree equal to 1), one of its most fragile parts, remained little investigated and understood. The border nodes may be involved in the evolution of structures such as geographical networks. Here we analyze the border trees of complex networks, which are defined as the subgraphs without cycles connected to the remainder of the network (containing cycles) and terminating into border nodes. In addition to describing an algorithm for identification of such tree subgraphs, we also consider how their topological properties can be quantified in terms of their depth and number of leaves. We investigate the properties of border trees for several theoretical models as well as real-world networks. Among the obtained results, we found that more than half of the nodes of some real-world networks belong to the border trees. A power-law with cut-off was observed for the distribution of the depth and number of leaves of the border trees. An analysis of the local role of the nodes in the border trees was also performed

A Method to Quantify Plant Availability and Initiating Event Frequency Using a Large Event Tree, Small Fault Tree Model

International Nuclear Information System (INIS)

Kee, Ernest J.; Sun, Alice; Rodgers, Shawn; Popova, ElmiraV; Nelson, Paul; Moiseytseva, Vera; Wang, Eric

2006-01-01

South Texas Project uses a large fault tree to produce scenarios (minimal cut sets) used in quantification of plant availability and event frequency predictions. On the other hand, the South Texas Project probabilistic risk assessment model uses a large event tree, small fault tree for quantifying core damage and radioactive release frequency predictions. The South Texas Project is converting its availability and event frequency model to use a large event tree, small fault in an effort to streamline application support and to provide additional detail in results. The availability and event frequency model as well as the applications it supports (maintenance and operational risk management, system engineering health assessment, preventive maintenance optimization, and RIAM) are briefly described. A methodology to perform availability modeling in a large event tree, small fault tree framework is described in detail. How the methodology can be used to support South Texas Project maintenance and operations risk management is described in detail. Differences with other fault tree methods and other recently proposed methods are discussed in detail. While the methods described are novel to the South Texas Project Risk Management program and to large event tree, small fault tree models, concepts in the area of application support and availability modeling have wider applicability to the industry. (authors)

Seasonal Variation in Soil Greenhouse Gas Emissions at Three Age-Stages of Dawn Redwood (Metasequoia glyptostroboides Stands in an Alluvial Island, Eastern China

Directory of Open Access Journals (Sweden)

Shan Yin

2016-11-01

Full Text Available Greenhouse gas (GHG emissions are an important part of the carbon (C and nitrogen (N cycle in forest soil. However, soil greenhouse gas emissions in dawn redwood (Metasequoia glyptostroboides stands of different ages are poorly understood. To elucidate the effect of plantation age and environmental factors on soil GHG emissions, we used static chamber/gas chromatography (GC system to measure soil GHG emissions in an alluvial island in eastern China for two consecutive years. The soil was a source of CO2 and N2O and a sink of CH4 with annual emissions of 5.5–7.1 Mg C ha−1 year−1, 0.15–0.36 kg N ha−1 year−1, and 1.7–4.5 kg C ha−1 year−1, respectively. A clear exponential correlation was found between soil temperature and CO2 emission, but a negative linear correlation was found between soil water content and CO2 emission. Soil temperature had a significantly positive effect on CH4 uptake and N2O emission, whereas no significant correlation was found between CH4 uptake and soil water content, and N2O emission and soil water content. These results implied that older forest stands might cause more GHG emissions from the soil into the atmosphere because of higher litter/root biomass and soil carbon/nitrogen content compared with younger stands.

Success tree method of resources evaluation

International Nuclear Information System (INIS)

Chen Qinglan; Sun Wenpeng

1994-01-01

By applying the reliability theory in system engineering, the success tree method is used to transfer the expert's recognition on metallogenetic regularities into the form of the success tree. The aim of resources evaluation is achieved by means of calculating the metallogenetic probability or favorability of the top event of the success tree. This article introduces in detail, the source, principle of the success tree method and three kinds of calculation methods, expounds concretely how to establish the success tree of comprehensive uranium metallogenesis as well as the procedure from which the resources evaluation is performed. Because this method has not restrictions on the number of known deposits and calculated area, it is applicable to resources evaluation for different mineral species, types and scales and possesses good prospects of development

Critical wind speed at which trees break

Science.gov (United States)

Virot, E.; Ponomarenko, A.; Dehandschoewercker, É.; Quéré, D.; Clanet, C.

2016-02-01

Data from storms suggest that the critical wind speed at which trees break is constant (≃42 m /s ), regardless of tree characteristics. We question the physical origin of this observation both experimentally and theoretically. By combining Hooke's law, Griffith's criterion, and tree allometry, we show that the critical wind speed indeed hardly depends on the height, diameter, and elastic properties of trees.

Critical wind speed at which trees break.

Science.gov (United States)

Virot, E; Ponomarenko, A; Dehandschoewercker, É; Quéré, D; Clanet, C

2016-02-01

Data from storms suggest that the critical wind speed at which trees break is constant (≃42m/s), regardless of tree characteristics. We question the physical origin of this observation both experimentally and theoretically. By combining Hooke's law, Griffith's criterion, and tree allometry, we show that the critical wind speed indeed hardly depends on the height, diameter, and elastic properties of trees.

Comprehensive decision tree models in bioinformatics.

Directory of Open Access Journals (Sweden)

Gregor Stiglic

Full Text Available PURPOSE: Classification is an important and widely used machine learning technique in bioinformatics. Researchers and other end-users of machine learning software often prefer to work with comprehensible models where knowledge extraction and explanation of reasoning behind the classification model are possible. METHODS: This paper presents an extension to an existing machine learning environment and a study on visual tuning of decision tree classifiers. The motivation for this research comes from the need to build effective and easily interpretable decision tree models by so called one-button data mining approach where no parameter tuning is needed. To avoid bias in classification, no classification performance measure is used during the tuning of the model that is constrained exclusively by the dimensions of the produced decision tree. RESULTS: The proposed visual tuning of decision trees was evaluated on 40 datasets containing classical machine learning problems and 31 datasets from the field of bioinformatics. Although we did not expected significant differences in classification performance, the results demonstrate a significant increase of accuracy in less complex visually tuned decision trees. In contrast to classical machine learning benchmarking datasets, we observe higher accuracy gains in bioinformatics datasets. Additionally, a user study was carried out to confirm the assumption that the tree tuning times are significantly lower for the proposed method in comparison to manual tuning of the decision tree. CONCLUSIONS: The empirical results demonstrate that by building simple models constrained by predefined visual boundaries, one not only achieves good comprehensibility, but also very good classification performance that does not differ from usually more complex models built using default settings of the classical decision tree algorithm. In addition, our study demonstrates the suitability of visually tuned decision trees for datasets

Comprehensive decision tree models in bioinformatics.

Science.gov (United States)

Stiglic, Gregor; Kocbek, Simon; Pernek, Igor; Kokol, Peter

2012-01-01

Classification is an important and widely used machine learning technique in bioinformatics. Researchers and other end-users of machine learning software often prefer to work with comprehensible models where knowledge extraction and explanation of reasoning behind the classification model are possible. This paper presents an extension to an existing machine learning environment and a study on visual tuning of decision tree classifiers. The motivation for this research comes from the need to build effective and easily interpretable decision tree models by so called one-button data mining approach where no parameter tuning is needed. To avoid bias in classification, no classification performance measure is used during the tuning of the model that is constrained exclusively by the dimensions of the produced decision tree. The proposed visual tuning of decision trees was evaluated on 40 datasets containing classical machine learning problems and 31 datasets from the field of bioinformatics. Although we did not expected significant differences in classification performance, the results demonstrate a significant increase of accuracy in less complex visually tuned decision trees. In contrast to classical machine learning benchmarking datasets, we observe higher accuracy gains in bioinformatics datasets. Additionally, a user study was carried out to confirm the assumption that the tree tuning times are significantly lower for the proposed method in comparison to manual tuning of the decision tree. The empirical results demonstrate that by building simple models constrained by predefined visual boundaries, one not only achieves good comprehensibility, but also very good classification performance that does not differ from usually more complex models built using default settings of the classical decision tree algorithm. In addition, our study demonstrates the suitability of visually tuned decision trees for datasets with binary class attributes and a high number of possibly

On Tree-Constrained Matchings and Generalizations

NARCIS (Netherlands)

S. Canzar (Stefan); K. Elbassioni; G.W. Klau (Gunnar); J. Mestre

2011-01-01

htmlabstractWe consider the following \\textsc{Tree-Constrained Bipartite Matching} problem: Given two rooted trees $T_1=(V_1,E_1)$, $T_2=(V_2,E_2)$ and a weight function $w: V_1\\times V_2 \\mapsto \\mathbb{R}_+$, find a maximum weight matching $\\mathcal{M}$ between nodes of the two trees, such that

Aspects of insertion in random trees

NARCIS (Netherlands)

Bagchi, Arunabha; Reingold, E.M.

1982-01-01

A method formulated by Yao and used by Brown has yielded bounds on the fraction of nodes with specified properties in trees bult by a sequence of random internal nodes in a random tree built by binary search and insertion, and show that in such a tree about bounds better than those now known. We

Visual exploration of parameter influence on phylogenetic trees.

Science.gov (United States)

Hess, Martin; Bremm, Sebastian; Weissgraeber, Stephanie; Hamacher, Kay; Goesele, Michael; Wiemeyer, Josef; von Landesberger, Tatiana

2014-01-01

Evolutionary relationships between organisms are frequently derived as phylogenetic trees inferred from multiple sequence alignments (MSAs). The MSA parameter space is exponentially large, so tens of thousands of potential trees can emerge for each dataset. A proposed visual-analytics approach can reveal the parameters' impact on the trees. Given input trees created with different parameter settings, it hierarchically clusters the trees according to their structural similarity. The most important clusters of similar trees are shown together with their parameters. This view offers interactive parameter exploration and automatic identification of relevant parameters. Biologists applied this approach to real data of 16S ribosomal RNA and protein sequences of ion channels. It revealed which parameters affected the tree structures. This led to a more reliable selection of the best trees.

GuiaTreeKey, a multi-access electronic key to identify tree genera in French Guiana.

Science.gov (United States)

Engel, Julien; Brousseau, Louise; Baraloto, Christopher

2016-01-01

The tropical rainforest of Amazonia is one of the most species-rich ecosystems on earth, with an estimated 16000 tree species. Due to this high diversity, botanical identification of trees in the Amazon is difficult, even to genus, often requiring the assistance of parataxonomists or taxonomic specialists. Advances in informatics tools offer a promising opportunity to develop user-friendly electronic keys to improve Amazonian tree identification. Here, we introduce an original multi-access electronic key for the identification of 389 tree genera occurring in French Guiana terra-firme forests, based on a set of 79 morphological characters related to vegetative, floral and fruit characters. Its purpose is to help Amazonian tree identification and to support the dissemination of botanical knowledge to non-specialists, including forest workers, students and researchers from other scientific disciplines. The electronic key is accessible with the free access software Xper ², and the database is publicly available on figshare: https://figshare.com/s/75d890b7d707e0ffc9bf (doi: 10.6084/m9.figshare.2682550).

Rooted triple consensus and anomalous gene trees

Directory of Open Access Journals (Sweden)

Schmidt Heiko A

2008-04-01

Full Text Available Abstract Background Anomalous gene trees (AGTs are gene trees with a topology different from a species tree that are more probable to observe than congruent gene trees. In this paper we propose a rooted triple approach to finding the correct species tree in the presence of AGTs. Results Based on simulated data we show that our method outperforms the extended majority rule consensus strategy, while still resolving the species tree. Applying both methods to a metazoan data set of 216 genes, we tested whether AGTs substantially interfere with the reconstruction of the metazoan phylogeny. Conclusion Evidence of AGTs was not found in this data set, suggesting that erroneously reconstructed gene trees are the most significant challenge in the reconstruction of phylogenetic relationships among species with current data. The new method does however rule out the erroneous reconstruction of deep or poorly resolved splits in the presence of lineage sorting.

Benefits of tree mixes in carbon plantings

Science.gov (United States)

Hulvey, Kristin B.; Hobbs, Richard J.; Standish, Rachel J.; Lindenmayer, David B.; Lach, Lori; Perring, Michael P.

2013-10-01

Increasingly governments and the private sector are using planted forests to offset carbon emissions. Few studies, however, examine how tree diversity -- defined here as species richness and/or stand composition -- affects carbon storage in these plantings. Using aboveground tree biomass as a proxy for carbon storage, we used meta-analysis to compare carbon storage in tree mixtures with monoculture plantings. Tree mixes stored at least as much carbon as monocultures consisting of the mixture's most productive species and at times outperformed monoculture plantings. In mixed-species stands, individual species, and in particular nitrogen-fixing trees, increased stand biomass. Further motivations for incorporating tree richness into planted forests include the contribution of diversity to total forest carbon-pool development, carbon-pool stability and the provision of extra ecosystem services. Our findings suggest a two-pronged strategy for designing carbon plantings including: (1) increased tree species richness; and (2) the addition of species that contribute to carbon storage and other target functions.