Residual densities affect growth of overstory trees and planted Douglas-fir, western hemlock, and western redcedar: results from the first decade

Treesearch

Leslie Chandler Brodie; Dean S. DeBell

2013-01-01

In recent years, interest has increased in silvicultural systems and harvest cuts that retain partial overstories, but there are few data available on the growth of the understory trees in such stands. We studied the response of overstory trees and underplanted seedlings, Douglas-fir (Pseudotsuga menziesii), western hemlock (Tsuga...

Detail of staircase (stepped ramp) and retaining wall at West ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

Detail of staircase (stepped ramp) and retaining wall at West 102nd Street, soccer field at right, looking south, with London Plane trees surrounding field. - Henry Hudson Parkway, Extending 11.2 miles from West 72nd Street to Bronx-Westchester border, New York County, NY

The morphological structure of leaves and the dust-retaining capability of afforested plants in urban Guangzhou, South China.

PubMed

Liu, Lu; Guan, Dongsheng; Peart, M R

2012-09-01

Air pollution is a serious health problem throughout the world, exacerbating a wide range of respiratory and vascular illnesses in urban areas. The mass artificial plantation is very helpful to absorb dust and reduce pollution for conservation of the urban environment. The foliar surface of plants is an important receptor of atmospheric pollutants. Therefore, selection of suitable plant species for urban environment is very important. The dust-retaining capability of urban trees in Guangzhou was determined at four different types of urban area, and the morphological traits of their leaves such as wax, cuticle, stomata, and trichomes were observed under a scanning electron microscope. It was determined that the dust-retaining capability of any given tree species is significantly different in the same place. Of the four studied tree species in the industrial area (IA) and commercial/traffic areas (CTA) type urban areas, the highest amounts of dust removed by Mangifera indica Linn was 12.723 and 1.482 g/m(2), respectively. However, in contrast, the equivalent maxima for Bauhinia blakeana is only 2.682 g/m(2) and 0.720 g/m(2), respectively. Different plant species have different leaf morphology. The leaf of M. indica has deep grooves and high stomata density which are in favor of dust-retained, and thus, their dust-retained capability is stronger, while B. blakeana has the cells and epicuticular wax with its stomata arranging regularly, resulting in poor dust catching capability. Leaf size was also shown to be related to dust capture for the four studied tree species. The dust removal capacity of individual tree species should be taken into account in the management of greening plantation in and around an urban area. It was also shown that temporal variation in dust accumulation occurred over the 28-day observation period and this was discussed. Furthermore, spatial contrasts in dust accumulation were evidenced by the data. This reflected the differing pollution loadings of the four urban-type areas. The highest amount of dust accumulation was associated with the industrial area in which shipyard and steelworks occurred whilst the lowest dust accumulation was associated with the grounds of the University which was the control area.

Level and pattern of overstory retention influence rates and forms of tree mortality in mature, coniferous forests of the Pacific Northwest, USA

Treesearch

Lauren S. Urgenson; Charles B. Halpern; Paul D. Anderson

2013-01-01

Mortality of retained trees can compromise the ecological objectives of variable-retention harvest. We used a large-scale experiment replicated at six locations in western Washington and Oregon to examine the influences of retention level (40% vs. 15% of original basal area) and its spatial pattern (aggregated vs.dispersed) on the rate and form of tree mortality for 11...

Management of almond leaf scorch disease: long term data on yield, tree vitality, and disease progress

USDA-ARS?s Scientific Manuscript database

Almond leaf scorch (ALS) disease has been a chronic problem for California almond growers. This disease is caused by the bacterial pathogen Xylella fastidiosa and is transmitted by xylem-feeding insects. Previous research suggested that retaining, rather than roguing, ALS-affected trees may be more ...

Agroforestry systems and valuation methodologies

Treesearch

Janaki R.R. Alavalapati; D. Evan Mercer; Jensen R. Montambault

2004-01-01

Agroforestry, the deliberate integration of trees with agricultural crops andor livestock either simultaneously or sequentially on the same unit of land, has been an established practice for centuries. Throughout the tropics and, to some extent, temperate zones, farmers have a long tradition of retaining trees on their fields and pastures, as well as growing crops or...

Biological legacies buffer local species extinction after logging

PubMed Central

Rudolphi, Jörgen; Jönsson, Mari T; Gustafsson, Lena

2014-01-01

Clearcutting has been identified as a main threat to forest biodiversity. In the last few decades, alternatives to clearcutting have gained much interest. Living and dead trees are often retained after harvest to serve as structural legacies to mitigate negative effects of forestry. However, this practice is widely employed without information from systematic before–after control-impact studies to assess the processes involved in species responses after clearcutting with retention. We performed a large-scale survey of the occurrence of logging-sensitive and red-listed bryophytes and lichens before and after clearcutting with the retention approach. A methodology was adopted that, for the first time in studies on retention approaches, enabled monitoring of location-specific substrates. We used uncut stands as controls to assess the variables affecting the survival of species after a major disturbance. In total, 12 bryophyte species and 27 lichen species were analysed. All were classified as sensitive to logging, and most species are also currently red-listed. We found that living and dead trees retained after final harvest acted as refugia in which logging-sensitive species were able to survive for 3 to 7 years after logging. Depending on type of retention and organism group, between 35% and 92% of the species occurrences persisted on retained structures. Most species observed outside retention trees or patches disappeared. Larger pre-harvest population sizes of bryophytes on dead wood increased the survival probability of the species and hence buffered the negative effects of logging. Synthesis and applications. Careful spatial planning of retention structures is required to fully embrace the habitats of logging-sensitive species. Bryophytes and lichens persisted to a higher degree in retention patches compared to solitary trees or in the clearcut area. Retaining groups of trees in logged areas will help to sustain populations of species over the clearcut phase. When possible, old logs should be moved into retention patches to provide a more beneficial environment for dead wood-dependent species. Our study also highlights the need for more before–after control-impact studies of retention forestry to explore factors influencing the survival of species after logging. PMID:25653456

Biological legacies buffer local species extinction after logging.

PubMed

Rudolphi, Jörgen; Jönsson, Mari T; Gustafsson, Lena; Bugmann, H

2014-02-01

Clearcutting has been identified as a main threat to forest biodiversity. In the last few decades, alternatives to clearcutting have gained much interest. Living and dead trees are often retained after harvest to serve as structural legacies to mitigate negative effects of forestry. However, this practice is widely employed without information from systematic before-after control-impact studies to assess the processes involved in species responses after clearcutting with retention. We performed a large-scale survey of the occurrence of logging-sensitive and red-listed bryophytes and lichens before and after clearcutting with the retention approach. A methodology was adopted that, for the first time in studies on retention approaches, enabled monitoring of location-specific substrates. We used uncut stands as controls to assess the variables affecting the survival of species after a major disturbance. In total, 12 bryophyte species and 27 lichen species were analysed. All were classified as sensitive to logging, and most species are also currently red-listed. We found that living and dead trees retained after final harvest acted as refugia in which logging-sensitive species were able to survive for 3 to 7 years after logging. Depending on type of retention and organism group, between 35% and 92% of the species occurrences persisted on retained structures. Most species observed outside retention trees or patches disappeared. Larger pre-harvest population sizes of bryophytes on dead wood increased the survival probability of the species and hence buffered the negative effects of logging. Synthesis and applications . Careful spatial planning of retention structures is required to fully embrace the habitats of logging-sensitive species. Bryophytes and lichens persisted to a higher degree in retention patches compared to solitary trees or in the clearcut area. Retaining groups of trees in logged areas will help to sustain populations of species over the clearcut phase. When possible, old logs should be moved into retention patches to provide a more beneficial environment for dead wood-dependent species. Our study also highlights the need for more before-after control-impact studies of retention forestry to explore factors influencing the survival of species after logging.

Metapopulation dynamics and future persistence of epiphytic cyanolichens in a European boreal forest ecosystem

PubMed Central

Fedrowitz, Katja; Kuusinen, Mikko; Snäll, Tord

2012-01-01

1. One approach to biodiversity conservation is to set aside small woodland key habitats (WKHs) in intensively managed landscapes. The aim is to support species, such as epiphytes, which often depend on old trees and are negatively affected by intensive forestry. However, it is not known whether the number of host trees within these areas can sustain species in the long term. 2. We studied metapopulation dynamics and assessed the future persistence of epiphytes assuming host tree numbers similar to those observed in large north European WKHs. The study species were seven cyanolichens confined to Populus tremula in the boreal study area. Colonizations and extinctions were recorded in 2008 on trees that had been surveyed 13 years earlier. We applied generalized (non)linear models to test the importance of environmental conditions, facilitation and spatial connectivity on the metapopulation dynamics. We also simulated the effects of tree numbers and tree fall rates on future species persistence. 3. Metapopulation dynamics were explained by tree quality, size or tree fall. In one species, colonizations increased with increasing connectivity, and in a second species it increased if other lichens sharing the photobiont with the focal species were present, suggesting facilitation. Both stochastic extinctions from standing trees and deterministic extinctions caused by tree fall should be accounted for in projecting epiphyte metapopulation dynamics. 4. One to three infrequent, sexually dispersed study species face a significant extinction risk within 50 years, especially in areas with low tree numbers. 5. Synthesis and applications. During the coming decades, infrequent, sexually dispersed, epiphytic lichens are likely to be lost from small woodland habitat set asides in intensively managed landscapes. Local extinction will be a consequence of low colonization rates and tree fall. Low colonization rates can be prevented by retaining large trees on which lichen species colonization rates are the highest and by assuring a high density of occupied trees. The negative effect of tree fall should be compensated for by assuring continuous availability of old trees. This can be achieved by decreasing the populations of large browsers, or by retaining trees with high conservation value during management operations. PMID:22745512

Semiautomated landscape feature extraction and modeling

NASA Astrophysics Data System (ADS)

Wasilewski, Anthony A.; Faust, Nickolas L.; Ribarsky, William

2001-08-01

We have developed a semi-automated procedure for generating correctly located 3D tree objects form overhead imagery. Cross-platform software partitions arbitrarily large, geocorrected and geolocated imagery into management sub- images. The user manually selected tree areas from one or more of these sub-images. Tree group blobs are then narrowed to lines using a special thinning algorithm which retains the topology of the blobs, and also stores the thickness of the parent blob. Maxima along these thinned tree grous are found, and used as individual tree locations within the tree group. Magnitudes of the local maxima are used to scale the radii of the tree objects. Grossly overlapping trees are culled based on a comparison of tree-tree distance to combined radii. Tree color is randomly selected based on the distribution of sample tree pixels, and height is estimated form tree radius. The final tree objects are then inserted into a terrain database which can be navigated by VGIS, a high-resolution global terrain visualization system developed at Georgia Tech.

The dust retention capacities of urban vegetation-a case study of Guangzhou, South China.

PubMed

Liu, Lu; Guan, Dongsheng; Peart, M R; Wang, Gang; Zhang, Hui; Li, Zhiwei

2013-09-01

Urban vegetation increasingly plays an important role in the improvement of the urban atmospheric environment. This paper deals with the dust retention capacities of four urban tree species (Ficus virens var. sublanceolata, Ficus microcarpa, Bauhinia blakeana, and Mangifera indica Linn) in Guangzhou. The dust-retaining capacities of four tree species are studied under different pollution intensities and for different seasons. Remote sensing imagery was used to estimate the total aboveground urban vegetation biomass in different functional areas of urban Guangzhou, information that was then used to estimate the dust-retaining capacities of the different functional areas and the total removal of airborne particulates in urban Guangzhou by foliage. The results showed that urban vegetation can remove dust from the atmosphere thereby improving air quality. The major findings are that dust retention, or capture, vary between the four species of tree studied; it also varied between season and between types of urban functional area, namely industrial, commercial/road traffic, residential, and clean areas. Dust accumulation over time was also studied and reached a maximum, and saturation, after about 24 days. The overall aboveground biomass of urban vegetation in Guangzhou was estimated to be 52.0 × 10(5) t, its total leaf area 459.01 km(2), and the dust-retaining capacity was calculated at 8012.89 t per year. The present study demonstrated that the foliage of tree species used in urban greening make a substantial contribution to atmospheric dust removal and retention in urban Guangzhou.

Ecological effects of variable retention harvests in the northwestern United States: the DEMO study.

Treesearch

Keith B. Aubry; Charles B. Halpern; Douglas A. Maguire

2004-01-01

The retention of trees in harvest units is an integral part of forest management practices on federal lands in the northwestern United States (U.S.), yet the ecological benefits that result from various levels or patterns of retained trees remain speculative. Large scale and long term silviculture experiments are needed to evaluate the effects of alternative forest...

Conserving and managing the trees of the future: genetic resources for Pacific Northwest forests.

Treesearch

Sally Duncan

2003-01-01

Genetic resource management has historically called for altering the genetic structure of plant populations through selection for traits of interest such as rapid growth. Although this is still a principal component of tree breeding programs in the Pacific Northwest, managing genetic resources now also brings a clear focus on retaining a broad diversity within and...

Deferment cutting in central Appalachian hardwoods: an update

Treesearch

Gary W. Miller; James E. Johnson; John E. Baumgras

1997-01-01

Deferment cutting is designed to regenerate a variety of high-quality hardwood species and promote a two-age stand structure for aesthetic, wildlife habitat, and other non-timber binefits. Basal area is reduced enough so that it resembles a seedtree or shelterwood practice in that some overstory trees are retained while all other trees are cut (Figure 1). However, in...

Canopy arthropod response to density and distribution of green trees retained after partial harvest.

Treesearch

Timothy D. Schowalter; Yanli Zhang; Robert A. Progar

2005-01-01

We measured canopy arthropod responses to six contrasting green-tree retention treatments at six locations (blocks) in western Oregon and Washington as part of the Demonstration of Ecosystem Management Options (DEMO) study. Treatments were 100% retention (uncut), 75% retention with three 1-ha harvested gaps, 40% dispersed retention, 40% aggregated retention with five 1...

Premature germination of forest tree seed during natural storage in duff

Treesearch

I. T. Haig

1932-01-01

For some years forest investigators in the Pacific Northwest have been aware of the considerable quantity of tree seed which accumulates in the duff of heavy virgin timber stands and apparently retains its vitality for a few years in a sort of natural cold-storage condition. The major portion of the luxuriant regeneration which frequently follows logging and forest...

Red Oak Research and Demonstration Area in Phelps Township, North Bay, Ontario-2004 to 2005

Treesearch

Dave Deugo; Andrée Morneault; Dianne Othmer; Megan Smith; Al Stinson; Murray Woods; Ian Kovacs; Ian Aho; Bill Parker; Rob Baker; Marinus Verwey; Guylaine Thauvette; Don Willis; Jeff Dech

2006-01-01

In July 2004, a large stand of red oak (Quercus rubra) was harvested in Phelps Township, North Bay District, North Bay, Ontario using the uniform shelterwood system. Most of the stand was harvested to retain 40 percent crown closure, while a very small portion was harvested to retain 70 percent crown closure. During tree marking, an active Northern...

Initial soil respiration response to biomass harvesting and green-tree retention in aspen-dominated forests of the Great Lakes region

USGS Publications Warehouse

Kurth, Valerie J.; Bradford, John B.; Slesak, Robert A.; D'Amato, Anthony W.

2014-01-01

Contemporary forest management practices are increasingly designed to optimize novel objectives, such as maximizing biomass feedstocks and/or maintaining ecological legacies, but many uncertainties exist regarding how these practices influence forest carbon (C) cycling. We examined the responses of soil respiration (Rs) to biomass harvesting and green-tree retention in an effort to empirically assess their impacts on C cycling. We measured Rs and soil microclimatic variables over four growing seasons following implementation of these management practices using a fully replicated, operational-scale experiment in aspen-dominated forests in northern Minnesota. Treatments included three levels of biomass removal within harvested areas: whole-tree harvest (no slash deliberately retained), 20% slash retained, and stem-only harvest (all slash retained), and two levels of green-tree retention: 0.1 ha aggregate or none. The relative amount of biomass removed had a negligible effect on Rs in harvested areas, but treatment effects were probably obscured by heterogeneous slash configurations and rapid post-harvest regeneration of aspen in all of the treatments. Discrete measurements of Rs and soil temperature within green-tree aggregates were not discernible from surrounding harvested areas or unharvested control stands until the fourth year following harvest, when Rs was higher in unharvested controls than in aggregates and harvested stands. Growing season estimates of Rs showed that unharvested control stands had higher Rs than both harvested stands and aggregates in the first and third years following harvest. Our results suggest that retention of larger forest aggregates may be necessary to maintain ecosystem-level responses similar to those in unharvested stands. Moreover, they highlight the innate complexity of operational-scale research and suggest that the initial impacts of biomass harvest on Rs may be indiscernible from traditional harvest in systems where incidental breakage is high.

Survival, growth and reproduction by big-leaf mahogany (Swietenia macrophylla) in open clearing vs. forested conditions in Brazil

Treesearch

James Grogan; Mark Schulze; Jurandir Galvao

2010-01-01

Big-leaf mahogany (Swietenia macrophylla) trees are often retained in agricultural fields and pastures for seed and timber production after selective logging and forest clearing in the Brazilian Amazon. At a forest management site in southeast Para´, we censused trees growing scattered across a large open clearing after forest removal and in heavily disturbed forest...

Variable-retention harvests in the Pacific Northwest: a review of short-term findings from the DEMO study

Treesearch

K.B. Aubry; C.B. Halpern; C.E. Peterson

2009-01-01

In the Pacific Northwest (PNW) region of the contiguous United States, retention of live (green) trees in harvest units is an integral part of forest management practices on federal lands, yet the ecological benefits that result from various levels or patterns of retained trees remain speculative. The Demonstration of Ecosystem Management Options (DEMO) study was...

Deer predation on leaf miners via leaf abscission

NASA Astrophysics Data System (ADS)

Yamazaki, Kazuo; Sugiura, Shinji

2008-03-01

The evergreen oak Quercus gilva Blume sheds leaves containing mines of the leaf miner Stigmella sp. (Lepidoptera: Nepticulidae) earlier than leaves with no mines in early spring in Nara, central Japan. The eclosion rates of the leaf miner in abscised and retained leaves were compared in the laboratory to clarify the effects of leaf abscission on leaf miner survival in the absence of deer. The leaf miner eclosed successfully from both fallen leaves and leaves retained on trees. However, sika deer ( Cervus nippon centralis Kishida) feed on the fallen mined leaves. Field observations showed that deer consume many fallen leaves under Q. gilva trees, suggesting considerable mortality of leaf miners due to deer predation via leaf abscission. This is a previously unreported relationship between a leaf miner and a mammalian herbivore via leaf abscission.

A tree-by-tree measure of site utilization for grand fir related to stand density index

Treesearch

Albert R. Stage

1968-01-01

The usefulness of stand density index (SDI) has been limited by lack of a way to partition its nonlinear expression into additive components to describe the relative stocking of a stand by species or quality classes. In this paper, a linear equation is derived to permit such a partition. A closely related expression for grand fir stocking is given that retains the...

Evaluating the effects of varying levels and patterns of green-tree retention: experimental design of the DEMO study.

Treesearch

Keith B. Aubry; Michael P. Amaranthus; Charles B. Haipern; James D. White; Brenda L. Woodard; Charles E. Peterson; Cynthia A. Lagoudakisi; Alan J. Horton

1999-01-01

In western Oregon and Washington, recent changes in federal forest management policy contained in the Northwest Forest Plan have led to new harvest prescriptions on millions of acres of public lands. For example. on upland sites, standards and guidelines now require that live (green) trees are retained in at least 15% of the area within each harvest unit and recommend...

Overstory cohort survival in an Appalachian hardwood deferment cutting: 35-year results

Treesearch

John P. Brown; Melissa A. Thomas-Van Gundy; Thomas M. Schuler

2018-01-01

Deferment cutting is a two-aged regeneration method in which the majority of the stand is harvested and a dispersed component of overstory trees—approximately 15–20% of the basal area – is retained for at least onehalf rotation and up one full rotation for reasons other than regeneration. Careful consideration of residual trees, in both characteristics and harvesting,...

Problem Solving and Learning in a Natural Task Domain

DTIC Science & Technology

1988-09-01

algorithm is demonstrated in two further examples. For clarity, all examples present a single path through the causal model, rather than the tree ...Any implications are added to the list. EDSEL1 keeps recent chains of reasoning. The tree form of any explorations is retained for future reasoning...9) (CAUSE (CRANK CRANKSHAFT) (OVEVIENT CAMSHAFT ) 9) (CAUSE (CRANK CRANKSHAFT) (TUR:N DRIVESHAFT) 9) STARTER (CAUSE (SWITCH-ACTION SOLENOID ON

Maintaining ecosystem resilience: functional responses of tree cavity nesters to logging in temperate forests of the Americas.

PubMed

Ibarra, José Tomás; Martin, Michaela; Cockle, Kristina L; Martin, Kathy

2017-06-30

Logging often reduces taxonomic diversity in forest communities, but little is known about how this biodiversity loss affects the resilience of ecosystem functions. We examined how partial logging and clearcutting of temperate forests influenced functional diversity of birds that nest in tree cavities. We used point-counts in a before-after-control-impact design to examine the effects of logging on the value, range, and density of functional traits in bird communities in Canada (21 species) and Chile (16 species). Clearcutting, but not partial logging, reduced diversity in both systems. The effect was much more pronounced in Chile, where logging operations removed critical nesting resources (large decaying trees), than in Canada, where decaying aspen Populus tremuloides were retained on site. In Chile, logging was accompanied by declines in species richness, functional richness (amount of functional niche occupied by species), community-weighted body mass (average mass, weighted by species densities), and functional divergence (degree of maximization of divergence in occupied functional niche). In Canada, clearcutting did not affect species richness but nevertheless reduced functional richness and community-weighted body mass. Although some cavity-nesting birds can persist under intensive logging operations, their ecosystem functions may be severely compromised unless future nest trees can be retained on logged sites.

Indicators: Human Disturbance

EPA Pesticide Factsheets

Human disturbance is a measure of the vulnerability of aquatic resources to a variety of harmful human activities such as tree removal, road building, construction near shorelines/streambanks, and artificial hardening of lakeshores with retaining walls.

Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies.

PubMed

Sayyari, Erfan; Mirarab, Siavash

2018-02-28

Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the inability to resolve relationships is often shown as a (soft) polytomy. Both types of polytomies have been traditionally studied in the context of gene tree reconstruction from sequence data. However, polytomies in the species tree cannot be detected or ruled out without considering gene tree discordance. In this paper, we describe a statistical test based on properties of the multi-species coalescent model to test the null hypothesis that a branch in an estimated species tree should be replaced by a polytomy. On both simulated and biological datasets, we show that the null hypothesis is rejected for all but the shortest branches, and in most cases, it is retained for true polytomies. The test, available as part of the Accurate Species TRee ALgorithm (ASTRAL) package, can help systematists decide whether their datasets are sufficient to resolve specific relationships of interest.

Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies

PubMed Central

Sayyari, Erfan

2018-01-01

Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the inability to resolve relationships is often shown as a (soft) polytomy. Both types of polytomies have been traditionally studied in the context of gene tree reconstruction from sequence data. However, polytomies in the species tree cannot be detected or ruled out without considering gene tree discordance. In this paper, we describe a statistical test based on properties of the multi-species coalescent model to test the null hypothesis that a branch in an estimated species tree should be replaced by a polytomy. On both simulated and biological datasets, we show that the null hypothesis is rejected for all but the shortest branches, and in most cases, it is retained for true polytomies. The test, available as part of the Accurate Species TRee ALgorithm (ASTRAL) package, can help systematists decide whether their datasets are sufficient to resolve specific relationships of interest. PMID:29495636

12. OVERVIEW FROM FORMER RESIDENTIAL AREA NORTH OF SAR2, SHOWING ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

12. OVERVIEW FROM FORMER RESIDENTIAL AREA NORTH OF SAR-2, SHOWING TRAIL UP TO FOREBAY, RETAINING WALL, PEPPER TREES, AND SAR-2 IN DISTANCE. VIEW TO SOUTH-SOUTHEAST. - Santa Ana River Hydroelectric System, Redlands, San Bernardino County, CA

Wavelet tree structure based speckle noise removal for optical coherence tomography

NASA Astrophysics Data System (ADS)

Yuan, Xin; Liu, Xuan; Liu, Yang

2018-02-01

We report a new speckle noise removal algorithm in optical coherence tomography (OCT). Though wavelet domain thresholding algorithms have demonstrated superior advantages in suppressing noise magnitude and preserving image sharpness in OCT, the wavelet tree structure has not been investigated in previous applications. In this work, we propose an adaptive wavelet thresholding algorithm via exploiting the tree structure in wavelet coefficients to remove the speckle noise in OCT images. The threshold for each wavelet band is adaptively selected following a special rule to retain the structure of the image across different wavelet layers. Our results demonstrate that the proposed algorithm outperforms conventional wavelet thresholding, with significant advantages in preserving image features.

Dimensional Reduction for the General Markov Model on Phylogenetic Trees.

PubMed

Sumner, Jeremy G

2017-03-01

We present a method of dimensional reduction for the general Markov model of sequence evolution on a phylogenetic tree. We show that taking certain linear combinations of the associated random variables (site pattern counts) reduces the dimensionality of the model from exponential in the number of extant taxa, to quadratic in the number of taxa, while retaining the ability to statistically identify phylogenetic divergence events. A key feature is the identification of an invariant subspace which depends only bilinearly on the model parameters, in contrast to the usual multi-linear dependence in the full space. We discuss potential applications including the computation of split (edge) weights on phylogenetic trees from observed sequence data.

Seasonal carbohydrate dynamics and growth in Douglas-fir trees experiencing chronic, fungal-mediated reduction in functional leaf area.

PubMed

Saffell, Brandy J; Meinzer, Frederick C; Woodruff, David R; Shaw, David C; Voelker, Steven L; Lachenbruch, Barbara; Falk, Kristen

2014-03-01

Stored non-structural carbohydrates (NSCs) could play an important role in tree survival in the face of a changing climate and associated stress-related mortality. We explored the effects of the stomata-blocking and defoliating fungal disease called Swiss needle cast on Douglas-fir carbohydrate reserves and growth to evaluate the extent to which NSCs can be mobilized under natural conditions of low water stress and restricted carbon supply in relation to potential demands for growth. We analyzed the concentrations of starch, sucrose, glucose and fructose in foliage, twig wood and trunk sapwood of 15 co-occurring Douglas-fir trees expressing a gradient of Swiss needle cast symptom severity quantified as previous-year functional foliage mass. Growth (mean basal area increment, BAI) decreased by ∼80% and trunk NSC concentration decreased by 60% with decreasing functional foliage mass. The ratio of relative changes in NSC concentration and BAI, an index of the relative priority of storage versus growth, more than doubled with increasing disease severity. In contrast, twig and foliage NSC concentrations remained nearly constant with decreasing functional foliage mass. These results suggest that under disease-induced reductions in carbon supply, Douglas-fir trees retain NSCs (either actively or due to sequestration) at the expense of trunk radial growth. The crown retains the highest concentrations of NSC, presumably to maintain foliage growth and shoot extension in the spring, partially compensating for rapid foliage loss in the summer and fall.

EFFECTS OF SUCCESSION ON NITROGEN EXPORT IN THE WEST-CENTRAL CASCADES, OREGON

EPA Science Inventory

Conceptual models predict that unpolluted, aggrading forest ecosystems tightly retain available nitrogen (N) until declining productivity by mature trees and storage in detritus reduces the demand for essential nutrients, and N export increases to equal input. Short-term nitrate ...

Cell longevity and sustained primary growth in palm stems.

PubMed

Tomlinson, P Barry; Huggett, Brett A

2012-12-01

Longevity, or organismal life span, is determined largely by the period over which constituent cells can function metabolically. Plants, with modular organization (the ability continually to develop new organs and tissues) differ from animals, with unitary organization (a fixed body plan), and this difference is reflected in their respective life spans, potentially much longer in plants than animals. We draw attention to the observation that palm trees, as a group of monocotyledons without secondary growth comparable to that of lignophytes (plants with secondary growth from a bifacial cambium), retain by means of sustained primary growth living cells in their trunks throughout their organismal life span. Does this make palms the longest-lived trees because they can grow as individuals for several centuries? No conventional lignophyte retains living metabolically active differentiated cell types in its trunk for this length of time, even though the tree as a whole can exist for millennia. Does this contrast also imply that the long-lived cells in a palm trunk have exceptional properties, which allows this seeming immortality? We document the long-life of many tall palm species and their inherent long-lived stem cell properties, comparing such plants to conventional trees. We provide a summary of aspects of cell age and life span in animals and plants. Cell replacement is a feature of animal function, whereas conventional trees rely on active growth centers (meristems) to sustain organismal development. However, the long persistence of living cells in palm trunks is seen not as evidence for unique metabolic processes that sustain longevity, but is a consequence of unique constructional features. This conclusion suggests that the life span of plant cells is not necessarily genetically determined.

NITROGEN FLUX FROM WEST CASCADE RANGE HEADWATER STREAMS DRAINING FORESTS ALONG A SUCCESSIONAL GRADIENT

EPA Science Inventory

Conceptual models predict that unpolluted, aggrading forest ecosystems tightly retain available nitrogen (N) until declining productivity by mature trees reduces the demand for essential nutrients and export increases to equal N inputs. Short-term nitrate loss following disturban...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Emms, David M.; Covshoff, Sarah; Hibberd, Julian M.

C4 photosynthesis is considered one of the most remarkable examples of evolutionary convergence in eukaryotes. However, it is unknown whether the evolution of C4 photosynthesis required the evolution of new genes. Genome-wide gene-tree species-tree reconciliation of seven monocot species that span two origins of C4 photosynthesis revealed that there was significant parallelism in the duplication and retention of genes coincident with the evolution of C4 photosynthesis in these lineages. Specifically, 21 orthologous genes were duplicated and retained independently in parallel at both C4 origins. Analysis of this gene cohort revealed that the set of parallel duplicated and retained genes ismore » enriched for genes that are preferentially expressed in bundle sheath cells, the cell type in which photosynthesis was activated during C4 evolution. Moreover, functional analysis of the cohort of parallel duplicated genes identified SWEET-13 as a potential key transporter in the evolution of C4 photosynthesis in grasses, and provides new insight into the mechanism of phloem loading in these C4 species.« less

CFIRP: What we learned in the first ten years

USGS Publications Warehouse

Chambers, C.L.; McComb, W.C.; Tappeiner, J. C.; Kellogg, L.D.; Johnson, R.L.; Spycher, G.

1999-01-01

In response to public dissatisfaction with forest management methods, we initiated the College of Forestry Integrated Research Project (CFIRP) to test alternative silvicultural systems in Douglas-fir (Pseudotsuga menziesii stands in western Oregon. We compared costs and biological and human responses among a control and three replicated silvicultural alternatives to clearcutting that retained structural features found in old Douglas-fir forests. Treatments were applied within 8- to 15-ha stands and attempted to mimic crown fires (modified clearcut), windthrow (green tree retention), and small-scale impacts such as root rot diseases (small patch group selection). We also compared costs in three unreplicated treatments (large patch group selection, wedge cut, and strip cut). Each treatment included differences in the pattern of retained dead trees (snags), as either scattered individuals or as clumps. Good communication among researchers and managers, a long-term commitment to the project, and careful documentation of research sites and data are important to the success of long-term silvicultural research projects. To date, over 30 publications have resulted from the project.

Fragment-based prediction of skin sensitization using recursive partitioning

NASA Astrophysics Data System (ADS)

Lu, Jing; Zheng, Mingyue; Wang, Yong; Shen, Qiancheng; Luo, Xiaomin; Jiang, Hualiang; Chen, Kaixian

2011-09-01

Skin sensitization is an important toxic endpoint in the risk assessment of chemicals. In this paper, structure-activity relationships analysis was performed on the skin sensitization potential of 357 compounds with local lymph node assay data. Structural fragments were extracted by GASTON (GrAph/Sequence/Tree extractiON) from the training set. Eight fragments with accuracy significantly higher than 0.73 ( p < 0.1) were retained to make up an indicator descriptor fragment. The fragment descriptor and eight other physicochemical descriptors closely related to the endpoint were calculated to construct the recursive partitioning tree (RP tree) for classification. The balanced accuracy of the training set, test set I, and test set II in the leave-one-out model were 0.846, 0.800, and 0.809, respectively. The results highlight that fragment-based RP tree is a preferable method for identifying skin sensitizers. Moreover, the selected fragments provide useful structural information for exploring sensitization mechanisms, and RP tree creates a graphic tree to identify the most important properties associated with skin sensitization. They can provide some guidance for designing of drugs with lower sensitization level.

Tree Growth Response to Drought Along a Depth to Groundwater Gradient in Northern Wisconsin

NASA Astrophysics Data System (ADS)

Ciruzzi, D. M.; Loheide, S. P., II

2017-12-01

Understanding complex spatial and temporal patterns of drought-induced forest stress requires knowledge of the physiological drivers and ecosystem attributes that lead to or inhibit tree mortality. Prevailing meteorological conditions leading to drought may have lesser effect on vegetation that has evolved to avoid drought by accessing deeper soil moisture reserves or shallow groundwater to meet evapotranspiration demand. This is especially true in arid and semi-arid regions, yet groundwater use by trees is rarely explored in temperate systems and the extent to which groundwater use reduces drought vulnerability in these climates and regions is unknown. We explored responses of radial growth in temperate tress to wet and dry years across a depth to groundwater gradient from 1 to 9 meters in sandy forests in northern Wisconsin. The spatial patterns of tree growth in this watershed show areas where tree growth is influenced by depth to groundwater. Preliminary results showed trees in areas of shallower groundwater with low variability in tree growth and indicated that tree growth remains consistent during both wet and dry years. Conversely, trees in areas of deeper groundwater showed higher variability in tree growth during wet and dry years. We hypothesize that even in this humid region, the sandy soils do not retain sufficient moisture leading to potentially frequent water stress in trees and reductions in productivity. However, where and when accessible, we suspect trees use shallow groundwater to sustain evapotranspiration and maintain consistent growth during dry periods.

Riparian Protection Rules for Oregon Forests

Treesearch

George G. Ice; Robert L. Beschta; Raymond S. Craig; James R. Sedell

1989-01-01

Forest Practice Rules under the Oregon Forest Practices Act were modified in 1987 to increase protection of riparian areas adjacent to timber harvest operations. These modifications addressed concerns about water quality protection and retaining trees as sources of large woody debris for future stream channel structure. The rule changes triggered debate about the...

Relationship of shoot dieback in pecan to fungi and fruiting stress

USDA-ARS?s Scientific Manuscript database

Two shoot dieback maladies (SDM) of pecan [Carya illinoinensis (Wangenh.) C. Koch] are of unknown cause and can adversely affect tree canopy health. They occur during either early spring (SpSDM) or early summer (SuSDM). Field studies found that both maladies predominately occur on shoots retaining...

Economic analysis of emerald ash borer (Coleoptera: Buprestidae) management options.

PubMed

Vannatta, A R; Hauer, R H; Schuettpelz, N M

2012-02-01

Emerald ash borer, Agrilus planipennis (Fairmaire) (Coleoptera: Buprestidae), plays a significant role in the health and extent of management of native North American ash species in urban forests. An economic analysis of management options was performed to aid decision makers in preparing for likely future infestations. Separate ash tree population valuations were derived from the i-Tree Streets program and the Council of Tree and Landscape Appraisers (CTLA) methodology. A relative economic analysis was used to compare a control option (do-nothing approach, only removing ash trees as they die) to three distinct management options: 1) preemptive removal of all ash trees over a 5 yr period, 2) preemptive removal of all ash trees and replacement with comparable nonash trees, or 3) treating the entire population of ash trees with insecticides to minimize mortality. For each valuation and management option, an annual analysis was performed for both the remaining ash tree population and those lost to emerald ash borer. Retention of ash trees using insecticide treatments typically retained greater urban forest value, followed by doing nothing (control), which was better than preemptive removal and replacement. Preemptive removal without tree replacement, which was the least expensive management option, also provided the lowest net urban forest value over the 20-yr simulation. A "no emerald ash borer" scenario was modeled to further serve as a benchmark for each management option and provide a level of economic justification for regulatory programs aimed at slowing the movement of emerald ash borer.

Remnant trees affect species composition but not structure of tropical second-growth forest.

PubMed

Sandor, Manette E; Chazdon, Robin L

2014-01-01

Remnant trees, spared from cutting when tropical forests are cleared for agriculture or grazing, act as nuclei of forest regeneration following field abandonment. Previous studies on remnant trees were primarily conducted in active pasture or old fields abandoned in the previous 2-3 years, and focused on structure and species richness of regenerating forest, but not species composition. Our study is among the first to investigate the effects of remnant trees on neighborhood forest structure, biodiversity, and species composition 20 years post-abandonment. We compared the woody vegetation around individual remnant trees to nearby plots without remnant trees in the same second-growth forests ("control plots"). Forest structure beneath remnant trees did not differ significantly from control plots. Species richness and species diversity were significantly higher around remnant trees. The species composition around remnant trees differed significantly from control plots and more closely resembled the species composition of nearby old-growth forest. The proportion of old-growth specialists and generalists around remnant trees was significantly greater than in control plots. Although previous studies show that remnant trees may initially accelerate secondary forest growth, we found no evidence that they locally affect stem density, basal area, and seedling density at later stages of regrowth. Remnant trees do, however, have a clear effect on the species diversity, composition, and ecological groups of the surrounding woody vegetation, even after 20 years of forest regeneration. To accelerate the return of diversity and old-growth forest species into regrowing forest on abandoned land, landowners should be encouraged to retain remnant trees in agricultural or pastoral fields.

Remnant Trees Affect Species Composition but Not Structure of Tropical Second-Growth Forest

PubMed Central

Sandor, Manette E.; Chazdon, Robin L.

2014-01-01

Remnant trees, spared from cutting when tropical forests are cleared for agriculture or grazing, act as nuclei of forest regeneration following field abandonment. Previous studies on remnant trees were primarily conducted in active pasture or old fields abandoned in the previous 2–3 years, and focused on structure and species richness of regenerating forest, but not species composition. Our study is among the first to investigate the effects of remnant trees on neighborhood forest structure, biodiversity, and species composition 20 years post-abandonment. We compared the woody vegetation around individual remnant trees to nearby plots without remnant trees in the same second-growth forests (“control plots”). Forest structure beneath remnant trees did not differ significantly from control plots. Species richness and species diversity were significantly higher around remnant trees. The species composition around remnant trees differed significantly from control plots and more closely resembled the species composition of nearby old-growth forest. The proportion of old-growth specialists and generalists around remnant trees was significantly greater than in control plots. Although previous studies show that remnant trees may initially accelerate secondary forest growth, we found no evidence that they locally affect stem density, basal area, and seedling density at later stages of regrowth. Remnant trees do, however, have a clear effect on the species diversity, composition, and ecological groups of the surrounding woody vegetation, even after 20 years of forest regeneration. To accelerate the return of diversity and old-growth forest species into regrowing forest on abandoned land, landowners should be encouraged to retain remnant trees in agricultural or pastoral fields. PMID:24454700

Geospatial Technologies and i-Tree Echo Inventory for Predicting Climate Change on Urban Environment

NASA Astrophysics Data System (ADS)

Sriharan, S.; Robinson, L.; Ghariban, N.; Comar, M.; Pope, B.; Frey, G.

2015-12-01

Urban forests can be useful both in mitigating climate change and in helping cities adapt to higher temperatures and other impacts of climate change. Understanding and managing the impacts of climate change on the urban forest trees and natural communities will help us maintain their environmental, cultural, and economic benefits. Tree Inventory can provide important information on tree species, height, crown width, overall condition, health and maintenance needs. This presentation will demonstrate that a trees database system is necessary for developing a sustainable urban tree program. Virginia State University (VSU) campus benefits from large number and diversity of trees that are helping us by cleaning the air, retaining water, and providing shade on the buildings to reduce energy cost. The objectives of this study were to develop campus inventory of the trees, identify the tree species, map the locations of the trees with user-friendly tools such as i-Tree Eco and geospatial technologies by assessing the cost/benefit of employing student labor for training and ground validation of the results, and help campus landscape managers implement adaptive responses to climate change impacts. Data was collected on the location, species, and size of trees by using i-Tree urban forestry analysis software. This data was transferred to i-Tree inventory system for demonstrating types of trees, diameter of the trees, height of the trees, and vintage of the trees. The study site was mapped by collecting waypoints with GPS (Global Positioning System) at the trees and uploading these waypoints in ArcMap. The results of this study showed that: (i) students make good field crews, (ii) if more trees were placed in the proper area, the heating and cooling costs will reduce, and (iii) trees database system is necessary for planning, designing, planting, and maintenance, and removal of campus trees Research sponsored by the NIFA Grant, "Urban Forestry Management" (2012-38821-20153).

The production and use of wood chips from Virginia pine thinnings

Treesearch

Richard H. Fenton

1956-01-01

In most forest-management plans, attention is usually directed to certain cultural treatments early in the life of a stand. These are generally some form of weeding or thinning to favor the ultimate crop trees by cutting out a proportion of the young stand that seems least desirable to retain.

Regeneration results using two-aged management

Treesearch

Arlyn W. Perkey; Gary W. Miller; Thomas M. Schuler

1999-01-01

Two-aged management is receiving increasing consideration by central Appalachian hardwood managers as a tool to accomplish multiple landowner goals. On non-industrial private forests where aesthetics are often important, two-aged management has the attribute of retaining some relatively large trees on the area at all times. For many landowners this is critical....

Acorn production in red oak

Treesearch

Daniel C. Dey

1995-01-01

Manipulation of stand stocking through thinning can increase the amount of oak in the upper crown classes and enhance individual tree characteristics that promote good acorn production. Identification of good acorn producers before thinning or shelterwood harvests can be used to retain them in a stand. Stocking charts can be used to time thinnings and to estimate acorn...

Understory Vegetation 3 Years after Implementing Uneven-Aged Silviculture in a Shortleaf Pine-Oak Stand

Treesearch

Michael G. Shelton; Paul A. Murphy

1997-01-01

The effects of retaining overstory hardwoods on understory vegetation were determined after implementing uneven-aged silviculture usingsingle-tree selection in a shortleaf pine-oak stand (Pinus echinata Mill. and Quercus spp.) in the Ouachita Mountains. Treatments were the following hardwood basal areas (square feet per acre) and...

Vegetation succession and impacts of biointrusion on covers used to limit acid mine drainage.

PubMed

Smirnova, Evgeniya; Bussière, Bruno; Tremblay, Francine; Bergeron, Yves

2011-01-01

A cover with capillary barrier effects (CCBE) was constructed in 1998 on the abandoned Lorraine mine tailings impoundment to limit the generation of acid mine drainage. The Ministry of Natural Resources and Fauna of Quebec (MRNF) is responsible for the site and for all restoration works on it, including CCBE construction. The CCBE is made up of three layers: a 0.3-m layer of sand used as a support and capillary break layer; a moisture-retaining layer with a thickness of 0.5 m (this layer is constructed of a nonplastic silt); and a 0.3-m sand and gravel layer on top. The main objective of the CCBE is to maintain one (or more) of the layers at a high degree of water saturation to impede oxygen migration and acid generation. Vegetation succession on the Lorraine CCBE results in an improvement in soil conditions, leading to the installation of deep-rooted species, which could represent a risk to CCBE long-term performance. Hence, the characterization of vegetation succession is an important aspect of the monitoring strategy for the Lorraine CCBE. Species occurrence was documented, and depth of tree roots was measured by excavation on a regular basis. Eight functional groups of plants were identified; herbaceous plants were the most abundant ecological plant groups. Tree ring counts confirmed that tree colonization started the year of CCBE construction (1999). Of the 11 tree species identified, the most abundant were poplar (Populus spp.), paper birch (Betula payrifera Marsh.), black spruce (Picea mariana Mill.), and willow (Salix spp.). Significant differences in occurrence related to environmental conditions were observed for most functional groups. Root excavation showed that tree roots exceeded the depth of the protective layer and started to reach the moisture-retaining layer; in 2008, root average depth was 0.4 m and the maximal root depth was 1.7 m.

Evidence for host plant preference by Iphiseiodes quadripilis (Acari: Phytoseiidae) on Citrus.

PubMed

Villanueva, Raul T; Childers, Carl C

2006-01-01

In this study, we present field and laboratory evidence on the preference of Iphiseiodes quadripilis (Banks) for grapefruit (Citrus paradisi Macfadyen) leaves compared with sweet orange (Citrus sinensis (L.) Osbeck) leaves. This preference was confirmed in four orchards whether leaf samples were taken from either border trees of contiguous grapefruit or sweet orange or interior row trees with both citrus species in adjacent rows. Iphiseiodes quadripilis was most abundant in grapefruit trees in spite of the greater abundance of the Texas citrus mite, Eutetranychus banksi (McGregor) (Acari: Tetranychidae) in sweet orange trees. Similar preference responses were observed in laboratory tests using a Y-tube olfactometer whether I. quadripilis were collected from sweet orange or grapefruit. Iphiseiodes quadripilis collected from grapefruit trees showed significant preference for grapefruit over sweet orange leaves in contact choice tests using an arena of alternating leaf strips (12 mm long x 2 mm wide) of sweet orange and grapefruit. However, I. quadripilis collected from sweet orange trees did not show preference for either grapefruit or sweet orange leaves. Based on these results, grapefruit leaves foster some unknown factor or factors that retain I. quadripilis in greater numbers compared with sweet orange leaves.

Living on the edge: Fig tree phenology at the northern range limit of monoecious Ficus in China

NASA Astrophysics Data System (ADS)

Zhang, Lu-Shui; Compton, Stephen G.; Xiao, Hui; Lu, Qian; Chen, Yan

2014-05-01

Fig trees (Ficus) are a species-rich group of mainly tropical and subtropical plants that are of ecological importance because of the large numbers of vertebrates that utilise their figs for food. Factors limiting their distributions to warmer regions are still poorly understood, but are likely to include factors linked to their specialised pollination biology, because each Ficus species is dependent on one or a small number of host-specific fig wasps (Agaonidae) for pollination. Adult fig wasps are short-lived, but some species are capable of dispersing extremely long distances to pollinate their hosts. Close to its northern range limit we investigated the phenology of Ficus virens, the monoecious fig tree that reaches furthest north in China. Relatively few trees produced any figs, and very few retained figs throughout the winter. Despite this, new crops produced in spring were pollinated, with seasonally migrant pollinators from plants growing further south the most likely pollen vectors. An inability to initiate new crops at low temperatures may limit the distribution of monoecious fig trees to warmer areas.

Positive versus negative environmental impacts of tree encroachment in South Africa

NASA Astrophysics Data System (ADS)

Grellier, Séraphine; Ward, David; Janeau, Jean-Louis; Podwojewski, Pascal; Lorentz, Simon; Abbadie, Luc; Valentin, Christian; Barot, Sébastien

2013-11-01

Woody plant encroachment in grasslands is a worldwide phenomenon. Despite many studies, the consequences of woody plant encroachment on sub-canopy vegetation and soil properties are still unclear. To better understand the impacts of trees on grassland properties we examined the following questions using a mountainous sub-tropical grassland of South Africa encroached by an indigenous tree, Acacia sieberiana as a case study: (1) Do trees increase sub-canopy herbaceous diversity, quality and biomass and soil nitrogen content? (2) Do large trees have a stronger effect than medium-sized trees on grass and soil properties? (3) Does the impact of trees change with the presence of livestock and position of trees in a catena? We studied grass and non-graminoid species diversity and biomass, grass quality and soil properties during the wet season of 2009. Nitrogen in grass leaves, soil cation exchange capacity and calcium and magnesium ion concentrations in the soil increased under tall Acacia versus open areas. Medium-sized Acacia decreased the gross energy content, digestibility and neutral detergent fibre of grasses but increased the species richness of non-graminoids. Tall and medium Acacia trees were associated with the presence of Senecio inaequidens, an indigenous species that is toxic to horses and cattle. The presence of livestock resulted in a decrease in herbaceous root biomass and an increase in soil carbon and leaf biomass of grass under Acacia. Tree position in the catena did not modify the impact of trees on the herbaceous layer and soil properties. For management of livestock we recommend retaining tall Acacia trees and partially removing medium-sized Acacia trees because the latter had negative effects on grass quality.

Rapid tree carbon stock recovery in managed Amazonian forests.

PubMed

Rutishauser, Ervan; Hérault, Bruno; Baraloto, Christopher; Blanc, Lilian; Descroix, Laurent; Sotta, Eleneide Doff; Ferreira, Joice; Kanashiro, Milton; Mazzei, Lucas; d'Oliveira, Marcus V N; de Oliveira, Luis C; Peña-Claros, Marielos; Putz, Francis E; Ruschel, Ademir R; Rodney, Ken; Roopsind, Anand; Shenkin, Alexander; da Silva, Katia E; de Souza, Cintia R; Toledo, Marisol; Vidal, Edson; West, Thales A P; Wortel, Verginia; Sist, Plinio

2015-09-21

While around 20% of the Amazonian forest has been cleared for pastures and agriculture, one fourth of the remaining forest is dedicated to wood production. Most of these production forests have been or will be selectively harvested for commercial timber, but recent studies show that even soon after logging, harvested stands retain much of their tree-biomass carbon and biodiversity. Comparing species richness of various animal taxa among logged and unlogged forests across the tropics, Burivalova et al. found that despite some variability among taxa, biodiversity loss was generally explained by logging intensity (the number of trees extracted). Here, we use a network of 79 permanent sample plots (376 ha total) located at 10 sites across the Amazon Basin to assess the main drivers of time-to-recovery of post-logging tree carbon (Table S1). Recovery time is of direct relevance to policies governing management practices (i.e., allowable volumes cut and cutting cycle lengths), and indirectly to forest-based climate change mitigation interventions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Calibrated birth-death phylogenetic time-tree priors for bayesian inference.

PubMed

Heled, Joseph; Drummond, Alexei J

2015-05-01

Here we introduce a general class of multiple calibration birth-death tree priors for use in Bayesian phylogenetic inference. All tree priors in this class separate ancestral node heights into a set of "calibrated nodes" and "uncalibrated nodes" such that the marginal distribution of the calibrated nodes is user-specified whereas the density ratio of the birth-death prior is retained for trees with equal values for the calibrated nodes. We describe two formulations, one in which the calibration information informs the prior on ranked tree topologies, through the (conditional) prior, and the other which factorizes the prior on divergence times and ranked topologies, thus allowing uniform, or any arbitrary prior distribution on ranked topologies. Although the first of these formulations has some attractive properties, the algorithm we present for computing its prior density is computationally intensive. However, the second formulation is always faster and computationally efficient for up to six calibrations. We demonstrate the utility of the new class of multiple-calibration tree priors using both small simulations and a real-world analysis and compare the results to existing schemes. The two new calibrated tree priors described in this article offer greater flexibility and control of prior specification in calibrated time-tree inference and divergence time dating, and will remove the need for indirect approaches to the assessment of the combined effect of calibration densities and tree priors in Bayesian phylogenetic inference. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

New Directions in Education Research: Using Data Mining Techniques to Explore Predictors of Grade Retention

ERIC Educational Resources Information Center

Kelley-Winstead, Deanna

2010-01-01

The purpose of this study was to use classification trees and logistic regression to identify subgroups of students more likely to be retained. The National Educational Longitudinal Study of 1988 (NELS:88) was used to identify the sociodemographic, family background and school related factors associated with grade retention. The sample size for…

Forest-floor disturbance reduces chipmunk (Tamias spp.) abundance two years after variable-retention harvest of Pacific Northwestern forests

Treesearch

Randall J. Wilk; Timothy B. Harrington; Robert A. Gitzen; Chris C. Maguire

2015-01-01

We evaluated the two-year effects of variable-retention harvest on chipmunk (Tamias spp.) abundance (N^) and habitat in mature coniferous forests in western Oregon and Washington because wildlife responses to density/pattern of retained trees remain largely unknown. In a randomized complete-block design, six...

Disturbance From the Initial Harvest Implementing Uneven-Aged Silviculture in a Pine-Hardwood Stand in Southwestern Mississippi

Treesearch

Michael G. Shelton; Paul A. Murphy

1999-01-01

Logging disturbance is important in uneven-aged stands because harvests are frequent, merchantable trees are retained, and regeneration may be present. Logging disturbance was monitored during the establishment of a study testing the application of uneven-aged silvicufture in an irregularly aged, pine-hardwood stand. Disturbances were: (1) seedbed conditions...

Biomass utilization opportunities to achieve diverse silvicultural goals

Treesearch

Barry Wynsma; Christopher R. Keyes

2010-01-01

Silviculturists and ecologists may recommend land management prescriptions that are designed to be resilient to changing climatic conditions. When considering biomass utilization opportunities that may result from climate-change treatments, it really doesn’t matter what species mix or stocking levels are to be retained: if there are trees that need to be harvested,...

Mortality and growth of dwarf mistletoe-infected red and white fir and the efficacy of thinning for reducing associated losses

Treesearch

H. K. Mehl; S. R. Mori; S. J. Frankel; D. M. Rizzo

2013-01-01

In managed forests dominated by true fir (Abies) species, stands are often restocked using understory trees retained during timber harvest, making the effects of dwarf mistletoe (Arceuthobium spp.) infestation on small true fir a concern. This study examined the response of small red (A. magnifica) and...

Long-term impacts of variable retention harvesting on ground-layer plant communities in Pinus resinosa forests

Treesearch

Margaret W. Roberts; Anthony W. D' Amato; Christel C. Kern; Brian J. Palik; Lorenzo Marini

2016-01-01

Concerns about loss of biodiversity and structural complexity in managed forests have recently increased and led to the development of new management strategies focused on restoring or maintaining ecosystem functions while also providing wood outputs. Variable retention harvest (VRH) systems, in which mature overstorey trees are retained in various spatial arrangements...

Seasonal Distributions of the Western Cherry Fruit Fly (Diptera: Tephritidae) Among Host and Nonhost Fruit Trees

PubMed Central

Yee, Wee L.

2014-01-01

Abstract Seasonal distributions of the western cherry fruit fly, Rhagoletis indifferens Curran (Diptera: Tephritidae), in sweet cherry ( Prunus avium (L.) L.) (major host), black hawthorn (occasional developmental host) ( Crataegus douglasii Lindley), and other trees were determined in a ponderosa pine ecosystem in Washington state, USA. The hypothesis that most fly dispersal from cherry trees occurs after fruit senesce or drop was tested, with emphasis on movement to black hawthorn trees. Sweet cherry fruit developed earlier than black hawthorn, bitter cherry (common host), choke cherry, and apple fruit. Flies were usually captured first in sweet cherry trees but were caught in bitter cherry and other trees throughout the season. Peak fly capture periods in sweet cherry began around the same time or slightly earlier than in other trees. However, peak fly capture periods in black hawthorn and other nonsweet cherry trees continued after peak periods in sweet cherry ended, or relative fly numbers within sweet cherry declined more quickly than those within other trees. Larvae were reared from sweet and bitter cherry but not black hawthorn fruit. Results provide partial support for the hypothesis in that although R. indifferens commonly disperses from sweet cherry trees with fruit, it could disperse more, or more flies are retained in nonsweet cherry trees after than before sweet cherries drop. This could allow opportunities for the flies to use other fruit for larval development. Although R . indifferens infestation in black hawthorn was not detected, early season fly dispersal to this and other trees and fly presence in bitter cherry could make fly management in sweet cherry difficult. PMID:25527581

Seasonal distributions of the western cherry fruit fly (Diptera: Tephritidae) among host and nonhost fruit trees.

PubMed

Yee, Wee L

2014-01-01

Seasonal distributions of the western cherry fruit fly, Rhagoletis indifferens Curran (Diptera: Tephritidae), in sweet cherry (Prunus avium (L.) L.) (major host), black hawthorn (occasional developmental host) (Crataegus douglasii Lindley), and other trees were determined in a ponderosa pine ecosystem in Washington state, USA. The hypothesis that most fly dispersal from cherry trees occurs after fruit senesce or drop was tested, with emphasis on movement to black hawthorn trees. Sweet cherry fruit developed earlier than black hawthorn, bitter cherry (common host), choke cherry, and apple fruit. Flies were usually captured first in sweet cherry trees but were caught in bitter cherry and other trees throughout the season. Peak fly capture periods in sweet cherry began around the same time or slightly earlier than in other trees. However, peak fly capture periods in black hawthorn and other nonsweet cherry trees continued after peak periods in sweet cherry ended, or relative fly numbers within sweet cherry declined more quickly than those within other trees. Larvae were reared from sweet and bitter cherry but not black hawthorn fruit. Results provide partial support for the hypothesis in that although R. indifferens commonly disperses from sweet cherry trees with fruit, it could disperse more, or more flies are retained in nonsweet cherry trees after than before sweet cherries drop. This could allow opportunities for the flies to use other fruit for larval development. Although R. indifferens infestation in black hawthorn was not detected, early season fly dispersal to this and other trees and fly presence in bitter cherry could make fly management in sweet cherry difficult. Published by Oxford University Press on behalf of the Entomological Society of America 2014. This work is written by a US Government employee and is in the public domain in the US.

Dying piece by piece: carbohydrate dynamics in aspen seedlings under severe carbon stress and starvation

NASA Astrophysics Data System (ADS)

Wiley, Erin; Chow, Pak; Landhäusser, Simon

2016-04-01

Carbon stress and starvation remain poorly understood in trees, despite their potential role in mortality from a variety of agents. To explore the effects of carbon stress on nonstructural carbohydrate (NSC) dynamics and recovery potential and to examine the process of starvation, we grew aspen seedlings under one of three levels of shade: 40% (light shade), 8% (medium shade), and 4% (dark shade) of full sunlight. We then exposed seedlings to 24 hours darkness at either 20° or 28° C until trees had died. Periodically, seedlings were harvested for NSC analysis and to measure stem and root respiration. In addition, some seedlings were moved back into the light to determine if recovery was possible at certain points during starvation. Specifically, we sought to address the following questions: 1) Do NSC concentrations or mass influence tree survival under carbon stress? 2) At what carbohydrate levels do trees fail to recover and starve? 3) Does temperature affect the NSC level at which trees starve? Increasing shade reduced growth, but surprisingly did not reduce NSC levels, except in a portion of deep shade seedlings that experienced dieback. Once in darkness, leaves died first, with final NSC levels ranging from ~4% (Medium shade, 28 degrees) to 7.5% (Light shade). Stem death generally occurred gradually down the stem. Stem tissues retained ~1-2% NSC when dead. Recovery was still possible when only the upper half of the stem had died; at this point, seedlings had relatively high root NSC levels in their remaining roots (7-10%), with 1-3% starch. No trees recovered after the whole stem had died, at which point, some trees root systems were completely dead. However, most retained substantial amounts of live roots, averaging 5-6% NSC, with 0.25-1.5% starch. Despite the initially similar NSC concentrations, light shade seedlings took longer to reach half stem and whole stem death than seedlings from medium and dark shade. Longer survival times were associated with greater initial NSC pool sizes and lower mass-specific respiration rates. Higher temperatures reduced the time until tissue death and also tended to reduce NSC levels at death in some tissues. Survival time during starvation appeared to be controlled not only by the size of initial reserves, but by the rate of respiration. Relatively high leaf NSC levels of dead leaves observed during drought and during fall leaf abscission are within the range of leaf NSC levels of starved leaves seen here. Patterns of nonzero tissue NSC and the piecewise progression of mortality often observed in mature trees are not inconsistent with the process of carbon starvation, which may contribute to tree death by many causes.

Spray deposition from ground-based applications of carbaryl to protect individual trees from bark beetle attack.

PubMed

Fettig, Christopher J; Munson, A Steven; McKelvey, Stephen R; Bush, Parshall B; Borys, Robert R

2008-01-01

Bark beetles (Coleoptera: Curculionidae, Scolytinae) are recognized as the most important tree mortality agent in western coniferous forests. A common method of protecting trees from bark beetle attack is to saturate the tree bole with carbaryl (1-naphthyl methylcarbamate) using a hydraulic sprayer. In this study, we evaluate the amount of carbaryl drift (ground deposition) occurring at four distances from the tree bole (7.6, 15.2, 22.9, and 38.1 m) during conventional spray applications for protecting individual lodgepole pine (Pinus contorta Dougl. ex Loud.) from mountain pine beetle (Dendroctonus ponderosae Hopkins) attack and Engelmann spruce (Picea engelmannii Parry ex Engelm.) from spruce beetle (D. rufipennis [Kirby]) attack. Mean deposition (carbaryl + alpha-naphthol) did not differ significantly among treatments (nozzle orifices) at any distance from the tree bole. Values ranged from 0.04 +/- 0.02 mg carbaryl m(-2) at 38.1 m to 13.30 +/- 2.54 mg carbaryl m(-2) at 7.6 m. Overall, distance from the tree bole significantly affected the amount of deposition. Deposition was greatest 7.6 m from the tree bole and quickly declined as distance from the tree bole increased. Approximately 97% of total spray deposition occurred within 15.2 m of the tree bole. Application efficiency (i.e., percentage of insecticide applied that is retained on trees) ranged from 80.9 to 87.2%. Based on review of the literature, this amount of drift poses little threat to adjacent aquatic environments. No-spray buffers of 7.6 m should be sufficient to protect freshwater fish, amphibians, crustaceans, bivalves, and most aquatic insects. Buffers >22.9 m appear sufficient to protect the most sensitive aquatic insects (Plecoptera).

In-vitro activity of essential oils, in particular Melaleuca alternifolia (tea tree) oil and tea tree oil products, against Candida spp.

PubMed

Hammer, K A; Carson, C F; Riley, T V

1998-11-01

The in-vitro activity of a range of essential oils, including tea tree oil, against the yeast candida was examined. Of the 24 essential oils tested by the agar dilution method against Candida albicans ATCC 10231, three did not inhibit C. albicans at the highest concentration tested, which was 2.0% (v/v) oil. Sandalwood oil had the lowest MIC, inhibiting C. albicans at 0.06%. Melaleuca alternifolia (tea tree) oil was investigated for activity against 81 C. albicans isolates and 33 non-albicans Candida isolates. By the broth microdilution method, the minimum concentration of oil inhibiting 90% of isolates for both C. albicans and non-albicans Candida species was 0.25% (v/v). The minimum concentration of oil killing 90% of isolates was 0.25% for C. albicans and 0.5% for non-albicans Candida species. Fifty-seven Candida isolates were tested for sensitivity to tea tree oil by the agar dilution method; the minimum concentration of oil inhibiting 90% of isolates was 0.5%. Tests on three intra-vaginal tea tree oil products showed these products to have MICs and minimum fungicidal concentrations comparable to those of non-formulated tea tree oil, indicating that the tea tree oil contained in these products has retained its anticandidal activity. These data indicate that some essential oils are active against Candida spp., suggesting that they may be useful in the topical treatment of superficial candida infections.

Recursive optimal pruning with applications to tree structured vector quantizers

NASA Technical Reports Server (NTRS)

Kiang, Shei-Zein; Baker, Richard L.; Sullivan, Gary J.; Chiu, Chung-Yen

1992-01-01

A pruning algorithm of Chou et al. (1989) for designing optimal tree structures identifies only those codebooks which lie on the convex hull of the original codebook's operational distortion rate function. The authors introduce a modified version of the original algorithm, which identifies a large number of codebooks having minimum average distortion, under the constraint that, in each step, only modes having no descendents are removed from the tree. All codebooks generated by the original algorithm are also generated by this algorithm. The new algorithm generates a much larger number of codebooks in the middle- and low-rate regions. The additional codebooks permit operation near the codebook's operational distortion rate function without time sharing by choosing from the increased number of available bit rates. Despite the statistical mismatch which occurs when coding data outside the training sequence, these pruned codebooks retain their performance advantage over full search vector quantizers (VQs) for a large range of rates.

Using convolutional neural networks to explore the microbiome.

PubMed

Reiman, Derek; Metwally, Ahmed; Yang Dai

2017-07-01

The microbiome has been shown to have an impact on the development of various diseases in the host. Being able to make an accurate prediction of the phenotype of a genomic sample based on its microbial taxonomic abundance profile is an important problem for personalized medicine. In this paper, we examine the potential of using a deep learning framework, a convolutional neural network (CNN), for such a prediction. To facilitate the CNN learning, we explore the structure of abundance profiles by creating the phylogenetic tree and by designing a scheme to embed the tree to a matrix that retains the spatial relationship of nodes in the tree and their quantitative characteristics. The proposed CNN framework is highly accurate, achieving a 99.47% of accuracy based on the evaluation on a dataset 1967 samples of three phenotypes. Our result demonstrated the feasibility and promising aspect of CNN in the classification of sample phenotype.

Ecological forestry in an uneven-aged, late-successional forest: Simulated effects of contrasting treatments on structure and yield

Treesearch

Jacob J. Hanson; Craig G. Lorimer; Corey R. Halpin; Brian J. Palik

2012-01-01

Ecological forestry practices are designed to retain species and structural features important for maintaining ecosystem function but which may be deficient in conventionally managed stands. We used the spatially-explicit, individual tree model CANOPY to assess tradeoffs in enhanced ecological attributes vs. reductions in timber yield for a wide variety of treatments...

Long-term regeneration responses to overstory retention and understory vegetation treatments in the northern Rocky Mountains

Treesearch

Woongsoon Jang; Christopher R. Keyes; Deborah S. Page-Dumroese

2017-01-01

Classic regeneration cuttings retaining trees at harvest (shelterwood with reserves, group selection) can be analyzed as analogs of variable-retention harvesting. A 1974 silvicultural experiment in the northern Rocky Mountains was analyzed at 38 years to evaluate the long-term effects of retention harvests on stand development, with a focus on both regeneration and...

Restoration of Aspen-Dominated Ecosystem in the Lake States

Treesearch

Douglas M. Stone; John D. Elioff; Donald V. Potter; Donald B. Peterson; Robert Wagner

2001-01-01

A reserve tree method(RTM)of harvesting was installed in six 70-to75-year-old aspen-dominated stands to determine if retaining 10 to 15 dominant aspen per acre would decrease sucker density to facilitate restoration of a conifer component. A reserve shelterwood cut was applied to three additional stands to evaluate performance of white pine planted under 50% crown...

Restoration of aspen-dominated ecosystems in the Lake States

Treesearch

Douglas M. Stone; John D. Elioff; Donald V. Potter; Donald B. Peterson; Robert Wagner

2000-01-01

A reserve tree method (RTM) of harvesting was installed in six 70-to75-year old aspen-dominated stands to determine if retaining 10 to 15 dominant aspen per acre would decrease sucker density to facilitate restoration of a conifer component. A reserve shelterwood cut was applied to three additional stands to evaluate performance of white pine planted under 50% crown...

Restoration of aspen-dominated ecosystems in the Lake States

Treesearch

Douglas M. Stone; John D. Elioff; Donald V. Potter; Donald B. Peterson; Robert Wagner

2001-01-01

A reserve tree method (RTM) of harvesting was installed in six 70- to 75-yearold aspen-dominated stands to determine if retaining 10 to 15 dominant aspen per acre would decrease sucker density to facilitate restoration of a conifer component. A reserve shelterwood cut was applied to three additional stands to evaluate performance of white pine planted under 50% crown...

Germination of Cherrybark and Nuttal Oak Acorns Following Flooding

Treesearch

C. B. Briscoe

1961-01-01

Frequency and duration of flooding is undoubtedly one of the most important environmental factors affecting species distribution in bottomland forests. In the life of a tree this influence is first exerted on the seed, and the capacity of seeds to retain viability after submergence by flood water may well be an important factor in determining the success of a species...

An 800-year fire history

Treesearch

Stanley G. Kitchen

2010-01-01

"Fire in the woods!" The words are a real heart stopper. Yet in spite of its capacity to destroy, fire plays an essential role in shaping plant communities. Knowledge of the patterns of fire over long time periods is critical for understanding this role. Trees often retain evidence of nonlethal fires in the form of injuries or scars in the annual growth rings...

Developing and managing sustainable forest ecosystems for spotted owls in the Sierra Nevada

Treesearch

J. Verner; K.S. McKelvey

1994-01-01

Studies of the California spotted owl have revealed significant selection for habitats with large, old trees; relatively high basal areas of snags; and relatively high biomass in large, downed logs. Based on planning documents for national forests in the Sierra Nevada, we projected declining amounts of older-forest attributes. Region 5 has adopted measures to retain...

Effects of overstory stand density and fire on ground layer vegetation in oak woodland and savanna habitats

Treesearch

John B. Taft

2009-01-01

Vegetation changes underway in oak woodland and savanna communities in the eastern and midwestern United States, primarily a result of reduced fire frequency or fire absence, include increased tree density and shading and loss of species diversity in the ground layer. However, some habitats, particularly on dry-mesic to xeric sites, retain considerable restoration...

Underplanting Shortleaf Pine Seedlings Beneath a Residual Hardwood Stand in the Ouachita Mountains: Results after Seven Growing Seasons

Treesearch

James M. Guldin; Gerald Heath

2001-01-01

An unreplicated demonstration was established in the Ouachita Mountains in which shortleaf pine (Pinus echinata Mill.) trees were harvested and overstory hardwoods were retained. A new stand was established by underplanting shortleaf pine seedlings. After the third growing season, five 0.5-acre plots were established, and one of five overstory...

Belowground carbon cycling in a humid tropical forest decreases with fertilization

Treesearch

C. Giardina; D. Binkley; M. Ryan; J. Fownes

2004-01-01

Only a small fraction of the carbon (C) allocated belowground by trees is retained by soils in long-lived, decay-resistant forms, yet because of the large magnitude of terrestrial primary productivity, even small changes in C allocation or retention can alter terrestrial C storage. The humid tropics exert a disproportionately large influence over terrestrial C storage...

Independent and parallel evolution of new genes by gene duplication in two origins of C4 photosynthesis provides new insight into the mechanism of phloem loading in C4 species

DOE PAGES

Emms, David M.; Covshoff, Sarah; Hibberd, Julian M.; ...

2016-03-24

C4 photosynthesis is considered one of the most remarkable examples of evolutionary convergence in eukaryotes. However, it is unknown whether the evolution of C4 photosynthesis required the evolution of new genes. Genome-wide gene-tree species-tree reconciliation of seven monocot species that span two origins of C4 photosynthesis revealed that there was significant parallelism in the duplication and retention of genes coincident with the evolution of C4 photosynthesis in these lineages. Specifically, 21 orthologous genes were duplicated and retained independently in parallel at both C4 origins. Analysis of this gene cohort revealed that the set of parallel duplicated and retained genes ismore » enriched for genes that are preferentially expressed in bundle sheath cells, the cell type in which photosynthesis was activated during C4 evolution. Moreover, functional analysis of the cohort of parallel duplicated genes identified SWEET-13 as a potential key transporter in the evolution of C4 photosynthesis in grasses, and provides new insight into the mechanism of phloem loading in these C4 species.« less

Treatment of an old-growth stand and its effects on birds, ants, and large woody debris: A case study. Forest Service general technical report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bull, E.L.; Torgersen, T.R.; Blumton, A.K.

1995-09-01

An old-structure stand with large amounts of tree mortality was treated to accelerate regeneration and reduce fuel loads but still maintain its function as old growth for selected bird species. The smll-diameter (less than 15 inches in diameter at breast height (d.b.h.)), dead trees were removed as was some of the down wood less than 15 inches in diameter at the large end. All live trees of any size and all dead trees equal to or greater than 15 inches d.b.h. were retained. Vaux`s swifts (Chaetura vauxi) and pileated woodpeckers (Dryocopus pileatus) continued to use the stand after harvest formore » nesting and roosting. Brown-headed cowbirds (molothrus ater) were more than twice as common in the treated stand as in an adjacent unlogged, control stand. In a comparison before and after harvest in the treated stand, the number of logs increased, the number of logs with ants increased, but the percentage of logs with ants decreased.« less

Genetic evaluation of the Association of Zoos and Aquariums Matschie's tree kangaroo (Dendrolagus matschiei) captive breeding program.

PubMed

McGreevy, Thomas J; Dabek, Lisa; Husband, Thomas P

2011-01-01

Matschie's tree kangaroo (Dendrolagus matschiei) is an endangered species that has been bred in captivity since the 1970s. In 1992, the Tree Kangaroo Species Survival Plan(®) (TKSSP) was established to coordinate the captive management of Association of Zoos and Aquariums (AZA) D. matschiei. The TKSSP makes annual breeding recommendations primarily based on the mean kinship (MK) strategy. Captive breeding programs often use the MK strategy to preserve genetic diversity in small populations-to avoid the negative consequences of inbreeding and retain their adaptive potential. The ability of a captive breeding program to retain the population's genetic diversity over time can be evaluated by comparing the genetic diversity of the captive population to wild populations. We analyzed DNA extracted from blood and fecal samples from AZA (n = 71), captive (n = 28), and wild (n = 22) D. matschiei using eight microsatellite markers and sequenced the partial mitochondrial DNA control region gene. AZA D. matschiei had a similar expected heterozygosity (H(e) = 0.595 ± 0.184) compared with wild D. matschiei (H(e) = 0.628 ± 0.143), but they had different allelic frequencies (F(ST) = 0.126; P < 0.001). AZA D. matschiei haplotype diversity was almost two times lower than wild D. matschiei Ĥ = 0.740 ± 0.063. These data will assist management of AZA D. matschiei and serve as a baseline for AZA and wild D. matschiei genetic diversity values that could be used to monitor future changes in their genetic diversity. © 2010 Wiley Periodicals, Inc.

Influence of individual reserve trees on nearby reproduction in two-aged Appalachian hardwood stands

Treesearch

Gary W. Miller; James N. Kochenderfer; Desta B. Fekedulegn

2006-01-01

In the 1970s, public opposition to clearcut harvesting in hardwood forests of the eastern United States led forest managers and scientists to consider alternative practices that retain a low-density overstory forest cover. From 1979 to 1984, a form of clearcut-with-reserves harvesting was applied in 80-year-old Appalachian mixed-hardwoods to create four experimental...

On the Effective Construction of Compactly Supported Wavelets Satisfying Homogenous Boundary Conditions on the Interval

NASA Technical Reports Server (NTRS)

Chiavassa, G.; Liandrat, J.

1996-01-01

We construct compactly supported wavelet bases satisfying homogeneous boundary conditions on the interval (0,1). The maximum features of multiresolution analysis on the line are retained, including polynomial approximation and tree algorithms. The case of H(sub 0)(sup 1)(0, 1)is detailed, and numerical values, required for the implementation, are provided for the Neumann and Dirichlet boundary conditions.

An alternative to clear-cutting in the boreal forest of Alaska: a 27-year study of regeneration after shelterwood harvesting.

Treesearch

T.L. Wurtz; J.C. Zasada

2001-01-01

We present 27-year results from a comparison of clear-cutting and shelterwood harvesting in the boreal forest of Alaska. Three patch clearcut and three shelterwood units were harvested in 1972; about 100 dispersed white spruce (Picea glauca (Moench) Voss) leave trees per hectare were retained in the shelterwoods. Units were mechanically scarified...

Profits from pruning ponderosa pine in relation to pruning diameter

Treesearch

Grant. Davis

1958-01-01

Pruning to obtain clear wood on the lower portion of forest trees has been practiced on a limited scale for many years. It became an important operation in the management of national forests after the enactment of the Knutson-Vandenberg Act in 1930. This act provided a means for retaining a portion of timber-sale receipts to finance pruning and other stand improvement...

Elevated root retention of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) in coniferous trees.

PubMed

Schoenmuth, Bernd; Mueller, Jakob O; Scharnhorst, Tanja; Schenke, Detlef; Büttner, Carmen; Pestemer, Wilfried

2014-03-01

For decades, the explosive RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) has been used for military and industrial applications. Residues of RDX pollute soils in large areas globally and the persistence and high soil mobility of these residues can lead to leaching into groundwater. Dendroremediation, i.e. the long-term use of trees to clean up polluted soils, is gaining acceptance as a green and sustainable strategy. Although the coniferous tree species Norway spruce and Scots pine cover large areas of military land in Central Europe, the potential of any coniferous tree for dendroremediation of RDX is still unknown. In this study, uptake experiments with a (14)C-labelled RDX solution (30 mg L(-1)) revealed that RDX was predominantly retained in the roots of 6-year-old coniferous trees. Only 23 % (pine) to 34 % (spruce) of RDX equivalents (RDXeq) taken up by the roots were translocated to aboveground tree compartments. This finding contrasts with the high aerial accumulation of RDXeq (up to 95 %) in the mass balances of all other plant species. Belowground retention of RDXeq is relatively stable in fine root fractions, since water leaching from tissue homogenates was less than 5 %. However, remobilisation from milled coarse roots and tree stubs reached up to 53 %. Leaching from homogenised aerial tree material was found to reach 64 % for needles, 58 % for stems and twigs and 40 % for spring sprouts. Leaching of RDX by precipitation increases the risk for undesired re-entry into the soil. However, it also opens the opportunity for microbial mineralisation in the litter layer or in the rhizosphere of coniferous forests and offers a chance for repeated uptake of RDX by the tree roots.

Construction of a Species-Level Tree of Life for the Insects and Utility in Taxonomic Profiling

PubMed Central

Chesters, Douglas

2017-01-01

Abstract Although comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis. I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta). Matrix-building requires separately optimized pipelines for nuclear transcriptomic, mitochondrial genomic, and species-rich markers, whereas tree-building requires hierarchical inference in order to capture species-breadth while retaining deep-level resolution. The phylogeny of insects contains 49,358 species, 13,865 genera, 760 families. Deep-level splits largely reflected previous findings for sections of the tree that are data rich or unambiguous, such as inter-ordinal Endopterygota and Dictyoptera, the recently evolved and relatively homogeneous Lepidoptera, Hymenoptera, Brachycera (Diptera), and Cucujiformia (Coleoptera). However, analysis of bias, matrix construction and gene-tree variation suggests confidence in some relationships (such as in Polyneoptera) is less than has been indicated by the matrix bootstrap method. To assess the utility of the insect tree as a tool in query profiling several tree-based taxonomic assignment methods are compared. Using test data sets with existing taxonomic annotations, a tendency is observed for greater accuracy of species-level assignments where using a fixed comprehensive tree of life in contrast to methods generating smaller de novo reference trees. Described herein is a solution to the discrepancy in the way data are fit into supermatrices. The resulting tree facilitates wider studies of insect diversification and application of advanced descriptions of diversity in community studies, among other presumed applications. PMID:27798407

Relative contributions of set-asides and tree retention to the long-term availability of key forest biodiversity structures at the landscape scale.

PubMed

Roberge, Jean-Michel; Lämås, Tomas; Lundmark, Tomas; Ranius, Thomas; Felton, Adam; Nordin, Annika

2015-05-01

Over previous decades new environmental measures have been implemented in forestry. In Fennoscandia, forest management practices were modified to set aside conservation areas and to retain trees at final felling. In this study we simulated the long-term effects of set-aside establishment and tree retention practices on the future availability of large trees and dead wood, two forest structures of documented importance to biodiversity conservation. Using a forest decision support system (Heureka), we projected the amounts of these structures over 200 years in two managed north Swedish landscapes, under management scenarios with and without set-asides and tree retention. In line with common best practice, we simulated set-asides covering 5% of the productive area with priority to older stands, as well as ∼5% green-tree retention (solitary trees and forest patches) including high-stump creation at final felling. We found that only tree retention contributed to substantial increases in the future density of large (DBH ≥35 cm) deciduous trees, while both measures made significant contributions to the availability of large conifers. It took more than half a century to observe stronger increases in the densities of large deciduous trees as an effect of tree retention. The mean landscape-scale volumes of hard dead wood fluctuated widely, but the conservation measures yielded values which were, on average over the entire simulation period, about 2.5 times as high as for scenarios without these measures. While the density of large conifers increased with time in the landscape initially dominated by younger forest, best practice conservation measures did not avert a long-term decrease in large conifer density in the landscape initially comprised of more old forest. Our results highlight the needs to adopt a long temporal perspective and to consider initial landscape conditions when evaluating the large-scale effects of conservation measures on forest biodiversity. Copyright © 2015 Elsevier Ltd. All rights reserved.

The harvested side of edges: effect of retained forests on the re-establishement of biodiversity in adjacent harvested areas

Treesearch

Susan C. Baker; Thomas A. Spies; Timothy J. Wardlaw; Jayne Balmer; Jerry F. Franklin

2013-01-01

Most silvicultural methods have been developed with the principal aim of ensuring adequate regeneration of commercial tree species after harvesting. Much less effort has been directed towards developing methods that benefit the re-establishment of all forest biodiversity. The concept of ‘forest influence’ relates the probability of species re-establishment to the...

12. LOOKING SOUTH ONTO PROPERTY FROM BODEGA AVENUE SHOWING HOUSING ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

12. LOOKING SOUTH ONTO PROPERTY FROM BODEGA AVENUE SHOWING HOUSING DEVELOPMENT. 'BURBANK FARM' ON RIGHT. TALL TREE TO RIGHT OF STREET LIGHT IS EUCALYPTUS ON WEST OF COTTAGE WHICH IS PLANNED FOR REMOVAL. 13. 'BURBANK FARM' SHOWING BANK CUT CREATED WHEN BODEGA AVENUE ROADBED WAS LOWERED. WPA STONE RETAINING WALL AT BASE OF CUT. LOOKING SOUTHWEST. - Gold Ridge Farm, 7777 Bodega Avenue, Sebastopol, Sonoma County, CA

Independent and Parallel Evolution of New Genes by Gene Duplication in Two Origins of C4 Photosynthesis Provides New Insight into the Mechanism of Phloem Loading in C4 Species.

PubMed

Emms, David M; Covshoff, Sarah; Hibberd, Julian M; Kelly, Steven

2016-07-01

C4 photosynthesis is considered one of the most remarkable examples of evolutionary convergence in eukaryotes. However, it is unknown whether the evolution of C4 photosynthesis required the evolution of new genes. Genome-wide gene-tree species-tree reconciliation of seven monocot species that span two origins of C4 photosynthesis revealed that there was significant parallelism in the duplication and retention of genes coincident with the evolution of C4 photosynthesis in these lineages. Specifically, 21 orthologous genes were duplicated and retained independently in parallel at both C4 origins. Analysis of this gene cohort revealed that the set of parallel duplicated and retained genes is enriched for genes that are preferentially expressed in bundle sheath cells, the cell type in which photosynthesis was activated during C4 evolution. Furthermore, functional analysis of the cohort of parallel duplicated genes identified SWEET-13 as a potential key transporter in the evolution of C4 photosynthesis in grasses, and provides new insight into the mechanism of phloem loading in these C4 species. C4 photosynthesis, gene duplication, gene families, parallel evolution. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Independent and Parallel Evolution of New Genes by Gene Duplication in Two Origins of C4 Photosynthesis Provides New Insight into the Mechanism of Phloem Loading in C4 Species

PubMed Central

Emms, David M.; Covshoff, Sarah; Hibberd, Julian M.; Kelly, Steven

2016-01-01

C4 photosynthesis is considered one of the most remarkable examples of evolutionary convergence in eukaryotes. However, it is unknown whether the evolution of C4 photosynthesis required the evolution of new genes. Genome-wide gene-tree species-tree reconciliation of seven monocot species that span two origins of C4 photosynthesis revealed that there was significant parallelism in the duplication and retention of genes coincident with the evolution of C4 photosynthesis in these lineages. Specifically, 21 orthologous genes were duplicated and retained independently in parallel at both C4 origins. Analysis of this gene cohort revealed that the set of parallel duplicated and retained genes is enriched for genes that are preferentially expressed in bundle sheath cells, the cell type in which photosynthesis was activated during C4 evolution. Furthermore, functional analysis of the cohort of parallel duplicated genes identified SWEET-13 as a potential key transporter in the evolution of C4 photosynthesis in grasses, and provides new insight into the mechanism of phloem loading in these C4 species. Key words: C4 photosynthesis, gene duplication, gene families, parallel evolution. PMID:27016024

Functional decay in tree community within tropical fragmented landscapes: Effects of landscape-scale forest cover.

PubMed

Rocha-Santos, Larissa; Benchimol, Maíra; Mayfield, Margaret M; Faria, Deborah; Pessoa, Michaele S; Talora, Daniela C; Mariano-Neto, Eduardo; Cazetta, Eliana

2017-01-01

As tropical rainforests are cleared, forest remnants are increasingly isolated within agricultural landscapes. Understanding how forest loss impacts on species diversity can, therefore, contribute to identifying the minimum amount of habitat required for biodiversity maintenance in human-modified landscapes. Here, we evaluate how the amount of forest cover, at the landscape scale, affects patterns of species richness, abundance, key functional traits and common taxonomic families of adult trees in twenty Brazilian Atlantic rainforest landscapes. We found that as forest cover decreases, both tree community richness and abundance decline, without exhibiting a threshold. At the family-level, species richness and abundance of the Myrtaceae and Sapotaceae were also negatively impacted by the percent forest remaining at the landscape scale. For functional traits, we found a reduction in shade-tolerant, animal-dispersed and small-seeded species following a decrease in the amount of forest retained in landscapes. These results suggest that the amount of forest in a landscape is driving non-random losses in phylogenetic and functional tree diversity in Brazil's remaining Atlantic rainforests. Our study highlights potential restraints on the conservation value of Atlantic rainforest remnants in deforested landscapes in the future.

Exploring the cosmic evolution of habitability with galaxy merger trees

NASA Astrophysics Data System (ADS)

Stanway, E. R.; Hoskin, M. J.; Lane, M. A.; Brown, G. C.; Childs, H. J. T.; Greis, S. M. L.; Levan, A. J.

2018-04-01

We combine inferred galaxy properties from a semi-analytic galaxy evolution model incorporating dark matter halo merger trees with new estimates of supernova and gamma-ray burst rates as a function of metallicity from stellar population synthesis models incorporating binary interactions. We use these to explore the stellar-mass fraction of galaxies irradiated by energetic astrophysical transients and its evolution over cosmic time, and thus the fraction which is potentially habitable by life like our own. We find that 18 per cent of the stellar mass in the Universe is likely to have been irradiated within the last 260 Myr, with GRBs dominating that fraction. We do not see a strong dependence of irradiated stellar-mass fraction on stellar mass or richness of the galaxy environment. We consider a representative merger tree as a Local Group analogue, and find that there are galaxies at all masses which have retained a high habitable fraction (>40 per cent) over the last 6 Gyr, but also that there are galaxies at all masses where the merger history and associated star formation have rendered galaxies effectively uninhabitable. This illustrates the need to consider detailed merger trees when evaluating the cosmic evolution of habitability.

Functional decay in tree community within tropical fragmented landscapes: Effects of landscape-scale forest cover

PubMed Central

Benchimol, Maíra; Mayfield, Margaret M.; Faria, Deborah; Pessoa, Michaele S.; Talora, Daniela C.; Mariano-Neto, Eduardo; Cazetta, Eliana

2017-01-01

As tropical rainforests are cleared, forest remnants are increasingly isolated within agricultural landscapes. Understanding how forest loss impacts on species diversity can, therefore, contribute to identifying the minimum amount of habitat required for biodiversity maintenance in human-modified landscapes. Here, we evaluate how the amount of forest cover, at the landscape scale, affects patterns of species richness, abundance, key functional traits and common taxonomic families of adult trees in twenty Brazilian Atlantic rainforest landscapes. We found that as forest cover decreases, both tree community richness and abundance decline, without exhibiting a threshold. At the family-level, species richness and abundance of the Myrtaceae and Sapotaceae were also negatively impacted by the percent forest remaining at the landscape scale. For functional traits, we found a reduction in shade-tolerant, animal-dispersed and small-seeded species following a decrease in the amount of forest retained in landscapes. These results suggest that the amount of forest in a landscape is driving non-random losses in phylogenetic and functional tree diversity in Brazil’s remaining Atlantic rainforests. Our study highlights potential restraints on the conservation value of Atlantic rainforest remnants in deforested landscapes in the future. PMID:28403166

Edge effects enhance selfing and seed harvesting efforts in the insect-pollinated Neotropical tree Copaifera langsdorffii (Fabaceae)

PubMed Central

Tarazi, R; Sebbenn, A M; Kageyama, P Y; Vencovsky, R

2013-01-01

Edge effects may affect the mating system of tropical tree species and reduce the genetic diversity and variance effective size of collected seeds at the boundaries of forest fragments because of a reduction in the density of reproductive trees, neighbour size and changes in the behaviour of pollinators. Here, edge effects on the genetic diversity, mating system and pollen pool of the insect-pollinated Neotropical tree Copaifera langsdorffii were investigated using eight microsatellite loci. Open-pollinated seeds were collected from 17 seed trees within continuous savannah woodland (SW) and were compared with seeds from 11 seed trees at the edge of the savannah remnant. Seeds collected from the SW had significantly higher heterozygosity levels (Ho=0.780; He=0.831) than seeds from the edge (Ho=0.702; He=0.800). The multilocus outcrossing rate was significantly higher in the SW (tm=0.859) than in the edge (tm=0.759). Pollen pool differentiation was significant, however, it did not differ between the SW (=0.105) and the edge (=0.135). The variance effective size within the progenies was significantly higher in the SW (Ne=2.65) than at the edge (Ne=2.30). The number of seed trees to retain the reference variance effective size of 500 was 189 at the SW and 217 at the edge. Therefore, it is preferable that seed harvesting for conservation and environmental restoration strategies be conducted in the SW, where genetic diversity and variance effective size within progenies are higher. PMID:23486081

Edge effects enhance selfing and seed harvesting efforts in the insect-pollinated Neotropical tree Copaifera langsdorffii (Fabaceae).

PubMed

Tarazi, R; Sebbenn, A M; Kageyama, P Y; Vencovsky, R

2013-06-01

Edge effects may affect the mating system of tropical tree species and reduce the genetic diversity and variance effective size of collected seeds at the boundaries of forest fragments because of a reduction in the density of reproductive trees, neighbour size and changes in the behaviour of pollinators. Here, edge effects on the genetic diversity, mating system and pollen pool of the insect-pollinated Neotropical tree Copaifera langsdorffii were investigated using eight microsatellite loci. Open-pollinated seeds were collected from 17 seed trees within continuous savannah woodland (SW) and were compared with seeds from 11 seed trees at the edge of the savannah remnant. Seeds collected from the SW had significantly higher heterozygosity levels (Ho=0.780; He=0.831) than seeds from the edge (Ho=0.702; He=0.800). The multilocus outcrossing rate was significantly higher in the SW (tm=0.859) than in the edge (tm=0.759). Pollen pool differentiation was significant, however, it did not differ between the SW (=0.105) and the edge (=0.135). The variance effective size within the progenies was significantly higher in the SW (Ne=2.65) than at the edge (Ne=2.30). The number of seed trees to retain the reference variance effective size of 500 was 189 at the SW and 217 at the edge. Therefore, it is preferable that seed harvesting for conservation and environmental restoration strategies be conducted in the SW, where genetic diversity and variance effective size within progenies are higher.

Impacts of post-harvest slash and live-tree retention on biomass and nutrient stocks in Populus tremuloides Michx.-dominated forests, northern Minnesota, USA

USGS Publications Warehouse

Klockow, Paul A.; D'Amato, Anthony W.; Bradford, John B.

2013-01-01

Globally, there is widespread interest in using forest-derived biomass as a source of bioenergy. While conventional timber harvesting generally removes only merchantable tree boles, harvesting biomass feedstock can remove all forms of woody biomass (i.e., live and dead standing woody vegetation, downed woody debris, and stumps) resulting in a greater loss of biomass and nutrients as well as more severe habitat alteration. To investigate the potential impacts of this practice, this study examined the initial impacts (pre- and post-harvest) of various levels of slash and live-tree retention on biomass and nutrient stocks, including carbon (C), nitrogen (N), calcium (Ca), potassium (K), and phosphorus (P), in Populus tremuloides Michx.-dominated forests of northern Minnesota, USA. Treatments examined included three levels of slash retention, whole-tree harvest (WTH), 20% slash retention (20SR), and stem-only harvest (SOH), factored with three levels of green-tree retention, no trees retained (NONE), dispersed retention (DISP), and aggregate retention (AGR). Slash retention was the primary factor affecting post-harvest biomass and nutrient stocks, including woody debris pools. Compared to the unharvested control, stocks of biomass, carbon, and nutrients, including N, Ca, K, and P, in woody debris were higher in all treatments. Stem-only harvests typically contained greater biomass and nutrient stocks than WTH, although biomass and nutrients within 20SR, a level recommended by biomass harvesting guidelines in the US and worldwide, generally did not differ from WTH or SOH. Biomass in smaller-diameter slash material (typically 2.5-22.5 cm in diameter) dominated the woody debris pool following harvest regardless of slash retention level. Trends among treatments in this diameter range were generally similar to those in the total woody debris pool. Specifically, SOH contained significantly greater amounts of biomass than WTH while 20SR was not different from either WTH or SOH. Within P. tremuloides systems, we observed high stocks of smaller diameter slash material for all prescribed slash retention treatments. Most notably, WTH retains much more material than anticipated, up to 50% of available slash. These results reflect the high levels of breakage during winter harvest operations in these stands and, consequently, warrant consideration when anticipating the impacts of biomass harvesting on woody debris pools. Further investigation is necessary to understand how deliberate slash retention levels and season-of-harvest impact woody debris in other forest systems.

Construction of a Species-Level Tree of Life for the Insects and Utility in Taxonomic Profiling.

PubMed

Chesters, Douglas

2017-05-01

Although comprehensive phylogenies have proven an invaluable tool in ecology and evolution, their construction is made increasingly challenging both by the scale and structure of publically available sequences. The distinct partition between gene-rich (genomic) and species-rich (DNA barcode) data is a feature of data that has been largely overlooked, yet presents a key obstacle to scaling supermatrix analysis. I present a phyloinformatics framework for draft construction of a species-level phylogeny of insects (Class Insecta). Matrix-building requires separately optimized pipelines for nuclear transcriptomic, mitochondrial genomic, and species-rich markers, whereas tree-building requires hierarchical inference in order to capture species-breadth while retaining deep-level resolution. The phylogeny of insects contains 49,358 species, 13,865 genera, 760 families. Deep-level splits largely reflected previous findings for sections of the tree that are data rich or unambiguous, such as inter-ordinal Endopterygota and Dictyoptera, the recently evolved and relatively homogeneous Lepidoptera, Hymenoptera, Brachycera (Diptera), and Cucujiformia (Coleoptera). However, analysis of bias, matrix construction and gene-tree variation suggests confidence in some relationships (such as in Polyneoptera) is less than has been indicated by the matrix bootstrap method. To assess the utility of the insect tree as a tool in query profiling several tree-based taxonomic assignment methods are compared. Using test data sets with existing taxonomic annotations, a tendency is observed for greater accuracy of species-level assignments where using a fixed comprehensive tree of life in contrast to methods generating smaller de novo reference trees. Described herein is a solution to the discrepancy in the way data are fit into supermatrices. The resulting tree facilitates wider studies of insect diversification and application of advanced descriptions of diversity in community studies, among other presumed applications. [Data integration; data mining; insects; phylogenomics; phyloinformatics; tree of life.]. © 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.

Mycorrhizal networks and distance from mature trees alter patterns of competition and facilitation in dry Douglas-fir forests.

PubMed

Teste, François P; Simard, Suzanne W

2008-11-01

The distribution of dry Douglas-fir forests in western North America is expected to shift northward with climate change and disappear from the grassland interface in the southern interior of British Columbia. This shift may be accentuated by clearcutting, a common harvesting practice that aims to reduce the competitive effects of residual mature trees on new regeneration, but in so doing, ignores their facilitative effects. In this study, we investigated the net effects of competition from and facilitation by mature trees retained on harvested sites on seedling establishment in the dry interface Douglas-fir forests. We demonstrate that access to a mycorrhizal network (MN) and proximity to trees have important influences on seedling performance. On six sites, we established trenched plots around 24 mature Pseudotsuga menziesii var. glauca (Douglas-fir) trees, then planted Douglas-fir seedlings into four mesh treatments that served to restrict MN access (i.e., planted into mesh bags with 0.5-, 35-, or 250-microm pores, or without mesh) or into impermeable bags (grown in isolation) at four distances (0.5, 1.0, 2.5, or 5.0 m). Seedling survival tended to be greater and water stress lower where seedlings had full access to the MN. Seedling height, shoot biomass, needle biomass, and nutrient uptake peaked at 2.5-5.0 m from mature trees. Seedlings 0.5 m from mature trees had lower CO2 assimilation rates and wood delta(13)C compared to seedlings 5.0 m away. Competition for soil resources was highest near mature trees but facilitation was relatively greater at further distances, resulting in a zone of net benefit for seedlings. These results show that intraspecific tree-seedling interactions are both competitive and facilitative in dry Douglas-fir forests, and that they are spatially dependent. After disturbance, maintaining residual mature trees may be important for their beneficial regeneration zones.

Comparative effects of urea fertilizer and red alder in a site III, coast Douglas-fir plantation in the Washington Cascade Range.

Treesearch

Richard E. Miller; Harry W. Anderson; Marshall Murray; Rick. Leon

2005-01-01

Five randomly assigned treatments were used to quantify effects of adding varying numbers of red alder (Alnus rubra Bong.) or nitrogen (N) fertilization on growth of a 10-year-old conifer plantation at a medium quality site in the western Washington Cascade Range. Zero, 20, 40, and 80 alder trees per acre were retained along with about 300 conifers...

Interspecific differences and commonalities in maternity roosting by tree cavity-roosting bats over a maternity season in a timber production landscape.

PubMed

Rueegger, Niels; Law, Brad; Goldingay, Ross

2018-01-01

Understanding maternity roost requirements is fundamental to guide timber production forest management given such roosts are vital to sustain bat populations. We tracked lactating females of three tree cavity-roosting species: Gould's long-eared bat (Nyctophilus gouldi) (n = 7), eastern broad-nosed bat (Scotorepens orion) (n = 6) and little forest bat (Vespadelus vulturnus) (n = 25), over five weeks in young (predominately <5 years old) forest regenerating from heavy timber harvest in southeast Australia. We aimed to investigate interspecific maternity roost selection in a regenerating landscape and by doing so, increase our understanding of the three species' roost ecology. Sixteen V. vulturnus, 15 N. gouldi and six S. orion unique maternity roost trees were located. Bats displayed a degree of maternity roost selection plasticity, however, interspecific differences were found. Nyctophilus gouldi roosted selectively in retained riparian buffers, in trees of high senescence and switched roosts every day. Vespadelus vulturnus roosted in logged areas and displayed high roost site fidelity, with one roost used for 33 consecutive days. Scotorepens orion selected large live trees of low senescence. The preliminary data for this species suggests that females roost most days in 'primary' roosts but display a roost switching behaviour conforming to the fission-fusion model. Dead trees were identified to be important for both N. gouldi and V. vulturnus. Historical and recent logging at our study area drastically reduced cavity-bearing tree density to 1.4 trees per hectare in the logging zones (outside of exclusion areas), potentially limiting local populations of tree cavity-roosting bats and other cavity-dependent wildlife. Our data demonstrate that forest management must consider a range of maternity roost requirements to accommodate differences among species and highlight the importance of exclusion areas for roost habitat. We propose that an expanded 'retention forestry' approach should be implemented in logged areas that includes in-perpetuity forest patch retention to increase habitat complexity and continuity.

Interspecific differences and commonalities in maternity roosting by tree cavity-roosting bats over a maternity season in a timber production landscape

PubMed Central

Law, Brad; Goldingay, Ross

2018-01-01

Understanding maternity roost requirements is fundamental to guide timber production forest management given such roosts are vital to sustain bat populations. We tracked lactating females of three tree cavity-roosting species: Gould's long-eared bat (Nyctophilus gouldi) (n = 7), eastern broad-nosed bat (Scotorepens orion) (n = 6) and little forest bat (Vespadelus vulturnus) (n = 25), over five weeks in young (predominately <5 years old) forest regenerating from heavy timber harvest in southeast Australia. We aimed to investigate interspecific maternity roost selection in a regenerating landscape and by doing so, increase our understanding of the three species’ roost ecology. Sixteen V. vulturnus, 15 N. gouldi and six S. orion unique maternity roost trees were located. Bats displayed a degree of maternity roost selection plasticity, however, interspecific differences were found. Nyctophilus gouldi roosted selectively in retained riparian buffers, in trees of high senescence and switched roosts every day. Vespadelus vulturnus roosted in logged areas and displayed high roost site fidelity, with one roost used for 33 consecutive days. Scotorepens orion selected large live trees of low senescence. The preliminary data for this species suggests that females roost most days in ‘primary’ roosts but display a roost switching behaviour conforming to the fission-fusion model. Dead trees were identified to be important for both N. gouldi and V. vulturnus. Historical and recent logging at our study area drastically reduced cavity-bearing tree density to 1.4 trees per hectare in the logging zones (outside of exclusion areas), potentially limiting local populations of tree cavity-roosting bats and other cavity-dependent wildlife. Our data demonstrate that forest management must consider a range of maternity roost requirements to accommodate differences among species and highlight the importance of exclusion areas for roost habitat. We propose that an expanded ‘retention forestry’ approach should be implemented in logged areas that includes in-perpetuity forest patch retention to increase habitat complexity and continuity. PMID:29543883

Biological significance of dead biomass retention trait in Mediterranean Basin species: an analysis between different successional niches and regeneration strategies as functional groups.

PubMed

Baeza, M J; Santana, V M

2015-11-01

Standing dead biomass retention is considered one of the most relevant fuel structural traits to affect plant flammability. However, very little is known about the biological significance of this trait and its distribution between different functional groups. Our aim was to analyse how the proportion of dead biomass produced in Mediterranean species is related to the successional niche of species (early-, mid- and late-successional stages) and the regeneration strategy of species (seeders and resprouters). We evaluated biomass distribution by size classes and standing dead biomass retention in nine dominant species from the Mediterranean Basin in different development stages (5, 9, 14 and 26 years since the last fire). The results revealed significant differences in the standing dead biomass retention of species that presented a distinct successional niche or regeneration strategy. These differences were restricted to the oldest ages studied (>9 years). Tree and small tree resprouters, typical in late-successional stages, presented slight variations with age and a less marked trend to retain dead biomass, while seeder shrubs and dwarf shrubs, characteristic of early-successional stages, showed high dead biomass loads. Our results suggest that the species that tend to retain more dead branches are colonising species that may promote fire in early-successional stages. © 2015 German Botanical Society and The Royal Botanical Society of the Netherlands.

LIFE CLIMATREE project: A novel approach for accounting and monitoring carbon sequestration of tree crops and their potential as carbon sink areas

NASA Astrophysics Data System (ADS)

Stergiou, John; Tagaris, Efthimios; -Eleni Sotiropoulou, Rafaella

2016-04-01

Climate Change Mitigation is one of the most important objectives of the Kyoto Convention, and is mostly oriented towards reducing GHG emissions. However, carbon sink is retained only in the calculation of the forests capacity since agricultural land and farmers practices for securing carbon stored in soils have not been recognized in GHG accounting, possibly resulting in incorrect estimations of the carbon dioxide balance in the atmosphere. The agricultural sector, which is a key sector in the EU, presents a consistent strategic framework since 1954, in the form of Common Agricultural Policy (CAP). In its latest reform of 2013 (reg. (EU) 1305/13) CAP recognized the significance of Agriculture as a key player in Climate Change policy. In order to fill this gap the "LIFE ClimaTree" project has recently founded by the European Commission aiming to provide a novel method for including tree crop cultivations in the LULUCF's accounting rules for GHG emissions and removal. In the framework of "LIFE ClimaTree" project estimation of carbon sink within EU through the inclusion of the calculated tree crop capacity will be assessed for both current and future climatic conditions by 2050s using the GISS-WRF modeling system in a very fine scale (i.e., 9km x 9km) using RCP8.5 and RCP4.5 climate scenarios. Acknowledgement: LIFE CLIMATREE project "A novel approach for accounting and monitoring carbon sequestration of tree crops and their potential as carbon sink areas" (LIFE14 CCM/GR/000635).

Emerald ash borer and the urban forest: Changes in landslide potential due to canopy loss scenarios in the City of Pittsburgh, PA.

PubMed

Pfeil-McCullough, Erin; Bain, Daniel J; Bergman, Jeffery; Crumrine, Danielle

2015-12-01

Emerald ash borer is expected to kill thousands of ash trees in the eastern U.S. This research develops tools to predict the effect of ash tree loss from the urban canopy on landslide susceptibility in Pittsburgh, PA. A spatial model was built using the SINMAP (Stability INdex MAPping) model coupled with spatially explicit scenarios of tree loss (0%, 25%, 50%, and 75% loss of ash trees from the canopy). Ash spatial distributions were estimated via Monte Carlo methods and available vegetation plot data. Ash trees are most prevalent on steeper slopes, likely due to urban development patterns. Therefore, ash loss disproportionately increases hillslope instability. A 75% loss of ash resulted in roughly 800 new potential landslide initiation locations. Sensitivity testing reveals that variations in rainfall rates, and friction angles produce minor changes to model results relative to the magnitude of parameter variation, but reveal high model sensitivity to soil density and root cohesion values. The model predictions demonstrate the importance of large canopy species to urban hillslope stability, particularly on steep slopes and in areas where soils tend to retain water. To improve instability predictions, better characterization of urban soils, particularly spatial patterns of compaction and species specific root cohesion is necessary. The modeling framework developed in this research will enhance assessment of changes in landslide risk due to tree mortality, improving our ability to design economically and ecologically sustainable urban systems. Copyright © 2015 Elsevier B.V. All rights reserved.

Optimising UK urban road verge contributions to biodiversity and ecosystem services with cost-effective management.

PubMed

O'Sullivan, Odhran S; Holt, Alison R; Warren, Philip H; Evans, Karl L

2017-04-15

Urban road verges can contain significant biodiversity, contribute to structural connectivity between other urban greenspaces, and due to their proximity to road traffic are well placed to provide ecosystem services. Using the UK as a case study we review and critically evaluate a broad range of evidence to assess how this considerable potential can be enhanced despite financial, contractual and public opinion constraints. Reduced mowing frequency and other alterations would enhance biodiversity, aesthetics and pollination services, whilst delivering costs savings and potentially being publically acceptable. Retaining mature trees and planting additional ones is favourable to residents and would enhance biodiversity, pollution and climate regulation, carbon storage, and stormwater management. Optimising these services requires improved selection of tree species, and creating a more diverse tree stock. Due to establishment costs additional tree planting and maintenance could benefit from payment for ecosystem service schemes. Verges could also provide areas for cultivation of biofuels and possibly food production. Maximising the contribution of verges to urban biodiversity and ecosystem services is economical and becoming an increasingly urgent priority as the road network expands and other urban greenspace is lost, requiring enhancement of existing greenspace to facilitate sustainable urban development. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Genetic diversity and mating system of Copaifera langsdorffii (Leguminosae/Caesalpinioideae).

PubMed

Gonela, A; Sebbenn, A M; Soriani, H H; Mestriner, M A; Martinez, C A; Alzate-Marin, A L

2013-02-27

Copaifera langsdorffii, locally known as copaíba, is a valuable tropical tree with medicinal properties of its oil. We studied the genetic variation, genetic structure, and the mating system of trees in stands of C. langsdorffii (Leguminosae/Caesalpinioideae) located in an extensive area between the Pardo and Mogi-Guaçu basins in São Paulo State, Brazil, and their offspring, conserved in an ex situ germplasm bank at the University of São Paulo in Ribeirão Preto, SP, Brazil, using six microsatellite loci. Leaves were collected from 80 seed trees and from 259 offspring and their DNA extracted. A total of 140 and 175 alleles were found in the seed trees and their offspring, respectively. Low genetic differentiation was observed between stands, indicating intense gene flow due to efficient pollen dispersion vectors. An estimation of the outcrossing rate showed that these stands are outcrossed (tm = 0.98, P > 0.05). The mean variance of the effective population size of each family in two of the stands was 3.69 and 3.43, while the total effective population size retained in the germplasm bank was between 81 and 96. The paternity correlation was low, ranging from 0.052 to 0.148, demonstrating that the families implanted in this germplasm bank are composed predominantly of half-sibs.

Water regime of mechanical-biological pretreated waste materials under fast-growing trees.

PubMed

Rüth, Björn; Lennartz, Bernd; Kahle, Petra

2007-10-01

In this study mechanical-biological pre-treated waste material (MBP) was tested for suitability to serve as an alternative surface layer in combination with fast-growing and water-consumptive trees for final covers at landfill sites. The aim was to quantify evapotranspiration and seepage losses by numerical model simulations for two sites in Germany. In addition, the leaf area index (LAI) of six tree species over the growing season as the driving parameter for transpiration calculations was determined experimentally. The maximum LAI varied between 3.8 and 6.1 m2 m(-2) for poplar and willow clones, respectively. The evapotranspiration calculations revealed that the use of MBP waste material for re-cultivation enhanced evapotranspiration by 40 mm year(-1) (10%) over an 11 year calculation period compared to a standard mineral soil. Between 82% (for LAI(max) = 3.8) and 87% (for LAI(max) = 6.1) of the average annual precipitation (506 mm) could be retained from the surface layer assuming eastern German climate conditions, compared with a retention efficiency between 79 and 82% for a mineral soil. Although a MBP layer in conjunction with water-consumptive trees can reduce vertical water losses as compared to mineral substrates, the effect is not sufficient to meet legal regulations.

Biogeochemistry of beetle-killed forests: Explaining a weak nitrate response

PubMed Central

Rhoades, Charles C.; McCutchan, James H.; Cooper, Leigh A.; Clow, David; Detmer, Thomas M.; Briggs, Jennifer S.; Stednick, John D.; Veblen, Thomas T.; Ertz, Rachel M.; Likens, Gene E.; Lewis, William M.

2013-01-01

A current pine beetle infestation has caused extensive mortality of lodgepole pine (Pinus contorta) in forests of Colorado and Wyoming; it is part of an unprecedented multispecies beetle outbreak extending from Mexico to Canada. In United States and European watersheds, where atmospheric deposition of inorganic N is moderate to low (<10 kg⋅ha⋅y), disturbance of forests by timber harvest or violent storms causes an increase in stream nitrate concentration that typically is close to 400% of predisturbance concentrations. In contrast, no significant increase in streamwater nitrate concentrations has occurred following extensive tree mortality caused by the mountain pine beetle in Colorado. A model of nitrate release from Colorado watersheds calibrated with field data indicates that stimulation of nitrate uptake by vegetation components unaffected by beetles accounts for significant nitrate retention in beetle-infested watersheds. The combination of low atmospheric N deposition (<10 kg⋅ha⋅y), tree mortality spread over multiple years, and high compensatory capacity associated with undisturbed residual vegetation and soils explains the ability of these beetle-infested watersheds to retain nitrate despite catastrophic mortality of the dominant canopy tree species. PMID:23319612

Insurance Contract Analysis for Company Decision Support in Acquisition Management

NASA Astrophysics Data System (ADS)

Chernovita, H. P.; Manongga, D.; Iriani, A.

2017-01-01

One of company activities to retain their business is marketing the products which include in acquisition management to get new customers. Insurance contract analysis using ID3 to produce decision tree and rules to be decision support for the insurance company. The decision tree shows 13 rules that lead to contract termination claim. This could be a guide for the insurance company in acquisition management to prevent contract binding with these contract condition because it has a big chance for the customer to terminate their insurance contract before its expired date. As the result, there are several strong points that could be the determinant of contract termination such as: 1) customer age whether too young or too old, 2) long insurance period (above 10 years), 3) big insurance amount, 4) big amount of premium charges, and 5) payment method.

Longevity of guard cell chloroplasts in falling leaves: implication for stomatal function and cellular aging.

PubMed

Zeiger, E; Schwartz, A

1982-11-12

Guard cell chloroplasts in senescing leaves from 12 species of perennial trees and three species of annual plants survived considerably longer than their mesophyll counterparts. In Ginkgo biloba, stomata from yellow leaves opened during the day and closed at night; guard cell chloroplasts from these leaves showed fluorescence transients associated with electron transport and photophosphorylation. These findings indicate that guard cell chloroplasts are highly conserved throughout the life-span of the leaf and that leaves retain stomatal control during senescence.

Longevity of guard cell chloroplasts in falling leaves: implication for stomatal function and cellular aging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zeiger, E.; Schwartz, A.

1982-11-12

Guard cell chloroplasts in senescing leaves from 12 species of perennial trees and three species of annual plants survived considerably longer than their mesophyll counterparts. In Ginkgo biloba, stomata from yellow leaves opened during the day and closed at night; guard cell chloroplasts from these leaves showed fluorescence transients associated with electron transport and photophosphorylation. These findings indicate that guard cell chloroplasts are highly conserved throughout the life-span of the leaf and that leaves retain stomatal control during senescence.

Phylogenomics Controlling for Base Compositional Bias Reveals a Single Origin of Eusociality in Corbiculate Bees.

PubMed

Romiguier, Jonathan; Cameron, Sydney A; Woodard, S Hollis; Fischman, Brielle J; Keller, Laurent; Praz, Christophe J

2016-03-01

As increasingly large molecular data sets are collected for phylogenomics, the conflicting phylogenetic signal among gene trees poses challenges to resolve some difficult nodes of the Tree of Life. Among these nodes, the phylogenetic position of the honey bees (Apini) within the corbiculate bee group remains controversial, despite its considerable importance for understanding the emergence and maintenance of eusociality. Here, we show that this controversy stems in part from pervasive phylogenetic conflicts among GC-rich gene trees. GC-rich genes typically have a high nucleotidic heterogeneity among species, which can induce topological conflicts among gene trees. When retaining only the most GC-homogeneous genes or using a nonhomogeneous model of sequence evolution, our analyses reveal a monophyletic group of the three lineages with a eusocial lifestyle (honey bees, bumble bees, and stingless bees). These phylogenetic relationships strongly suggest a single origin of eusociality in the corbiculate bees, with no reversal to solitary living in this group. To accurately reconstruct other important evolutionary steps across the Tree of Life, we suggest removing GC-rich and GC-heterogeneous genes from large phylogenomic data sets. Interpreted as a consequence of genome-wide variations in recombination rates, this GC effect can affect all taxa featuring GC-biased gene conversion, which is common in eukaryotes. © The Author 2015. 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.

Phylesystem: a git-based data store for community-curated phylogenetic estimates.

PubMed

McTavish, Emily Jane; Hinchliff, Cody E; Allman, James F; Brown, Joseph W; Cranston, Karen A; Holder, Mark T; Rees, Jonathan A; Smith, Stephen A

2015-09-01

Phylogenetic estimates from published studies can be archived using general platforms like Dryad (Vision, 2010) or TreeBASE (Sanderson et al., 1994). Such services fulfill a crucial role in ensuring transparency and reproducibility in phylogenetic research. However, digital tree data files often require some editing (e.g. rerooting) to improve the accuracy and reusability of the phylogenetic statements. Furthermore, establishing the mapping between tip labels used in a tree and taxa in a single common taxonomy dramatically improves the ability of other researchers to reuse phylogenetic estimates. As the process of curating a published phylogenetic estimate is not error-free, retaining a full record of the provenance of edits to a tree is crucial for openness, allowing editors to receive credit for their work and making errors introduced during curation easier to correct. Here, we report the development of software infrastructure to support the open curation of phylogenetic data by the community of biologists. The backend of the system provides an interface for the standard database operations of creating, reading, updating and deleting records by making commits to a git repository. The record of the history of edits to a tree is preserved by git's version control features. Hosting this data store on GitHub (http://github.com/) provides open access to the data store using tools familiar to many developers. We have deployed a server running the 'phylesystem-api', which wraps the interactions with git and GitHub. The Open Tree of Life project has also developed and deployed a JavaScript application that uses the phylesystem-api and other web services to enable input and curation of published phylogenetic statements. Source code for the web service layer is available at https://github.com/OpenTreeOfLife/phylesystem-api. The data store can be cloned from: https://github.com/OpenTreeOfLife/phylesystem. A web application that uses the phylesystem web services is deployed at http://tree.opentreeoflife.org/curator. Code for that tool is available from https://github.com/OpenTreeOfLife/opentree. mtholder@gmail.com. © The Author 2015. Published by Oxford University Press.

Access to mycorrhizal networks and roots of trees: importance for seedling survival and resource transfer.

PubMed

Teste, François P; Simard, Suzanne W; Durall, Daniel M; Guy, Robert D; Jones, Melanie D; Schoonmaker, Amanda L

2009-10-01

Mycorrhizal networks (MNs) are fungal hyphae that connect roots of at least two plants. It has been suggested that these networks are ecologically relevant because they may facilitate interplant resource transfer and improve regeneration dynamics. This study investigated the effects of MNs on seedling survival, growth and physiological responses, interplant resource (carbon and nitrogen) transfer, and ectomycorrhizal (EM) fungal colonization of seedlings by trees in dry interior Douglas-fir (Pseudotsuga menziesii var. glauca) forests. On a large, recently harvested site that retained some older trees, we established 160 isolated plots containing pairs of older Douglas-fir "donor" trees and either manually sown seed or planted Douglas-fir "receiver" seedlings. Seed- and greenhouse-grown seedlings were sown and planted into four mesh treatments that served to restrict MN access (i.e., planted into mesh bags with 0.5-, 35-, 250-microm pores, or without mesh). Older trees were pulse labeled with carbon (13CO2) and nitrogen (15NH4(15)NO3) to quantify resource transfer. After two years, seedlings grown from seed in the field had the greatest survival and received the greatest amounts of transferred carbon (0.0063% of donor photo-assimilates) and nitrogen (0.0018%) where they were grown without mesh; however, planted seedlings were not affected by access to tree roots and hyphae. Size of "donor" trees was inversely related to the amount of carbon transferred to seedlings. The potential for MNs to form was high (based on high similarity of EM communities between hosts), and MN-mediated colonization appeared only to be important for seedlings grown from seed in the field. These results demonstrate that MNs and mycorrhizal roots of trees may be ecologically important for natural regeneration in dry forests, but it is still uncertain whether resource transfer is an important mechanism underlying seedling establishment.

Ion homeostasis, osmoregulation, and physiological changes in the roots and leaves of pistachio rootstocks in response to salinity.

PubMed

Akbari, Mohammad; Mahna, Nasser; Ramesh, Katam; Bandehagh, Ali; Mazzuca, Silvia

2018-03-12

Pistachio, one of the important tree nuts, is cultivated in arid and semi-arid regions where salinity is the most common abiotic stress encountered by this tree. However, the mechanisms underlying salinity tolerance in this plant are not well understood. In the present study, five 1-year-old pistachio rootstocks (namely Akbari, Badami, Ghazvini, Kale-Ghouchi, and UCB-1) were treated with four saline water regimes (control, 8, 12, and 16 dS m -1 ) for 100 days. At high salinity level, all rootstocks showed decreased relative water content (RWC), total chlorophyll content (TCHC), and carotenoids in the leaf, while ascorbic acid (AsA) and total soluble proteins (TSP) were reduced in both leaf and root organs. In addition, the total phenolic compounds (TPC), proline, glycine betaine, total soluble carbohydrate (TSC), and H 2 O 2 content increased under salinity stress in all studied rootstocks. Three different ion exclusion strategies were observed in the studied rootstocks: (i) Na + exclusion in UCB-1, because most of its Na + is retained in the roots; (ii) Cl - exclusion in Badami, in which most of its Cl - remained in the roots; and (iii) similar concentrations of Na + and Cl - were observed in the leaves and roots of Ghazvini, Akbari, and Kale-Ghouchi. Transport capacity (ST value) of K + over Na + from the roots to the leaves was more observable in UCB-1 and Ghazvini. Overall, the root system cooperated more effectively in UCB-1 and Badami for retaining and detoxifying an excessive amount of Na + and Cl - . The results presented here provide important inputs to better understand the salt tolerance mechanism in a tree species for developing more salt-tolerant genotypes. Based on the results obtained here, the studied rootstocks from tolerant to susceptible are arranged as follows: UCB-1 > Badami > Ghazvini > Kale-Ghouchi > Akbari.

Explaining Match Outcome During The Men’s Basketball Tournament at The Olympic Games

PubMed Central

Leicht, Anthony S.; Gómez, Miguel A.; Woods, Carl T.

2017-01-01

In preparation for the Olympics, there is a limited opportunity for coaches and athletes to interact regularly with team performance indicators providing important guidance to coaches for enhanced match success at the elite level. This study examined the relationship between match outcome and team performance indicators during men’s basketball tournaments at the Olympic Games. Twelve team performance indicators were collated from all men’s teams and matches during the basketball tournament of the 2004-2016 Olympic Games (n = 156). Linear and non-linear analyses examined the relationship between match outcome and team performance indicator characteristics; namely, binary logistic regression and a conditional interference (CI) classification tree. The most parsimonious logistic regression model retained ‘assists’, ‘defensive rebounds’, ‘field-goal percentage’, ‘fouls’, ‘fouls against’, ‘steals’ and ‘turnovers’ (delta AIC <0.01; Akaike weight = 0.28) with a classification accuracy of 85.5%. Conversely, four performance indicators were retained with the CI classification tree with an average classification accuracy of 81.4%. However, it was the combination of ‘field-goal percentage’ and ‘defensive rebounds’ that provided the greatest probability of winning (93.2%). Match outcome during the men’s basketball tournaments at the Olympic Games was identified by a unique combination of performance indicators. Despite the average model accuracy being marginally higher for the logistic regression analysis, the CI classification tree offered a greater practical utility for coaches through its resolution of non-linear phenomena to guide team success. Key points A unique combination of team performance indicators explained 93.2% of winning observations in men’s basketball at the Olympics. Monitoring of these team performance indicators may provide coaches with the capability to devise multiple game plans or strategies to enhance their likelihood of winning. Incorporation of machine learning techniques with team performance indicators may provide a valuable and strategic approach to explain patterns within multivariate datasets in sport science. PMID:29238245

Phytoscreening for chlorinated solvents using rapid in vitro SPME sampling: Application to urban plume in Verl, Germany

USGS Publications Warehouse

Limmer, M.A.; Balouet, J.-C.; Karg, F.; Vroblesky, D.A.; Burken, J.G.

2011-01-01

Rapid detection and delineation of contaminants in urban settings is critically important in protecting human health. Cores from trees growing above a plume of contaminated groundwater in Verl, Germany, were collected in 1 day, with subsequent analysis and plume mapping completed over several days. Solid-phase microextraction (SPME) analysis was applied to detect tetrachloroethene (PCE) and trichloroethene (TCE) to below nanogram/liter levels in the transpiration stream of the trees. The tree core concentrations showed a clear areal correlation to the distribution of PCE and TCE in the groundwater. Concentrations in tree cores were lower than the underlying groundwater, as anticipated; however, the tree core water retained the PCE:TCE signature of the underlying groundwater in the urban, populated area. The PCE:TCE ratio can indicate areas of differing degradation activity. Therefore, the phytoscreening analysis was capable not only of mapping the spatial distribution of groundwater contamination but also of delineating zones of potentially differing contaminant sources and degradation. The simplicity of tree coring and the ability to collect a large number of samples in a day with minimal disruption or property damage in the urban setting demonstrates that phytoscreening can be a powerful tool for gaining reconnaissance-level information on groundwater contaminated by chlorinated solvents. The use of SPME decreases the detection level considerably and increases the sensitivity of phytoscreening as an assessment, monitoring, and phytoforensic tool. With rapid, inexpensive, and noninvasive methods of detecting and delineating contaminants underlying homes, as in this case, human health can be better protected through screening of broader areas and with far faster response times. ?? 2011 American Chemical Society.

Photosynthetic response to low sink demand after fruit removal in relation to photoinhibition and photoprotection in peach trees.

PubMed

Duan, Wei; Fan, Pei G; Wang, Li J; Li, Wei D; Yan, Shu T; Li, Shao H

2008-01-01

Diurnal variations in photosynthesis, chlorophyll fluorescence, xanthophyll cycle, antioxidant enzymes and antioxidant metabolism in leaves in response to low sink demand caused by fruit removal (-fruit) were studied in 'Zaojiubao' peach (Prunus persica (L.) Batch) trees during the final stage of rapid fruit growth. Compared with the retained fruit treatment (+fruit), the -fruit treatment resulted in a significantly lower photosynthetic rate, stomatal conductance and transpiration rate, but generally higher internal CO(2) concentration, leaf-to-air vapor pressure difference and leaf temperature. The low photosynthetic rate in the -fruit trees paralleled reductions in maximal efficiency of photosystem II (PSII) photochemistry and carboxylation efficiency. The midday depression in photosynthetic rate in response to low sink demand resulting from fruit removal was mainly caused by non-stomatal limitation. Fruit removal resulted in lower quantum efficiency of PSII as a result of both a decrease in the efficiency of excitation capture by open PSII reaction centers and an increase in closure of PSII reaction centers. Both xanthophyll-dependent thermal dissipation and the antioxidant system were up-regulated providing protection from photo-oxidative damage to leaves during low sink demand. Compared with the leaves of +fruit trees, leaves of -fruit trees had a larger xanthophyll cycle pool size and a higher de-epoxidation state, as well as significantly higher activities of antioxidant enzymes, including superoxide dismutase, ascorbate peroxidase, monodehydroascorbate reductase, dehydroascorbate reductase, glutathione reductase and a higher reduction state of ascorbate and glutathione. However, the -fruit treatment resulted in higher hydrogen peroxide and malondialdehyde concentrations compared with the +fruit treatment, indicating photo-oxidative damage.

A perfect storm: multiple stressors interact to drive postfire regeneration failure of lodgepole pine and Douglas-fir forests in Yellowstone

NASA Astrophysics Data System (ADS)

Hansen, W. D.; Braziunas, K. H.; Rammer, W.; Seidl, R.; Turner, M. G.

2017-12-01

Twenty-first century forests will experience increased stress as environmental conditions and disturbance regimes change. Whether forests retain their structure or transitions to alternate states, particularly when affected by multiple stressors, remains unresolved. Subalpine forests in Yellowstone National Park, WY experience large severe wildfires, and postfire-tree regeneration is necessary to assure resilience. Drying is projected, causing frequent larger wildfires that could reduce seed supply and drought that could constrain postfire-seedling establishment. We asked what combinations of warming-drying conditions, increased fire frequency, and increased burned-patch size cause postfire tree-regeneration failure in Yellowstone? We conducted a simulation experiment to identify combinations of fire frequency, fire size, postfire climate, substrate type, and elevation where lodgepole-pine and Douglas-fir regeneration failed. We expected postfire densities to be reduced if burned-patch sizes exceeded effective dispersal distance, sequential fires burned before trees reached reproductive maturity, or drought occurred after fire. We also expected regeneration failure only where multiple stressors occurred simultaneously at low elevation or on poor substrates.Douglas-fir stands were most vulnerable to regeneration failure. 98% of simulated Douglas-fir stands located in the middle of large burned patches failed to regenerate 30 years post fire. Lodgepole-pine stands in the middle of large burned patches failed to regenerate if they were also located at low elevations (93%) or at higher elevations on soils with poor water retention (73%). Stands of serotinous lodgepole (i.e., trees with closed cones that open when heated) also failed to regenerate if fire recurred before trees were reproductively mature (82%). Drought constrained postfire regeneration, yet, enhanced establishment due to release from cold-temperatures during mid-to-late 21st century often outweighed drought effects. Postfire tree regeneration arises from the interplay between multiple factors; some constraining establishment and others enhancing it. To understand 21st-century climate and fire effects on postfire tree regeneration and forest resilience, a reductionist approach is insufficient.

Management of Agroforestry Practices in Assosa District, Benishangul Gumuze Region, Ethiopia

NASA Astrophysics Data System (ADS)

Kifle, E. T.; Asfaw, Z.; Abdelkadir, A.

2017-12-01

Trees on farms have evolved from the selective retention of useful trees on agricultural lands following the severe forest destruction and degradation for agriculture and other uses. As a consequence, trees on farms form the main vegetation types in much of rural Ethiopia in general and Assosa district in particular. In order to increase the products and services of these important agroforestry species there is a need to identify and document the species type and their management practices. To this end, this study is intended to:1) identify agroforestry types, species richness, use-diversity and management of the woody and non-woody plant species 2) record on-farm tree management practices and 3) assess the perception and attitude of farmers towards tree management. A combination of assessment methods including species inventory, key informant discussions and questionnaire surveys were employed in the study. The key findings of the study have shown that a) there were four major agroforestry practices namely homrgardens, parklands, alley cropping and farm boundary plantings with homegardens and parklands appearing to be the dominant practices, b) a total of 57 woody and non-woody species were found to form the main vegetation species with about 21 species commonly shared by both homegardens and parklands c)the difference in mean number of stems in homegardens and parklands was significantly different (p<0.05), d) retained trees in the study area are multifunctional with more than six use types and were managed by more than five management practices including slant-cut of mango (Mangifera indica) trees. According to household respondents and key informants land tenure insecurity, prevalence of pests/diseases, scarcity of water and poor survival of seedlings were the major problems. Therefore, land certification, water resource development, integrated pest management(IPM), training of farmers and further research on the cultural management practices are key recommendations for further development of agroforestry in the study area. Keywords: homegardens; parklands; local knowledge; slant-cut; inventory; key informants; questionnaire

A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments.

PubMed

Rajan, Vaibhav

2013-03-01

Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common practice in phylogenetic analysis. Although masking is often done manually, automated methods are necessary to handle the much larger data sets being prepared today. In this study, we introduce the concept of subsplits and demonstrate their use in extracting phylogenetic signal from alignments. We design a clustering approach for alignment masking where each cluster contains similar columns-similarity being defined on the basis of compatible subsplits; our approach then identifies noisy clusters and eliminates them. Trees inferred from the columns in the retained clusters are found to be topologically closer to the reference trees. We test our method on numerous standard benchmarks (both synthetic and biological data sets) and compare its performance with other methods of alignment masking. We find that our method can eliminate sites more accurately than other methods, particularly on divergent data, and can improve the topologies of the inferred trees in likelihood-based analyses. Software available upon request from the author.

Insect herbivores associated with an evergreen tree Goniorrhachis marginata Taub. (Leguminosae: Caesalpinioideae) in a tropical dry forest.

PubMed

Silva, J O; Neves, F S

2014-08-01

Goniorrhachis marginata Taub. (Leguminosae: Caesalpinioideae) is a tree species found in Brazilian tropical dry forests that retain their leaves during the dry season. That being, we addressed the following question: i) How do insect diversity (sap-sucking and chewing), leaf herbivory and defensive traits (tannin and leaf sclerophylly) vary on the evergreen tree species G. marginata between seasons? The abundance of sap-sucking insects was higher in the dry season than in the rainy season. However, we did not verify any difference in the species richness and abundance of chewing insects between seasons. Leaf herbivory was higher in the rainy season, whereas leaf sclerophylly was higher in the dry season. However, herbivory was not related to sclerophylly. Insect herbivores likely decrease their folivory activity during the dry season due to life history patterns or changes in behaviour, possibly entering diapause or inactivity during this period. Therefore, G. marginata acts as a likely keystone species, serving as a moist refuge for the insect fauna during the dry season in tropical dry forest, and the presence of this evergreen species is crucial to conservation strategies of this threatened ecosystem.

Advancing dendrochronological studies of fire in the United States

USGS Publications Warehouse

Harley, Grant L.; Baisan, Christopher H.; Brown, Peter M.; Falk, Donald A.; Flatley, William T.; Grissino-Mayer, Henri D.; Hessl, Amy; Heyerdahl, Emily K.; Kaye, Margot W.; Lafon, Charles W.; Margolis, Ellis; Maxwell, R. Stockton; Naito, Adam T.; Platt, William J.; Rother, Monica T.; Saladyga, Thomas; Sherriff, Rosemary L.; Stachowiak, Lauren A.; Stambaugh, Michael C.; Sutherland, Elaine Kennedy; Taylor, Alan H.

2018-01-01

Dendroecology is the science that dates tree rings to their exact calendar year of formation to study processes that influence forest ecology (e.g., Speer 2010, Amoroso et al., 2017). Reconstruction of past fire regimes is a core application of dendroecology, linking fire history to population dynamics and climate effects on tree growth and survivorship. Since the early 20th century when dendrochronologists recognized that tree rings retained fire scars (e.g., Figure 1), and hence a record of past fires, they have conducted studies worldwide to reconstruct the historical range and variability of fire regimes (e.g., frequency, severity, seasonality, spatial extent), the influence of fire regimes on forest structure and ecosystem dynamics, and the top-down (e.g., climate) and bottom-up (e.g., fuels, topography) drivers of fire that operate at a range of temporal and spatial scales. As in other scientific fields, continued application of dendrochronological techniques to study fires has shaped new trajectories for the science. Here we highlight some important current directions in the United States (US) and call on our international colleagues to continue the conversation with perspectives from other countries.

Effects of forests, roads and mistletoe on bird diversity in monoculture rubber plantations

NASA Astrophysics Data System (ADS)

Sreekar, Rachakonda; Huang, Guohualing; Yasuda, Mika; Quan, Rui-Chang; Goodale, Eben; Corlett, Richard T.; Tomlinson, Kyle W.

2016-02-01

Rising global demand for natural rubber is expanding monoculture rubber (Hevea brasilensis) at the expense of natural forests in the Old World tropics. Conversion of forests into rubber plantations has a devastating impact on biodiversity and we have yet to identify management strategies that can mitigate this. We determined the life-history traits that best predict bird species occurrence in rubber plantations in SW China and investigated the effects of surrounding forest cover and distance to roads on bird diversity. Mistletoes provide nectar and fruit resources in rubber so we examined mistletoe densities and the relationship with forest cover and rubber tree diameter. In rubber plantations, we recorded less than half of all bird species extant in the surrounding area. Birds with wider habitat breadths and low conservation value had a higher probability of occurrence. Species richness and diversity increased logarithmically with surrounding forest cover, but roads had little effect. Mistletoe density increased exponentially with rubber tree diameters, but was unrelated to forest cover. To maximize bird diversity in rubber-dominated landscapes it is therefore necessary to preserve as much forest as possible, construct roads through plantations and not forest, and retain some large rubber trees with mistletoes during crop rotations.

Effects of forests, roads and mistletoe on bird diversity in monoculture rubber plantations.

PubMed

Sreekar, Rachakonda; Huang, Guohualing; Yasuda, Mika; Quan, Rui-Chang; Goodale, Eben; Corlett, Richard T; Tomlinson, Kyle W

2016-02-23

Rising global demand for natural rubber is expanding monoculture rubber (Hevea brasilensis) at the expense of natural forests in the Old World tropics. Conversion of forests into rubber plantations has a devastating impact on biodiversity and we have yet to identify management strategies that can mitigate this. We determined the life-history traits that best predict bird species occurrence in rubber plantations in SW China and investigated the effects of surrounding forest cover and distance to roads on bird diversity. Mistletoes provide nectar and fruit resources in rubber so we examined mistletoe densities and the relationship with forest cover and rubber tree diameter. In rubber plantations, we recorded less than half of all bird species extant in the surrounding area. Birds with wider habitat breadths and low conservation value had a higher probability of occurrence. Species richness and diversity increased logarithmically with surrounding forest cover, but roads had little effect. Mistletoe density increased exponentially with rubber tree diameters, but was unrelated to forest cover. To maximize bird diversity in rubber-dominated landscapes it is therefore necessary to preserve as much forest as possible, construct roads through plantations and not forest, and retain some large rubber trees with mistletoes during crop rotations.

Evolutionary heritage influences Amazon tree ecology.

PubMed

Coelho de Souza, Fernanda; Dexter, Kyle G; Phillips, Oliver L; Brienen, Roel J W; Chave, Jerome; Galbraith, David R; Lopez Gonzalez, Gabriela; Monteagudo Mendoza, Abel; Pennington, R Toby; Poorter, Lourens; Alexiades, Miguel; Álvarez-Dávila, Esteban; Andrade, Ana; Aragão, Luis E O C; Araujo-Murakami, Alejandro; Arets, Eric J M M; Aymard C, Gerardo A; Baraloto, Christopher; Barroso, Jorcely G; Bonal, Damien; Boot, Rene G A; Camargo, José L C; Comiskey, James A; Valverde, Fernando Cornejo; de Camargo, Plínio B; Di Fiore, Anthony; Elias, Fernando; Erwin, Terry L; Feldpausch, Ted R; Ferreira, Leandro; Fyllas, Nikolaos M; Gloor, Emanuel; Herault, Bruno; Herrera, Rafael; Higuchi, Niro; Honorio Coronado, Eurídice N; Killeen, Timothy J; Laurance, William F; Laurance, Susan; Lloyd, Jon; Lovejoy, Thomas E; Malhi, Yadvinder; Maracahipes, Leandro; Marimon, Beatriz S; Marimon-Junior, Ben H; Mendoza, Casimiro; Morandi, Paulo; Neill, David A; Vargas, Percy Núñez; Oliveira, Edmar A; Lenza, Eddie; Palacios, Walter A; Peñuela-Mora, Maria C; Pipoly, John J; Pitman, Nigel C A; Prieto, Adriana; Quesada, Carlos A; Ramirez-Angulo, Hirma; Rudas, Agustin; Ruokolainen, Kalle; Salomão, Rafael P; Silveira, Marcos; Stropp, Juliana; Ter Steege, Hans; Thomas-Caesar, Raquel; van der Hout, Peter; van der Heijden, Geertje M F; van der Meer, Peter J; Vasquez, Rodolfo V; Vieira, Simone A; Vilanova, Emilio; Vos, Vincent A; Wang, Ophelia; Young, Kenneth R; Zagt, Roderick J; Baker, Timothy R

2016-12-14

Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of traits and evolutionary relationships among species. The Amazonian tree flora comprises a high diversity of angiosperm lineages and species with widely differing life-history characteristics, providing an excellent system to investigate the combined influences of evolutionary heritage and selection in determining trait variation. We used trait data related to the major axes of life-history variation among tropical trees (e.g. growth and mortality rates) from 577 inventory plots in closed-canopy forest, mapped onto a phylogenetic hypothesis spanning more than 300 genera including all major angiosperm clades to test for evolutionary constraints on traits. We found significant phylogenetic signal (PS) for all traits, consistent with evolutionarily related genera having more similar characteristics than expected by chance. Although there is also evidence for repeated evolution of pioneer and shade tolerant life-history strategies within independent lineages, the existence of significant PS allows clearer predictions of the links between evolutionary diversity, ecosystem function and the response of tropical forests to global change. © 2016 The Authors.

Evolutionary heritage influences Amazon tree ecology

PubMed Central

Coelho de Souza, Fernanda; Dexter, Kyle G.; Phillips, Oliver L.; Brienen, Roel J. W.; Chave, Jerome; Galbraith, David R.; Lopez Gonzalez, Gabriela; Monteagudo Mendoza, Abel; Pennington, R. Toby; Poorter, Lourens; Alexiades, Miguel; Álvarez-Dávila, Esteban; Andrade, Ana; Aragão, Luis E. O. C.; Araujo-Murakami, Alejandro; Arets, Eric J. M. M.; Aymard C, Gerardo A.; Baraloto, Christopher; Barroso, Jorcely G.; Bonal, Damien; Boot, Rene G. A.; Camargo, José L. C.; Comiskey, James A.; Valverde, Fernando Cornejo; de Camargo, Plínio B.; Di Fiore, Anthony; Erwin, Terry L.; Feldpausch, Ted R.; Ferreira, Leandro; Fyllas, Nikolaos M.; Gloor, Emanuel; Herault, Bruno; Herrera, Rafael; Higuchi, Niro; Honorio Coronado, Eurídice N.; Killeen, Timothy J.; Laurance, William F.; Laurance, Susan; Lloyd, Jon; Lovejoy, Thomas E.; Malhi, Yadvinder; Maracahipes, Leandro; Marimon, Beatriz S.; Marimon-Junior, Ben H.; Mendoza, Casimiro; Morandi, Paulo; Neill, David A.; Vargas, Percy Núñez; Oliveira, Edmar A.; Lenza, Eddie; Palacios, Walter A.; Peñuela-Mora, Maria C.; Pipoly, John J.; Pitman, Nigel C. A.; Prieto, Adriana; Quesada, Carlos A.; Ramirez-Angulo, Hirma; Rudas, Agustin; Ruokolainen, Kalle; Salomão, Rafael P.; Silveira, Marcos; ter Steege, Hans; Thomas-Caesar, Raquel; van der Hout, Peter; van der Heijden, Geertje M. F.; van der Meer, Peter J.; Vasquez, Rodolfo V.; Vieira, Simone A.; Vilanova, Emilio; Vos, Vincent A.; Wang, Ophelia; Young, Kenneth R.; Zagt, Roderick J.; Baker, Timothy R.

2016-01-01

Lineages tend to retain ecological characteristics of their ancestors through time. However, for some traits, selection during evolutionary history may have also played a role in determining trait values. To address the relative importance of these processes requires large-scale quantification of traits and evolutionary relationships among species. The Amazonian tree flora comprises a high diversity of angiosperm lineages and species with widely differing life-history characteristics, providing an excellent system to investigate the combined influences of evolutionary heritage and selection in determining trait variation. We used trait data related to the major axes of life-history variation among tropical trees (e.g. growth and mortality rates) from 577 inventory plots in closed-canopy forest, mapped onto a phylogenetic hypothesis spanning more than 300 genera including all major angiosperm clades to test for evolutionary constraints on traits. We found significant phylogenetic signal (PS) for all traits, consistent with evolutionarily related genera having more similar characteristics than expected by chance. Although there is also evidence for repeated evolution of pioneer and shade tolerant life-history strategies within independent lineages, the existence of significant PS allows clearer predictions of the links between evolutionary diversity, ecosystem function and the response of tropical forests to global change. PMID:27974517

Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria.

PubMed

Padial, José M; Grant, Taran; Frost, Darrel R

2014-06-26

Brachycephaloidea is a monophyletic group of frogs with more than 1000 species distributed throughout the New World tropics, subtropics, and Andean regions. Recently, the group has been the target of multiple molecular phylogenetic analyses, resulting in extensive changes in its taxonomy. Here, we test previous hypotheses of phylogenetic relationships for the group by combining available molecular evidence (sequences of 22 genes representing 431 ingroup and 25 outgroup terminals) and performing a tree-alignment analysis under the parsimony optimality criterion using the program POY. To elucidate the effects of alignment and optimality criterion on phylogenetic inferences, we also used the program MAFFT to obtain a similarity-alignment for analysis under both parsimony and maximum likelihood using the programs TNT and GARLI, respectively. Although all three analytical approaches agreed on numerous points, there was also extensive disagreement. Tree-alignment under parsimony supported the monophyly of the ingroup and the sister group relationship of the monophyletic marsupial frogs (Hemiphractidae), while maximum likelihood and parsimony analyses of the MAFFT similarity-alignment did not. All three methods differed with respect to the position of Ceuthomantis smaragdinus (Ceuthomantidae), with tree-alignment using parsimony recovering this species as the sister of Pristimantis + Yunganastes. All analyses rejected the monophyly of Strabomantidae and Strabomantinae as originally defined, and the tree-alignment analysis under parsimony further rejected the recently redefined Craugastoridae and Pristimantinae. Despite the greater emphasis in the systematics literature placed on the choice of optimality criterion for evaluating trees than on the choice of method for aligning DNA sequences, we found that the topological differences attributable to the alignment method were as great as those caused by the optimality criterion. Further, the optimal tree-alignment indicates that insertions and deletions occurred in twice as many aligned positions as implied by the optimal similarity-alignment, confirming previous findings that sequence turnover through insertion and deletion events plays a greater role in molecular evolution than indicated by similarity-alignments. Our results also provide a clear empirical demonstration of the different effects of wildcard taxa produced by missing data in parsimony and maximum likelihood analyses. Specifically, maximum likelihood analyses consistently (81% bootstrap frequency) provided spurious resolution despite a lack of evidence, whereas parsimony correctly depicted the ambiguity due to missing data by collapsing unsupported nodes. We provide a new taxonomy for the group that retains previously recognized Linnaean taxa except for Ceuthomantidae, Strabomantidae, and Strabomantinae. A phenotypically diagnosable superfamily is recognized formally as Brachycephaloidea, with the informal, unranked name terrarana retained as the standard common name for these frogs. We recognize three families within Brachycephaloidea that are currently diagnosable solely on molecular grounds (Brachycephalidae, Craugastoridae, and Eleutherodactylidae), as well as five subfamilies (Craugastorinae, Eleutherodactylinae, Holoadeninae, Phyzelaphryninae, and Pristimantinae) corresponding in large part to previous families and subfamilies. Our analyses upheld the monophyly of all tested genera, but we found numerous subgeneric taxa to be non-monophyletic and modified the taxonomy accordingly.

Object-based assessment of burn severity in diseased forests using high-spatial and high-spectral resolution MASTER airborne imagery

NASA Astrophysics Data System (ADS)

Chen, Gang; Metz, Margaret R.; Rizzo, David M.; Dillon, Whalen W.; Meentemeyer, Ross K.

2015-04-01

Forest ecosystems are subject to a variety of disturbances with increasing intensities and frequencies, which may permanently change the trajectories of forest recovery and disrupt the ecosystem services provided by trees. Fire and invasive species, especially exotic disease-causing pathogens and insects, are examples of disturbances that together could pose major threats to forest health. This study examines the impacts of fire and exotic disease (sudden oak death) on forests, with an emphasis on the assessment of post-fire burn severity in a forest where trees have experienced three stages of disease progression pre-fire: early-stage (trees retaining dried foliage and fine twigs), middle-stage (trees losing fine crown fuels), and late-stage (trees falling down). The research was conducted by applying Geographic Object-Based Image Analysis (GEOBIA) to MASTER airborne images that were acquired immediately following the fire for rapid assessment and contained both high-spatial (4 m) and high-spectral (50 bands) resolutions. Although GEOBIA has gradually become a standard tool for analyzing high-spatial resolution imagery, high-spectral resolution data (dozens to hundreds of bands) can dramatically reduce computation efficiency in the process of segmentation and object-based variable extraction, leading to complicated variable selection for succeeding modeling. Hence, we also assessed two widely used band reduction algorithms, PCA (principal component analysis) and MNF (minimum noise fraction), for the delineation of image objects and the subsequent performance of burn severity models using either PCA or MNF derived variables. To increase computation efficiency, only the top 5 PCA and MNF and top 10 PCA and MNF components were evaluated, which accounted for 10% and 20% of the total number of the original 50 spectral bands, respectively. Results show that if no band reduction was applied the models developed for the three stages of disease progression had relatively similar performance, where both spectral responses and texture contributed to burn assessments. However, the application of PCA and MNF introduced much greater variation among models across the three stages. For the early-stage disease progression, neither band reduction algorithms improved or retained the accuracy of burn severity modeling (except for the use of 10 MNF components). Compared to the no-band-reduction scenario, band reduction led to a greater level of overestimation of low-degree burns and underestimation of medium-degree burns, suggesting that the spectral variation removed by PCA and MNF was vital for distinguishing between the spectral reflectance from disease-induced dried crowns (still retaining high structural complexity) and fire ash. For the middle-stage, both algorithms improved the model R2 values by 2-37%, while the late-stage models had comparable or better performance to those using the original 50 spectral bands. This could be explained by the loss of tree crowns enabling better signal penetration, thus leading to reduced spectral variation from canopies. Hence, spectral bands containing a high degree of random noise were correctly removed by the band reduction algorithms. Compared to the middle-stage, the late-stage forest stands were covered by large piles of fallen trees and branches, resulting in higher variability of MASTER imagery. The ability of band reduction to improve the model performance for these late-stage forest stands was reduced, because the valuable spectral variation representing the actual late-stage forest status was partially removed by both algorithms as noise. Our results indicate that PCA and MNF are promising for balancing computation efficiency and the performance of burn severity models in forest stands subject to the middle and late stages of sudden oak death disease progression. Compared to PCA, MNF dramatically reduced image spectral variation, generating larger image objects with less complexity of object shapes. Whereas, PCA-based models delivered superior performance in most evaluated cases suggesting that some key spectral variability contributing to the accuracy of burn severity models in diseased forests may have been removed together with true spectral noise through MNF transformations.

Assessment of imperfect detection of blister rust in whitebark pine within the Greater Yellowstone Ecosystem

USGS Publications Warehouse

Wright, Wilson J.; Irvine, Kathryn M.

2017-01-01

We examined data on white pine blister rust (blister rust) collected during the monitoring of whitebark pine trees in the Greater Yellowstone Ecosystem (from 2004-2015). Summaries of repeat observations performed by multiple independent observers are reviewed and discussed. These summaries show variability among observers and the potential for errors being made in blister rust status. Based on this assessment, we utilized occupancy models to analyze blister rust prevalence while explicitly accounting for imperfect detection. Available covariates were used to model both the probability of a tree being infected with blister rust and the probability of an observer detecting the infection. The fitted model provided strong evidence that the probability of blister rust infection increases as tree diameter increases and decreases as site elevation increases. Most importantly, we found evidence of heterogeneity in detection probabilities related to tree size and average slope of a transect. These results suggested that detecting the presence of blister rust was more difficult in larger trees. Also, there was evidence that blister rust was easier to detect on transects located on steeper slopes. Our model accounted for potential impacts of observer experience on blister rust detection probabilities and also showed moderate variability among the different observers in their ability to detect blister rust. Based on these model results, we suggest that multiple observer sampling continue in future field seasons in order to allow blister rust prevalence estimates to be corrected for imperfect detection. We suggest that the multiple observer effort be spread out across many transects (instead of concentrated at a few each field season) while retaining the overall proportion of trees with multiple observers around 5-20%. Estimates of prevalence are confounded with detection unless it is explicitly accounted for in an analysis and we demonstrate how an occupancy model can be used to do account for this source of observation error.

Liftoff of the 18 May 1980 surge of Mount St. Helens (USA) and the deposits left behind

NASA Astrophysics Data System (ADS)

Gardner, James E.; Andrews, Benjamin J.; Dennen, Robert

2017-01-01

The distance that ground-hugging pyroclastic density currents travel is limited partly by when they reverse buoyancy and liftoff into the atmosphere. It is not clear, however, what deposits are left behind by lofting flows. One current that was seen to liftoff was the surge erupted from Mount St. Helens on the morning of 18 May 1980. Before lofting, it had leveled a large area of thick forest (the blowdown zone). The outer edge of the devastated area—where trees were scorched but left standing (the scorched zone)—is where the surge is thought to have lifted off. Deposits in the outer parts of the blowdown and in the scorched zone were examined at 32 sites. The important finding is that the laterally moving surge traveled through the scorched zone, and hence, the change in tree damage does not mark the runout distance of the surge. Buoyancy reversal and liftoff are thus not preserved in the deposits where the surge lofted upwards. We propose, based on interpretation of eyewitness accounts and the impacts of the surge on trees and vehicles, that the surge consisted of a faster, dilute "overcurrent" and a slower "undercurrent," where most of the mass (and heat) was retained. Reasonable estimates for flow density and velocity show that dynamic pressure of the surge (i.e., its ability to topple trees) peaked near the base of the overcurrent. We propose that where the overcurrent began to liftoff, the height of peak dynamic pressure rose above the trees and stopped toppling them. The slower undercurrent continued forward, however, scorching trees, but lacked the dynamic pressure needed to topple them. Grain-size variations argue that it slowed from ˜30 m s-1 when it entered the scorched zone to ˜3 m s-1 at the far end.

Runout distance and dynamic pressure of pyroclastic density currents: Evidence from 18 May 1980 blast surge of Mount St. Helens

NASA Astrophysics Data System (ADS)

Gardner, J. E.; Andrews, B. J.

2016-12-01

Pyroclastic density currents (flows and surges) are one of the most deadly hazards associated with volcanic eruptions. Understanding what controls how far such currents will travel, and how their dynamic pressure evolves, could help mitigate their hazards. The distance a ground hugging, pyroclastic density current travels is partly limited by when it reverses buoyancy and lifts off into the atmosphere. The 1980 blast surge of Mount St. Helens offers an example of a current seen to lift off. Before lofting, it had traveled up to 20 km and leveled more than 600 km3 of thick forest (the blowdown zone). The outer edge of the devastated area - where burned trees that were left standing (the singe zone) - is where the surge is thought to have lifted off. We recently examined deposits in the outer parts of the blowdown and in the singe zone at 32 sites. The important finding is that the laterally moving surge travelled into the singe zone, and hence the change in tree damage does not mark the run out distance of the ground hugging surge. Eyewitness accounts and impacts on trees and vehicles reveal that the surge consisted of a fast, dilute "overcurrent" and a slower "undercurrent", where most of the mass (and heat) was retained. Reasonable estimates for flow density and velocity show that dynamic pressure of the surge (i.e., its ability to topple trees) peaked near the base of the overcurrent. We propose that when the overcurrent began to lift off, the height of peak dynamic pressure rose above the trees and stopped toppling them. The slower undercurrent continued forward, burning trees but it lacked the dynamic pressure needed to topple them. Grain-size variations argue that it slowed from 30 m/s when it entered the singe zone to 3 m/s at the far end. Buoyancy reversal and liftoff are thus not preserved in the deposits where the surge lofted upwards.

Continuous fields of land cover for the conterminous United States using Landsat data: First results from the Web-Enabled Landsat Data (WELD) project

USGS Publications Warehouse

Hansen, M.C.; Egorov, Alexey; Roy, David P.; Potapov, P.; Ju, J.; Turubanova, S.; Kommareddy, I.; Loveland, Thomas R.

2011-01-01

Vegetation Continuous Field (VCF) layers of 30 m percent tree cover, bare ground, other vegetation and probability of water were derived for the conterminous United States (CONUS) using Landsat 7 Enhanced Thematic Mapper Plus (ETM+) data sets from the Web-Enabled Landsat Data (WELD) project. Turnkey approaches to land cover characterization were enabled due to the systematic WELD Landsat processing, including conversion of digital numbers to calibrated top of atmosphere reflectance and brightness temperature, cloud masking, reprojection into a continental map projection and temporal compositing. Annual, seasonal and monthly WELD composites for 2008 were used as spectral inputs to a bagged regression and classification tree procedure using a large training data set derived from very high spatial resolution imagery and available ancillary data. The results illustrate the ability to perform Landsat land cover characterizations at continental scales that are internally consistent while retaining local spatial and thematic detail.

Decoupling of unpolluted temperate forests from rock nutrient sources revealed by natural (87)Sr/(86)Sr and (84)Sr tracer addition.

PubMed

Kennedy, Martin J; Hedin, Lars O; Derry, Louis A

2002-07-23

An experimental tracer addition of (84)Sr to an unpolluted temperate forest site in southern Chile, as well as the natural variation of (87)Sr/(86)Sr within plants and soils, indicates that mechanisms in shallow soil organic horizons are of key importance for retaining and recycling atmospheric cation inputs at scales of decades or less. The dominant tree species Nothofagus nitida feeds nearly exclusively (>90%) on cations of atmospheric origin, despite strong variations in tree size and location in the forest landscape. Our results illustrate that (i) unpolluted temperate forests can become nutritionally decoupled from deeper weathering processes, virtually functioning as atmospherically fed ecosystems, and (ii) base cation turnover times are considerably more rapid than previously recognized in the plant available pool of soil. These results challenge the prevalent paradigm that plants largely feed on rock-derived cations and have important implications for understanding sensitivity of forests to air pollution.

Effects of forests, roads and mistletoe on bird diversity in monoculture rubber plantations

PubMed Central

Sreekar, Rachakonda; Huang, Guohualing; Yasuda, Mika; Quan, Rui-Chang; Goodale, Eben; Corlett, Richard T.; Tomlinson, Kyle W.

2016-01-01

Rising global demand for natural rubber is expanding monoculture rubber (Hevea brasilensis) at the expense of natural forests in the Old World tropics. Conversion of forests into rubber plantations has a devastating impact on biodiversity and we have yet to identify management strategies that can mitigate this. We determined the life-history traits that best predict bird species occurrence in rubber plantations in SW China and investigated the effects of surrounding forest cover and distance to roads on bird diversity. Mistletoes provide nectar and fruit resources in rubber so we examined mistletoe densities and the relationship with forest cover and rubber tree diameter. In rubber plantations, we recorded less than half of all bird species extant in the surrounding area. Birds with wider habitat breadths and low conservation value had a higher probability of occurrence. Species richness and diversity increased logarithmically with surrounding forest cover, but roads had little effect. Mistletoe density increased exponentially with rubber tree diameters, but was unrelated to forest cover. To maximize bird diversity in rubber-dominated landscapes it is therefore necessary to preserve as much forest as possible, construct roads through plantations and not forest, and retain some large rubber trees with mistletoes during crop rotations. PMID:26903032

Reconstructions of Soil Moisture for the Upper Colorado River Basin Using Tree-Ring Chronologies

NASA Astrophysics Data System (ADS)

Tootle, G.; Anderson, S.; Grissino-Mayer, H.

2012-12-01

Soil moisture is an important factor in the global hydrologic cycle, but existing reconstructions of historic soil moisture are limited. Tree-ring chronologies (TRCs) were used to reconstruct annual soil moisture in the Upper Colorado River Basin (UCRB). Gridded soil moisture data were spatially regionalized using principal components analysis and k-nearest neighbor techniques. Moisture sensitive tree-ring chronologies in and adjacent to the UCRB were correlated with regional soil moisture and tested for temporal stability. TRCs that were positively correlated and stable for the calibration period were retained. Stepwise linear regression was applied to identify the best predictor combinations for each soil moisture region. The regressions explained 42-78% of the variability in soil moisture data. We performed reconstructions for individual soil moisture grid cells to enhance understanding of the disparity in reconstructive skill across the regions. Reconstructions that used chronologies based on ponderosa pines (Pinus ponderosa) and pinyon pines (Pinus edulis) explained increased variance in the datasets. Reconstructed soil moisture was standardized and compared with standardized reconstructed streamflow and snow water equivalent from the same region. Soil moisture reconstructions were highly correlated with streamflow and snow water equivalent reconstructions, indicating reconstructions of soil moisture in the UCRB using TRCs successfully represent hydrologic trends, including the identification of periods of prolonged drought.

Labeling RDF Graphs for Linear Time and Space Querying

NASA Astrophysics Data System (ADS)

Furche, Tim; Weinzierl, Antonius; Bry, François

Indices and data structures for web querying have mostly considered tree shaped data, reflecting the view of XML documents as tree-shaped. However, for RDF (and when querying ID/IDREF constraints in XML) data is indisputably graph-shaped. In this chapter, we first study existing indexing and labeling schemes for RDF and other graph datawith focus on support for efficient adjacency and reachability queries. For XML, labeling schemes are an important part of the widespread adoption of XML, in particular for mapping XML to existing (relational) database technology. However, the existing indexing and labeling schemes for RDF (and graph data in general) sacrifice one of the most attractive properties of XML labeling schemes, the constant time (and per-node space) test for adjacency (child) and reachability (descendant). In the second part, we introduce the first labeling scheme for RDF data that retains this property and thus achieves linear time and space processing of acyclic RDF queries on a significantly larger class of graphs than previous approaches (which are mostly limited to tree-shaped data). Finally, we show how this labeling scheme can be applied to (acyclic) SPARQL queries to obtain an evaluation algorithm with time and space complexity linear in the number of resources in the queried RDF graph.

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules

PubMed Central

Ashkenazy, Haim; Abadi, Shiran; Martz, Eric; Chay, Ofer; Mayrose, Itay; Pupko, Tal; Ben-Tal, Nir

2016-01-01

The degree of evolutionary conservation of an amino acid in a protein or a nucleic acid in DNA/RNA reflects a balance between its natural tendency to mutate and the overall need to retain the structural integrity and function of the macromolecule. The ConSurf web server (http://consurf.tau.ac.il), established over 15 years ago, analyses the evolutionary pattern of the amino/nucleic acids of the macromolecule to reveal regions that are important for structure and/or function. Starting from a query sequence or structure, the server automatically collects homologues, infers their multiple sequence alignment and reconstructs a phylogenetic tree that reflects their evolutionary relations. These data are then used, within a probabilistic framework, to estimate the evolutionary rates of each sequence position. Here we introduce several new features into ConSurf, including automatic selection of the best evolutionary model used to infer the rates, the ability to homology-model query proteins, prediction of the secondary structure of query RNA molecules from sequence, the ability to view the biological assembly of a query (in addition to the single chain), mapping of the conservation grades onto 2D RNA models and an advanced view of the phylogenetic tree that enables interactively rerunning ConSurf with the taxa of a sub-tree. PMID:27166375

Deposition of organic material in a coral reef lagoon, One Tree Island, Great Barrier Reef

NASA Astrophysics Data System (ADS)

Koop, K.; Larkum, A. W. D.

1987-07-01

Deposition of organic material was measured at four sites on One Tree Island coral reef using fixed sediment traps. Although no reliable data were obtained for the reef crest area because of problems of resuspension, mean deposition in the backreef area amounted to some 4 g organic C m -2 day -1 whereas in the lagoon it was about 1·5 g C m -2 day -1. This amounted to mean nitrogen deposition rates of 160 and 95 mg N m -2 day -1, respectively. As primary production by turf algae, the principal producers at One Tree Island, has been estimated at about 2·3 g C m -2 day -1 for the whole reef system and the weighted mean carbon deposition is estimated at 2·2 g C m -2 day -1, it is clear that the carbon produced by plants is largely retained in the system. Nitrogen deposition, on the other hand, amounted to only about 60% of that produced by turf algae and it must be assumed that much of this leached into the water during sedimentation. Losses of nitrogen may be minimized by incorporation of dissolved nitrogen by pelagic microheterotrophs which may in turn be consumed by filter feeders before they leave the reef.

Seed gum of Stryphnodendron barbatiman (Barbatimao)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reicher, F.; Leitner, S.C.S.; Fontana, J.D.

1991-12-31

Stryphnodendron barbatiman (barbatimao) is a native tree that is found throughout the {open_quotes}Cerrados,{close_quotes} a region of Central Brazil. Plant seeds, on water extraction, furnished 28 g% galactomannan (dry-weight basis), the monosaccharide composition of which (galactose to mannose ratio, 1.0:1.5) fits in the legume heteromannan group. This seed gum, after Sevag deproteinization, still retained 6 g% of associated protein and had a molecular weight of about 1.8 MD on gel filtration. A high intrinsic viscosity (1300 cP) was observed for the polysaccharide sample obtained after reflux of the crushed seeds in 80% aqueous methanol.

Sinks for Inorganic Nitrogen Deposition in Forest Ecosystems with Low and High Nitrogen Deposition in China

PubMed Central

Sheng, Wenping; Yu, Guirui; Fang, Huajun; Jiang, Chunming; Yan, Junhua; Zhou, Mei

2014-01-01

We added the stable isotope 15N in the form of (15NH4)2SO4 and K15NO3 to forest ecosystems in eastern China under two different N deposition levels to study the fate of the different forms of deposited N. Prior to the addition of the 15N tracers, the natural 15N abundance ranging from −3.4‰ to +10.9‰ in the forest under heavy N deposition at Dinghushan (DHS), and from −3.92‰ to +7.25‰ in the forest under light N deposition at Daxinganling (DXAL). Four months after the tracer application, the total 15N recovery from the major ecosystem compartments ranged from 55.3% to 90.5%. The total 15N recoveries were similar under the (15NH4)2SO4 tracer treatment in both two forest ecosystems, whereas the total 15N recovery was significantly lower in the subtropical forest ecosystem at DHS than in the boreal forest ecosystem at DXAL under the K15NO3 tracer treatment. The 15N assimilated into the tree biomass represented only 8.8% to 33.7% of the 15N added to the forest ecosystems. In both of the tracer application treatments, more 15N was recovered from the tree biomass in the subtropical forest ecosystem at DHS than the boreal forest ecosystem at DXAL. The amount of 15N assimilated into tree biomass was greater under the K15NO3 tracer treatment than that of the (15NH4)2SO4 treatment in both forest ecosystems. This study suggests that, although less N was immobilized in the forest ecosystems under more intensive N deposition conditions, forest ecosystems in China strongly retain N deposition, even in areas under heavy N deposition intensity or in ecosystems undergoing spring freezing and thawing melts. Compared to ammonium deposition, deposited nitrate is released from the forest ecosystem more easily. However, nitrate deposition could be retained mostly in the plant N pool, which might lead to more C sequestration in these ecosystems. PMID:24586688

Highly Active Ice Nuclei from Tree Leaf Litters Retain Activity for Decades

NASA Astrophysics Data System (ADS)

Schnell, R. C.; Hill, T. C. J.

2015-12-01

Biogenic ice nuclei (IN) studied since the 1960s were first observed in tree leaf litters, in a few bacteria species and later in fungi and lichens. Recently, viable IN bacteria in precipitation have been used as a metric of their possible role in precipitation formation. Although bacterial IN activity is deactivated by a variety of common environmental stresses, we present data showing that IN found in a potpourri of decayed plant leaves, bacteria, molds and fungi etc. in plant litters are exceptionally stable and active over decades while in storage. As such, their atmospheric IN potential is worthy of further study due to their environmental persistence. In August 1970 litter collected in a grove of deciduous trees near Red Deer, AB, Canada was tested for IN (drop freezing technique). The sample initiated ice at -4C with 109 IN per gram of litter active at -10C. A few kilograms were stored in a plastic bag and tested every few years for IN content; the IN activity remained essentially unchanged over 40 years. In 2011, litter collected in the same grove had the same IN activity as the sample tested over the intervening 40 years. Boiling a gram sample of this litter in 100 grams of water deactivated 99 % of the IN activity down to -13C. None of 88 different bacteria cultures several of which appeared to Pseudomonads (common IN producing bacteria) from the fresh litter produced any active IN. A sample of the litter was placed on the top of a 15 cm column of laboratory grade kaolin and water dripped onto the litter. Ten days later the water reached the bottom of the column. The kaolin was dried and tested for IN. The prior essentially IN free kaolin now exhibited IN activity at -4C with 105 IN active at -10C. The litter exposed kaolin retained the IN activity for 25 years. Baking the kaolin removed the active IN. This suggests that IN activity attributed to kaolin particles sometimes seen at the nucleus of snow crystals could be of biological origin.

Sinks for inorganic nitrogen deposition in forest ecosystems with low and high nitrogen deposition in China.

PubMed

Sheng, Wenping; Yu, Guirui; Fang, Huajun; Jiang, Chunming; Yan, Junhua; Zhou, Mei

2014-01-01

We added the stable isotope (15)N in the form of ((15)NH4)2SO4 and K(15)NO3 to forest ecosystems in eastern China under two different N deposition levels to study the fate of the different forms of deposited N. Prior to the addition of the (15)N tracers, the natural (15)N abundance ranging from -3.4‰ to +10.9‰ in the forest under heavy N deposition at Dinghushan (DHS), and from -3.92‰ to +7.25‰ in the forest under light N deposition at Daxinganling (DXAL). Four months after the tracer application, the total (15)N recovery from the major ecosystem compartments ranged from 55.3% to 90.5%. The total (15)N recoveries were similar under the ((15)NH4)2SO4 tracer treatment in both two forest ecosystems, whereas the total (15)N recovery was significantly lower in the subtropical forest ecosystem at DHS than in the boreal forest ecosystem at DXAL under the K(15)NO3 tracer treatment. The (15)N assimilated into the tree biomass represented only 8.8% to 33.7% of the (15)N added to the forest ecosystems. In both of the tracer application treatments, more (15)N was recovered from the tree biomass in the subtropical forest ecosystem at DHS than the boreal forest ecosystem at DXAL. The amount of (15)N assimilated into tree biomass was greater under the K(15)NO3 tracer treatment than that of the ((15)NH4)2SO4 treatment in both forest ecosystems. This study suggests that, although less N was immobilized in the forest ecosystems under more intensive N deposition conditions, forest ecosystems in China strongly retain N deposition, even in areas under heavy N deposition intensity or in ecosystems undergoing spring freezing and thawing melts. Compared to ammonium deposition, deposited nitrate is released from the forest ecosystem more easily. However, nitrate deposition could be retained mostly in the plant N pool, which might lead to more C sequestration in these ecosystems.

Does tree harvesting in riparian areas increase stream sedimentation and turbidity - world-wide experience relative to Australia.

NASA Astrophysics Data System (ADS)

Neary, D.; Smethurst, P.; Petrone, K.

2009-04-01

A typical improved-pasture property in the high-rainfall zone of Australia contains 0.5-2.0 km of waterways per 100 ha. Nationwide, some 25-30 million ha of improved pasture contains about 100,000 km of streams, of which about 75% are currently un-buffered and contributing to soil and water degradation. Farmers and natural resource managers are considering ways to enhance environmental outcomes at farm and catchment scales using stream-side buffers of trees and other perennial vegetation. Benefits of buffers include improved water quality, biodiversity, carbon sequestration and aesthetics. Lack of sound information and funding for establishing and managing buffer zones is hindering wide-scale adoption of this practice. Stream-side areas of farms are generally highly productive (wet and nutrient-rich) and contain a high biodiversity, but they are also high-risk zones for soil and water values and stock safety. Development of options based on a balance between environmental and economic outcomes would potentially promote wider adoption. Australian codes of forest practice currently discourage or prevent harvesting of trees in streamside buffers. These codes were developed exclusively for large-scale native forests and industrial-scale plantations, and were applicable to farm forestry as now required. In countries including USA and Germany trees in stream-side buffers are harvested using Best Management Practices. Trees may grow at a faster rate in riparian zones and provide a commercial return, but the impacts of tree establishment and harvesting on water yield and quality must be evaluated. However, there have been few designed experiments investigating this problem. Australia has recently initiated studies to explore the use of high-value timber species and associated vegetation in riparian zones to improve water quality, particularly suspended sediment. Preliminary information from the Yan Yan Gurt Catchment in Victoria indicate that forested riparian strips can retain 98% of the sediment entrained in runoff from agricultural sections of the catchment. This paper examines the science background from North American and European experiences relative to Australia, with particular emphasis on sediment relationships after tree harvesting using Best Management Practices.

Belowground Carbon Allocation to Ectomycorrhizal Fungi Links Biogeochemical Cycles of Boron and Nitrogen

NASA Astrophysics Data System (ADS)

Lucas, R. W.; Högberg, P.; Ingri, J. N.

2011-12-01

Boron (B) is an essential micronutrient to most trees and represents an important limiting resource in some regions, deficient trees experiencing the loss of apical dominance, altered stem growth, and even tree death in extreme cases. Similar to the acquisition of most soil nutrients, B is likely supplied to host trees by mycorrhizal symbionts in exchange for recently fixed carbohydrates. In this way, belowground allocation of photosynthate, which drives the majority of biological processes belowground, links the biogeochemical cycles of B and nitrogen (N). Using a long-term N addition experiment in a Pinus sylvestris forest that has been ongoing for 41 years, we examined how the availability of inorganic N mediates the response of B isotopes in the tree needles, organic soil, and fungal pools in a boreal forest in northern Sweden. Using archived needle samples collected annually from the current year's needle crop, we observed δ11B to increase from 30.8 (0.5 se) to 41.8 (0.7 se)% in N fertilized plots from 1970 to 1979, a period of increasing B deficiency stress induced by N fertilization; the concentration of B in tree needles during 1979 dropping as low as 3.0 μg g-2. During the same period, B concentrations in tree needles from control plots remained relatively unchanged and δ11B remained at a steady state value of 34.1 (1.0 se)%. Following a distinct, large-scale, pulse labeling event in 1980 in which 2.5 kg ha-1 of isotopically distinct B was applied to all treatment and control plots to alleviate the N-induced B deficiency, concentrations of B in current needles increased immediately in all treatments, the magnitude of the response being dependent upon the N treatment. But unlike other pool dilution studies, δ11B of current tree needles did not return to pre-addition, steady-state levels. Instead, δ11B continued to decrease over time in both N addition and control treatments. This unexpected pattern has not been previously described but can be explained by the preferential translocation of 10B to their host trees by ectomycorrhizal fungi, while the fungal partner retains the heavier 11B. Repeated fractionation over time leads to progressively larger differences in δ11B in both current tree needles and also fungal tissue, analogous to the repeated fractionation of N isotopes by ectomycorrhizal fungi.

Spatial Variability of Tree Transpiration Along a Soil Drainage Gradient of Boreal Black Spruce Forest

NASA Astrophysics Data System (ADS)

Angstmann, J. L.; Ewers, B. E.; Kwon, H.; Bond-Lamberty, B.; Amiro, B.; Gower, S. T.

2008-12-01

Boreal forests are an integral component in obtaining a predictive understanding of global climate change because they comprise 33% of the world's forests and store large amounts of carbon. Much of this carbon storage is a result of peat formation in cold, poorly-drained soils. Transpiration plays a crucial role in the interaction between carbon and water cycles due to stomatal control of these fluxes. The primary focus of this study is to quantify the spatial variability and drivers of tree transpiration in boreal forest stands across a well- to poorly-drained soil drainage gradient. Species composition of this region of boreal forest changes during succession in well-drained soils from being primarily dominated by Picea mariana with co-dominant Pinus banksiana and Populus tremuloides in younger stands to being dominated solely by Picea marianain older stands. Poorly-drained soils are dominated by Picea mariana and change little with succession. Previous work in well-drained stands showed that 1) tree transpiration changed substantially with stand age due to sapwood-to-leaf area ratio dynamics and 2) minimum leaf water potential (Ψ) was kept constant to prevent excessive cavitation. We hypothesized that 1) minimum Ψ would be constant, 2) transpiration would be proportional to the sapwood-to-leaf area ratio across a soil drainage gradient, and 3) spatial relationships between trees would vary depending on stomatal responses to vapor pressure deficit (D). We tested these hypotheses by measuring Ψ of 33 trees and sap flux from 204 trees utilizing cyclic sampling constructed to study spatial relationships. Measurements were conducted at a 42-year-old stand representing maximum tree diversity during succession. There were no significant differences between growing season averaged Ψ in well- (-0.35 and -1.37 for pre-dawn and mid-day respectively) and poorly- drained soil conditions (-0.38 and -1.41 for pre-dawn and mid-day respectively) for Picea mariana. Water use results of Picea mariana differed between drainage conditions when expressed per unit xylem area with trees in poorly-drained soils experiencing higher rates than trees in well-drained areas (101.79 and 83.02 g cm-2 day-1 respectively). In contrast, when expressed as transpiration per tree, trees on well-drained soils had higher rates than those in poorly-drained locations (366.96 and 216.82 g tree-1 day-1 respectively). This indicates that tree size, reflected in sapwood area per ground area, which is constrained by anaerobic conditions across well- to poorly-drained areas, is driving differences in tree transpiration. Initial spatial analyses show that spatial autocorrelation decreases from 51.3 to 24.6 meters as D increases from 0.9 to 2.1 kPa. This phenomenon is explained by tree hydraulics and more patchy stomatal response as trees regulate water loss. Thus, regional scale bottom-up process models of boreal forest transpiration can be simplified with respect to soil drainage while retaining mechanistic rigor with respect to plant hydraulics.

Forest structure of oak plantations after silvicultural treatment to enhance habitat for wildlife

USGS Publications Warehouse

Twedt, Daniel J.; Phillip, Cherrie-Lee P.; Guilfoyle, Michael P.; Wilson, R. Randy; Schweitzer, Callie Jo; Clatterbuck, Wayne K.; Oswalt, Christopher M.

2016-01-01

During the past 30 years, thousands of hectares of oak-dominated bottomland hardwood plantations have been planted on agricultural fields in the Mississippi Alluvial Valley. Many of these plantations now have closed canopies and sparse understories. Silvicultural treatments could create a more heterogeneous forest structure, with canopy gaps and increased understory vegetation for wildlife. Lack of volume sufficient for commercial harvest in hardwood plantations has impeded treatments, but demand for woody biomass for energy production may provide a viable means to introduce disturbance beneficial for wildlife. We assessed forest structure in response to prescribed pre-commercial perturbations in hardwood plantations resulting from silvicultural treatments: 1) row thinning by felling every fourth planted row; 2) multiple patch cuts with canopy gaps of <1 0.25 – 2 ha; and 3) tree removal on intersecting corridors diagonal to planted rows. These 3 treatments, and an untreated control, were applied to oak plantations (20 - 30 years post-planting) on three National Wildlife Refuges (Cache River, AR; Grand Cote, LA; and Yazoo, MS) during summer 2010. We sampled habitat using fixed-radius plots in 2009 (pre-treatment) and in 2012 (post-treatment) at random locations. Retained basal area was least in diagonal corridor treatments but had greater variance in patch-cut treatments. All treatments increased canopy openness and the volume of coarse woody debris. Occurrence of birds using early successional habitats was greater on sites treated with patch cuts and diagonal intersections. Canopy openings on row-thinned stands are being filled by lateral crown growth of retained trees whereas patch cut and diagonal intersection gaps appear likely to be filled by regenerating saplings.

A dynamic processes study of PM retention by trees under different wind conditions.

PubMed

Xie, Changkun; Kan, Liyan; Guo, Jiankang; Jin, Sijia; Li, Zhigang; Chen, Dan; Li, Xin; Che, Shengquan

2018-02-01

Particulate matter (PM) is one of the most serious environmental problems, exacerbating respiratory and vascular illnesses. Plants have the ability to reduce non-point source PM pollution through retention on leaves and branches. Studies of the dynamic processes of PM retention by plants and the mechanisms influencing this process will help to improve the efficiency of urban greening for PM reduction. We examined dynamic processes of PM retention and the major factors influencing PM retention by six trees with different branch structure characteristics in wind tunnel experiments at three different wind speeds. The results showed that the changes of PM numbers retained by plant leaves over time were complex dynamic processes for which maximum values could exceed minimum values by over 10 times. The average value of PM measured in multiple periods and situations can be considered a reliable indicator of the ability of the plant to retain PM. The dynamic processes were similar for PM 10 and PM 2.5 . They could be clustered into three groups simulated by continually-rising, inverse U-shaped, and U-shaped polynomial functions, respectively. The processes were the synthetic effect of characteristics such as species, wind speed, period of exposure and their interactions. Continually-rising functions always explained PM retention in species with extremely complex branch structure. Inverse U-shaped processes explained PM retention in species with relatively simple branch structure and gentle wind. The U-shaped processes mainly explained PM retention at high wind speeds and in species with a relatively simple crown. These results indicate that using plants with complex crowns in urban greening and decreasing wind speed in plant communities increases the chance of continually-rising or inverse U-shaped relationships, which have a positive effect in reducing PM pollution. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molecular proxies for climate maladaptation in a long-lived tree (Pinus pinaster Aiton, Pinaceae).

PubMed

Jaramillo-Correa, Juan-Pablo; Rodríguez-Quilón, Isabel; Grivet, Delphine; Lepoittevin, Camille; Sebastiani, Federico; Heuertz, Myriam; Garnier-Géré, Pauline H; Alía, Ricardo; Plomion, Christophe; Vendramin, Giovanni G; González-Martínez, Santiago C

2015-03-01

Understanding adaptive genetic responses to climate change is a main challenge for preserving biological diversity. Successful predictive models for climate-driven range shifts of species depend on the integration of information on adaptation, including that derived from genomic studies. Long-lived forest trees can experience substantial environmental change across generations, which results in a much more prominent adaptation lag than in annual species. Here, we show that candidate-gene SNPs (single nucleotide polymorphisms) can be used as predictors of maladaptation to climate in maritime pine (Pinus pinaster Aiton), an outcrossing long-lived keystone tree. A set of 18 SNPs potentially associated with climate, 5 of them involving amino acid-changing variants, were retained after performing logistic regression, latent factor mixed models, and Bayesian analyses of SNP-climate correlations. These relationships identified temperature as an important adaptive driver in maritime pine and highlighted that selective forces are operating differentially in geographically discrete gene pools. The frequency of the locally advantageous alleles at these selected loci was strongly correlated with survival in a common garden under extreme (hot and dry) climate conditions, which suggests that candidate-gene SNPs can be used to forecast the likely destiny of natural forest ecosystems under climate change scenarios. Differential levels of forest decline are anticipated for distinct maritime pine gene pools. Geographically defined molecular proxies for climate adaptation will thus critically enhance the predictive power of range-shift models and help establish mitigation measures for long-lived keystone forest trees in the face of impending climate change. Copyright © 2015 by the Genetics Society of America.

Initial responses of rove and ground beetles (Coleoptera, Staphylinidae, Carabidae) to removal of logging residues following clearcut harvesting in the boreal forest of Quebec, Canada

PubMed Central

Work, Timothy T.; Klimaszewski, Jan; Thiffault, Evelyne; Bourdon, Caroline; Paré, David; Bousquet, Yves; Venier, Lisa; Titus, Brian

2013-01-01

Abstract Increased interest in biomass harvesting for bioenergetic applications has raised questions regarding the potential ecological consequences on forest biodiversity. Here we evaluate the initial changes in the abundance, species richness and community composition of rove (Staphylinidae) and ground beetles (Carabidae), immediately following 1) stem-only harvesting (SOH), in which logging debris (i.e., tree tops and branches) are retained on site, and 2) whole-tree harvesting (WTH), in which stems, tops and branches are removed in mature balsam fir stands in Quebec, Canada. Beetles were collected throughout the summer of 2011, one year following harvesting, using pitfall traps. Overall catch rates were greater in uncut forest (Control) than either stem-only or whole-tree harvested sites. Catch rates in WTH were greater than SOH sites. Uncut stands were characterized primarily by five species: Atheta capsularis, Atheta klagesi, Atheta strigosula, Tachinus fumipennis/frigidus complex (Staphylinidae) and to a lesser extent to Pterostichus punctatissimus (Carabidae). Increased catch rates in WTH sites, where post-harvest biomass was less, were attributable to increased catches of rove beetles Pseudopsis subulata, Quedius labradorensis and to a lesser extent Gabrius brevipennis. We were able to characterize differences in beetle assemblages between harvested and non-harvested plots as well as differences between whole tree (WTH) and stem only (SOH) harvested sites where logging residues had been removed or left following harvest. However, the overall assemblage response was largely a recapitulation of the responses of several abundant species. PMID:23653498

Initial responses of rove and ground beetles (Coleoptera, Staphylinidae, Carabidae) to removal of logging residues following clearcut harvesting in the boreal forest of Quebec, Canada.

PubMed

Work, Timothy T; Klimaszewski, Jan; Thiffault, Evelyne; Bourdon, Caroline; Paré, David; Bousquet, Yves; Venier, Lisa; Titus, Brian

2013-01-01

Increased interest in biomass harvesting for bioenergetic applications has raised questions regarding the potential ecological consequences on forest biodiversity. Here we evaluate the initial changes in the abundance, species richness and community composition of rove (Staphylinidae) and ground beetles (Carabidae), immediately following 1) stem-only harvesting (SOH), in which logging debris (i.e., tree tops and branches) are retained on site, and 2) whole-tree harvesting (WTH), in which stems, tops and branches are removed in mature balsam fir stands in Quebec, Canada. Beetles were collected throughout the summer of 2011, one year following harvesting, using pitfall traps. Overall catch rates were greater in uncut forest (Control) than either stem-only or whole-tree harvested sites. Catch rates in WTH were greater than SOH sites. Uncut stands were characterized primarily by five species: Atheta capsularis, Atheta klagesi, Atheta strigosula, Tachinus fumipennis/frigidus complex (Staphylinidae) and to a lesser extent to Pterostichus punctatissimus(Carabidae). Increased catch rates in WTH sites, where post-harvest biomass was less, were attributable to increased catches of rove beetles Pseudopsis subulata, Quedius labradorensis and to a lesser extent Gabrius brevipennis. We were able to characterize differences in beetle assemblages between harvested and non-harvested plots as well as differences between whole tree (WTH) and stem only (SOH) harvested sites where logging residues had been removed or left following harvest. However, the overall assemblage response was largely a recapitulation of the responses of several abundant species.

Omega-3 long-chain polyunsaturated fatty acids support aerial insectivore performance more than food quantity.

PubMed

Twining, Cornelia W; Brenna, J Thomas; Lawrence, Peter; Shipley, J Ryan; Tollefson, Troy N; Winkler, David W

2016-09-27

Once-abundant aerial insectivores, such as the Tree Swallow (Tachycineta bicolor), have declined steadily in the past several decades, making it imperative to understand all aspects of their ecology. Aerial insectivores forage on a mixture of aquatic and terrestrial insects that differ in fatty acid composition, specifically long-chain omega-3 polyunsaturated fatty acid (LCPUFA) content. Aquatic insects contain high levels of both LCPUFA and their precursor omega-3 PUFA, alpha-linolenic acid (ALA), whereas terrestrial insects contain much lower levels of both. We manipulated both the quantity and quality of food for Tree Swallow chicks in a full factorial design. Diets were either high-LCPUFA or low in LCPUFA but high in ALA, allowing us to separate the effects of direct LCPUFA in diet from the ability of Tree Swallows to convert their precursor, ALA, into LCPUFA. We found that fatty acid composition was more important for Tree Swallow chick performance than food quantity. On high-LCPUFA diets, chicks grew faster, were in better condition, and had greater immunocompetence and lower basal metabolic rates compared with chicks on both low LCPUFA diets. Increasing the quantity of high-LCPUFA diets resulted in improvements to all metrics of performance while increasing the quantity of low-LCPUFA diets only resulted in greater immunocompetence and lower metabolic rates. Chicks preferentially retained LCPUFA in brain and muscle when both food quantity and LCPUFA were limited. Our work suggests that fatty acid composition is an important dimension of aerial insectivore nutritional ecology and reinforces the importance of high-quality aquatic habitat for these declining birds.

Molecular Proxies for Climate Maladaptation in a Long-Lived Tree (Pinus pinaster Aiton, Pinaceae)

PubMed Central

Jaramillo-Correa, Juan-Pablo; Rodríguez-Quilón, Isabel; Grivet, Delphine; Lepoittevin, Camille; Sebastiani, Federico; Heuertz, Myriam; Garnier-Géré, Pauline H.; Alía, Ricardo; Plomion, Christophe; Vendramin, Giovanni G.; González-Martínez, Santiago C.

2015-01-01

Understanding adaptive genetic responses to climate change is a main challenge for preserving biological diversity. Successful predictive models for climate-driven range shifts of species depend on the integration of information on adaptation, including that derived from genomic studies. Long-lived forest trees can experience substantial environmental change across generations, which results in a much more prominent adaptation lag than in annual species. Here, we show that candidate-gene SNPs (single nucleotide polymorphisms) can be used as predictors of maladaptation to climate in maritime pine (Pinus pinaster Aiton), an outcrossing long-lived keystone tree. A set of 18 SNPs potentially associated with climate, 5 of them involving amino acid-changing variants, were retained after performing logistic regression, latent factor mixed models, and Bayesian analyses of SNP–climate correlations. These relationships identified temperature as an important adaptive driver in maritime pine and highlighted that selective forces are operating differentially in geographically discrete gene pools. The frequency of the locally advantageous alleles at these selected loci was strongly correlated with survival in a common garden under extreme (hot and dry) climate conditions, which suggests that candidate-gene SNPs can be used to forecast the likely destiny of natural forest ecosystems under climate change scenarios. Differential levels of forest decline are anticipated for distinct maritime pine gene pools. Geographically defined molecular proxies for climate adaptation will thus critically enhance the predictive power of range-shift models and help establish mitigation measures for long-lived keystone forest trees in the face of impending climate change. PMID:25549630

Electroweak penguin amplitudes and constraints on γ in charmless B-->VP decays

NASA Astrophysics Data System (ADS)

Gronau, Michael

2000-07-01

Electroweak penguin (EWP) amplitudes are studied model independently in B meson decays to charmless final states consisting of a vector meson (V) and a pseudoscalar meson (P). A set of SU(3) relations is derived between EWP contributions and tree amplitudes, in the approximation of retaining only the dominant EWP operators Q9 and Q10. Two applications are described for constraining the weak phase γ, in B+/--->ρ+/-K0 and B+/--->ρ0K+/- (or B+/--->K*+/-π0 and B+/--->K*0π+/-), and in B0-->K*+/-π-/+ and B+/--->φK+/-. Theoretical uncertainties are discussed.

Recent growth of conifer species of western North America: Assessing spatial patterns of radial growth trends

USGS Publications Warehouse

McKenzie, D.; Hessl, Amy E.; Peterson, D.L.

2001-01-01

We explored spatial patterns of low-frequency variability in radial tree growth among western North American conifer species and identified predictors of the variability in these patterns. Using 185 sites from the International Tree-Ring Data Bank, each of which contained 10a??60 raw ring-width series, we rebuilt two chronologies for each site, using two conservative methods designed to retain any low-frequency variability associated with recent environmental change. We used factor analysis to identify regional low-frequency patterns in site chronologies and estimated the slope of the growth trend since 1850 at each site from a combination of linear regression and time-series techniques. This slope was the response variable in a regression-tree model to predict the effects of environmental gradients and species-level differences on growth trends. Growth patterns at 27 sites from the American Southwest were consistent with quasi-periodic patterns of drought. Either 12 or 32 of the 185 sites demonstrated patterns of increasing growth between 1850 and 1980 A.D., depending on the standardization technique used. Pronounced growth increases were associated with high-elevation sites (above 3000 m) and high-latitude sites in maritime climates. Future research focused on these high-elevation and high-latitude sites should address the precise mechanisms responsible for increased 20th century growth.

Comparison of plastid 16S rRNA (rrn16) genes from Helicosporidium spp.: evidence supporting the reclassification of Helicosporidia as green algae (Chlorophyta).

PubMed

Tartar, Aurélien; Boucias, Drion G; Becnel, James J; Adams, Byron J

2003-11-01

The Helicosporidia are invertebrate pathogens that have recently been identified as non-photosynthetic green algae (Chlorophyta). In order to confirm the algal nature of the genus Helicosporidium, the presence of a retained chloroplast genome in Helicosporidia cells was investigated. Fragments homologous to plastid 16S rRNA (rrn16) genes were amplified successfully from cellular DNA extracted from two different Helicosporidium isolates. The fragment sequences are 1269 and 1266 bp long, are very AT-rich (60.7 %) and are similar to homologous genes sequenced from non-photosynthetic green algae. Maximum-parsimony, maximum-likelihood and neighbour-joining methods were used to infer phylogenetic trees from an rrn16 sequence alignment. All trees depicted the Helicosporidia as sister taxa to the non-photosynthetic, pathogenic alga Prototheca zopfii. Moreover, the trees identified Helicosporidium spp. as members of a clade that included the heterotrophic species Prototheca spp. and the mesotrophic species Chlorella protothecoides. The clade is always strongly supported by bootstrap values, suggesting that all these organisms share a most recent common ancestor. Phylogenetic analyses inferred from plastid 16S rRNA genes confirmed that the Helicosporidia are non-photosynthetic green algae, close relatives of the genus Prototheca (Chlorophyta, Trebouxiophyceae). Such phylogenetic affinities suggest that Helicosporidium spp. are likely to possess Prototheca-like organelles and organelle genomes.

Rapid and sensitive detection of Little cherry virus 2 using isothermal reverse transcription-recombinase polymerase amplification.

PubMed

Mekuria, Tefera A; Zhang, Shulu; Eastwell, Kenneth C

2014-09-01

Little cherry virus 2 (LChV2) (genus Ampelovirus) is the primary causal agent of little cherry disease (LCD) in sweet cherry (Prunus avium) in North America and other parts of the world. This mealybug-transmitted virus does not induce significant foliar symptoms in most sweet cherry cultivars, but does cause virus-infected trees to yield unevenly ripened small fruits with poor flavor. Most fruits from infected trees are unmarketable. In the present study, an isothermal reverse transcription-recombinase polymerase amplification (RT-RPA) technique was developed using LChV2 coat protein specific primers and probe. Detection of terminally labeled amplicons was achieved with a high affinity lateral flow strip. The RT-RPA is confirmed to be simple, fast, and specific. In comparison, although it retains the sensitivity of RT-PCR, it is a more cost-effective procedure. RT-RPA will be a very useful tool for detecting LChV2 from crude extracts in any growth stage of sweet cherry from field samples. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

A resource-saving collective approach to biomedical semantic role labeling

PubMed Central

2014-01-01

Background Biomedical semantic role labeling (BioSRL) is a natural language processing technique that identifies the semantic roles of the words or phrases in sentences describing biological processes and expresses them as predicate-argument structures (PAS’s). Currently, a major problem of BioSRL is that most systems label every node in a full parse tree independently; however, some nodes always exhibit dependency. In general SRL, collective approaches based on the Markov logic network (MLN) model have been successful in dealing with this problem. However, in BioSRL such an approach has not been attempted because it would require more training data to recognize the more specialized and diverse terms found in biomedical literature, increasing training time and computational complexity. Results We first constructed a collective BioSRL system based on MLN. This system, called collective BIOSMILE (CBIOSMILE), is trained on the BioProp corpus. To reduce the resources used in BioSRL training, we employ a tree-pruning filter to remove unlikely nodes from the parse tree and four argument candidate identifiers to retain candidate nodes in the tree. Nodes not recognized by any candidate identifier are discarded. The pruned annotated parse trees are used to train a resource-saving MLN-based system, which is referred to as resource-saving collective BIOSMILE (RCBIOSMILE). Our experimental results show that our proposed CBIOSMILE system outperforms BIOSMILE, which is the top BioSRL system. Furthermore, our proposed RCBIOSMILE maintains the same level of accuracy as CBIOSMILE using 92% less memory and 57% less training time. Conclusions This greatly improved efficiency makes RCBIOSMILE potentially suitable for training on much larger BioSRL corpora over more biomedical domains. Compared to real-world biomedical corpora, BioProp is relatively small, containing only 445 MEDLINE abstracts and 30 event triggers. It is not large enough for practical applications, such as pathway construction. We consider it of primary importance to pursue SRL training on large corpora in the future. PMID:24884358

Assessing fire effects on forest spatial structure using a fusion of Landsat and airborne LiDAR data in Yosemite National Park

USGS Publications Warehouse

Kane, Van R.; North, Malcolm P.; Lutz, James A.; Churchill, Derek J.; Roberts, Susan L.; Smith, Douglas F.; McGaughey, Robert J.; Kane, Jonathan T.; Brooks, Matthew L.

2014-01-01

Mosaics of tree clumps and openings are characteristic of forests dominated by frequent, low- and moderate-severity fires. When restoring these fire-suppressed forests, managers often try to reproduce these structures to increase ecosystem resilience. We examined unburned and burned forest structures for 1937 0.81 ha sample areas in Yosemite National Park, USA. We estimated severity for fires from 1984 to 2010 using the Landsat-derived Relativized differenced Normalized Burn Ratio (RdNBR) and measured openings and canopy clumps in five height strata using airborne LiDAR data. Because our study area lacked concurrent field data, we identified methods to allow structural analysis using LiDAR data alone. We found three spatial structures, canopy-gap, clump-open, and open, that differed in spatial arrangement and proportion of canopy and openings. As fire severity increased, the total area in canopy decreased while the number of clumps increased, creating a patchwork of openings and multistory tree clumps. The presence of openings > 0.3 ha, an approximate minimum gap size needed to favor shade-intolerant pine regeneration, increased rapidly with loss of canopy area. The range and variation of structures for a given fire severity were specific to each forest type. Low- to moderate-severity fires best replicated the historic clump-opening patterns that were common in forests with frequent fire regimes. Our results suggest that managers consider the following goals for their forest restoration: 1) reduce total canopy cover by breaking up large contiguous areas into variable-sized tree clumps and scattered large individual trees; 2) create a range of opening sizes and shapes, including ~ 50% of the open area in gaps > 0.3 ha; 3) create multistory clumps in addition to single story clumps; 4) retain historic densities of large trees; and 5) vary treatments to include canopy-gap, clump-open, and open mosaics across project areas to mimic the range of patterns found for each forest type in our study.

An economic evaluation of maxillary implant overdentures based on six vs. four implants.

PubMed

Listl, Stefan; Fischer, Leonhard; Giannakopoulos, Nikolaos Nikitas

2014-08-18

The purpose of the present study was to assess the value for money achieved by bar-retained implant overdentures based on six implants compared with four implants as treatment alternatives for the edentulous maxilla. A Markov decision tree model was constructed and populated with parameter estimates for implant and denture failure as well as patient-centred health outcomes as available from recent literature. The decision scenario was modelled within a ten year time horizon and relied on cost reimbursement regulations of the German health care system. The cost-effectiveness threshold was identified above which the six-implant solution is preferable over the four-implant solution. Uncertainties regarding input parameters were incorporated via one-way and probabilistic sensitivity analysis based on Monte-Carlo simulation. Within a base case scenario of average treatment complexity, the cost-effectiveness threshold was identified to be 17,564 € per year of denture satisfaction gained above of which the alternative with six implants is preferable over treatment including four implants. Sensitivity analysis yielded that, depending on the specification of model input parameters such as patients' denture satisfaction, the respective cost-effectiveness threshold varies substantially. The results of the present study suggest that bar-retained maxillary overdentures based on six implants provide better patient satisfaction than bar-retained overdentures based on four implants but are considerably more expensive. Final judgements about value for money require more comprehensive clinical evidence including patient-centred health outcomes.

An economic evaluation of maxillary implant overdentures based on six vs. four implants

PubMed Central

2014-01-01

Background The purpose of the present study was to assess the value for money achieved by bar-retained implant overdentures based on six implants compared with four implants as treatment alternatives for the edentulous maxilla. Methods A Markov decision tree model was constructed and populated with parameter estimates for implant and denture failure as well as patient-centred health outcomes as available from recent literature. The decision scenario was modelled within a ten year time horizon and relied on cost reimbursement regulations of the German health care system. The cost-effectiveness threshold was identified above which the six-implant solution is preferable over the four-implant solution. Uncertainties regarding input parameters were incorporated via one-way and probabilistic sensitivity analysis based on Monte-Carlo simulation. Results Within a base case scenario of average treatment complexity, the cost-effectiveness threshold was identified to be 17,564 € per year of denture satisfaction gained above of which the alternative with six implants is preferable over treatment including four implants. Sensitivity analysis yielded that, depending on the specification of model input parameters such as patients’ denture satisfaction, the respective cost-effectiveness threshold varies substantially. Conclusions The results of the present study suggest that bar-retained maxillary overdentures based on six implants provide better patient satisfaction than bar-retained overdentures based on four implants but are considerably more expensive. Final judgements about value for money require more comprehensive clinical evidence including patient-centred health outcomes. PMID:25135370

Avian species richness in relation to intensive forest management practices in early seral tree plantations.

PubMed

Jones, Jay E; Kroll, Andrew J; Giovanini, Jack; Duke, Steven D; Ellis, Tana M; Betts, Matthew G

2012-01-01

Managers of landscapes dedicated to forest commodity production require information about how practices influence biological diversity. Individual species and communities may be threatened if management practices truncate or simplify forest age classes that are essential for reproduction and survival. For instance, the degradation and loss of complex diverse forest in young age classes have been associated with declines in forest-associated Neotropical migrant bird populations in the Pacific Northwest, USA. These declines may be exacerbated by intensive forest management practices that reduce hardwood and broadleaf shrub cover in order to promote growth of economically valuable tree species in plantations. We used a Bayesian hierarchical model to evaluate relationships between avian species richness and vegetation variables that reflect stand management intensity (primarily via herbicide application) on 212 tree plantations in the Coast Range, Oregon, USA. Specifically, we estimated the influence of broadleaf hardwood vegetation cover, which is reduced through herbicide applications, on bird species richness and individual species occupancy. Our model accounted for imperfect detection. We used average predictive comparisons to quantify the degree of association between vegetation variables and species richness. Both conifer and hardwood cover were positively associated with total species richness, suggesting that these components of forest stand composition may be important predictors of alpha diversity. Estimates of species richness were 35-80% lower when imperfect detection was ignored (depending on covariate values), a result that has critical implications for previous efforts that have examined relationships between forest composition and species richness. Our results revealed that individual and community responses were positively associated with both conifer and hardwood cover. In our system, patterns of bird community assembly appear to be associated with stand management strategies that retain or increase hardwood vegetation while simultaneously regenerating the conifer cover in commercial tree plantations.

The utility of a classificatory decision tree approach to assist clinical differentiation of melancholic and non-melancholic depression.

PubMed

Parker, G; McCraw, S; Hadzi-Pavlovic, D

2015-07-15

Studies suggest that differentiating melancholic from non-melancholic depressive disorders is advanced by use of illness course as well as symptom variables but, in practice, potentially differentiating variables are generally positioned as having equal value. Judging that differentiating features are more likely to vary in their signal intensity, we sought to determine the number of features required to effect differentiation and their hierarchical order. The 24-item clinician-rated Sydney Melancholia Prototype Index (SMPI-CR) was completed for 364 unipolar depressed patients. The sample was divided into two cohorts according to the recruitment period. An RPART classification tree analysis identified the most discriminating SMPI items in the development sample of 197 patients, and examined the sensitivity and specificity of the diagnostic decisions, then sought to replicate findings in a validation sample of 169 patients. Independent analyses of putative SMPI items identified only seven items as required to discriminate those with clinically-diagnosed melancholic or non-melancholic depression when the conditions were examined separately. An RPART analysis considering differentiation of melancholic and non-melancholic depression in the total samples retained five of those items in the classification tree, three of which were non-symptom items, and with 92% sensitivity and 80% specificity in the development sample. This reduced item set showed 93% sensitivity and 82% specificity in the validation sample. Our clinical judgment of melancholic or non-melancholic depression may not correspond with the clinical logic employed by other clinicians. Only five SMPI items were required to derive a succinct and efficient decision tree, comprising high sensitivity and specificity in differentiating melancholic and non-melancholic depression. Current study findings provide an empirical model that could enrich clinicians׳ approach to differentiating melancholic and non-melancholic depression. Copyright © 2015 Elsevier B.V. All rights reserved.

Integrating gene flow, crop biology, and farm management in on-farm conservation of avocado (Persea americana, Lauraceae).

PubMed

Birnbaum, Kenneth; Desalle, Rob; Peters, Charles M; Benfey, Philip N

2003-11-01

Maintaining crop diversity on farms where cultivars can evolve is a conservation goal, but few tools are available to assess the long-term maintenance of genetic diversity on farms. One important issue for on-farm conservation is gene flow from crops with a narrow genetic base into related populations that are genetically diverse. In a case study of avocado (Persea americana var. americana) in one of its centers of diversity (San Jerónimo, Costa Rica), we used 10 DNA microsatellite markers in a parentage analysis to estimate gene flow from commercialized varieties into a traditional crop population. Five commercialized genotypes comprised nearly 40% of orchard trees, but they contributed only about 14.5% of the gametes to the youngest cohort of trees. Although commercialized varieties and the diverse population were often planted on the same farm, planting patterns appeared to keep the two types of trees separated on small scales, possibly explaining the limited gene flow. In a simulation that combined gene flow estimates, crop biology, and graft tree management, loss of allelic diversity was less than 10% over 150 yr, and selection was effective in retaining desirable alleles in the diverse subpopulation. Simulations also showed that, in addition to gene flow, managing the genetic makeup and life history traits of the invasive commercialized varieties could have a significant impact on genetic diversity in the target population. The results support the feasibility of on-farm crop conservation, but simulations also showed that higher levels of gene flow could lead to severe losses of genetic diversity even if farmers continue to plant diverse varieties.

Whole genome duplication events in plant evolution reconstructed and predicted using myosin motor proteins

PubMed Central

2013-01-01

Background The evolution of land plants is characterized by whole genome duplications (WGD), which drove species diversification and evolutionary novelties. Detecting these events is especially difficult if they date back to the origin of the plant kingdom. Established methods for reconstructing WGDs include intra- and inter-genome comparisons, KS age distribution analyses, and phylogenetic tree constructions. Results By analysing 67 completely sequenced plant genomes 775 myosins were identified and manually assembled. Phylogenetic trees of the myosin motor domains revealed orthologous and paralogous relationships and were consistent with recent species trees. Based on the myosin inventories and the phylogenetic trees, we have identified duplications of the entire myosin motor protein family at timings consistent with 23 WGDs, that had been reported before. We also predict 6 WGDs based on further protein family duplications. Notably, the myosin data support the two recently reported WGDs in the common ancestor of all extant angiosperms. We predict single WGDs in the Manihot esculenta and Nicotiana benthamiana lineages, two WGDs for Linum usitatissimum and Phoenix dactylifera, and a triplication or two WGDs for Gossypium raimondii. Our data show another myosin duplication in the ancestor of the angiosperms that could be either the result of a single gene duplication or a remnant of a WGD. Conclusions We have shown that the myosin inventories in angiosperms retain evidence of numerous WGDs that happened throughout plant evolution. In contrast to other protein families, many myosins are still present in extant species. They are closely related and have similar domain architectures, and their phylogenetic grouping follows the genome duplications. Because of its broad taxonomic sampling the dataset provides the basis for reliable future identification of further whole genome duplications. PMID:24053117

Whole genome duplication events in plant evolution reconstructed and predicted using myosin motor proteins.

PubMed

Mühlhausen, Stefanie; Kollmar, Martin

2013-09-22

The evolution of land plants is characterized by whole genome duplications (WGD), which drove species diversification and evolutionary novelties. Detecting these events is especially difficult if they date back to the origin of the plant kingdom. Established methods for reconstructing WGDs include intra- and inter-genome comparisons, KS age distribution analyses, and phylogenetic tree constructions. By analysing 67 completely sequenced plant genomes 775 myosins were identified and manually assembled. Phylogenetic trees of the myosin motor domains revealed orthologous and paralogous relationships and were consistent with recent species trees. Based on the myosin inventories and the phylogenetic trees, we have identified duplications of the entire myosin motor protein family at timings consistent with 23 WGDs, that had been reported before. We also predict 6 WGDs based on further protein family duplications. Notably, the myosin data support the two recently reported WGDs in the common ancestor of all extant angiosperms. We predict single WGDs in the Manihot esculenta and Nicotiana benthamiana lineages, two WGDs for Linum usitatissimum and Phoenix dactylifera, and a triplication or two WGDs for Gossypium raimondii. Our data show another myosin duplication in the ancestor of the angiosperms that could be either the result of a single gene duplication or a remnant of a WGD. We have shown that the myosin inventories in angiosperms retain evidence of numerous WGDs that happened throughout plant evolution. In contrast to other protein families, many myosins are still present in extant species. They are closely related and have similar domain architectures, and their phylogenetic grouping follows the genome duplications. Because of its broad taxonomic sampling the dataset provides the basis for reliable future identification of further whole genome duplications.

Stable annual pattern of water use by Acacia tortilis in Sahelian Africa.

PubMed

Do, Frederic C; Rocheteau, Alain; Diagne, Amadou L; Goudiaby, Venceslas; Granier, André; Lhomme, Jean-Paul

2008-01-01

Water use by mature trees of Acacia tortilis (Forsk.) Hayne ssp. raddiana (Savi) Brenan var. raddiana growing in the northern Sahel was continuously recorded over 4 years. Water use was estimated from xylem sap flow measured by transient heat dissipation. Concurrently, cambial growth, canopy phenology, leaf water potential, climatic conditions and soil water availability (SWA) were monitored. In addition to the variation attributable to interannual variation in rainfall, SWA was increased by irrigation during one wet season. The wet season lasted from July to September, and annual rainfall ranged between 146 and 367 mm. The annual amount and pattern of tree water use were stable from year-to-year despite interannual and seasonal variations in SWA in the upper soil layers. Acacia tortilis transpired readily throughout the year, except for one month during the dry season when defoliation was at a maximum. Maximum water use of about 23 l (dm sapwood area)(-2) day(-1) was recorded at the end of the wet season. While trees retained foliage in the dry season, the decline in water use was modest at around 30%. Variation in predawn leaf water potential indicated that the trees were subject to soil water constraint. The rapid depletion of water in the uppermost soil layers after the wet season implies that there was extensive use of water from deep soil layers. The deep soil profile revealed (1) the existence of living roots at 25 m and (2) that the availability of soil water was low (-1.6 MPa) down to the water table at a depth of 31 m. However, transpiration was recorded at a predawn leaf water potential of -2.0 MPa, indicating that the trees used water from both intermediary soil layers and the water table. During the full canopy stage, mean values of whole-tree hydraulic conductance were similar in the wet and dry seasons. We propose that the stability of water use at the seasonal and annual scales resulted from a combination of features, including an extensive rooting habit related to deep water availability and an effective regulation of canopy conductance. Despite a limited effect on tree water use, irrigation during the wet season sharply increased predawn leaf water potential and cambial growth of trunks and branches.

Agents for gallstone dissolution.

PubMed

Pitt, H A; McFadden, D W; Gadacz, T R

1987-02-01

Numerous methods are presently available for gallstone dissolution, including oral bile salts; cholesterol solvents such as mono-octanoin and methyl tert-butyl ether; calcium or pigment solvents such as EDTA and polysorbate; mechanical extraction techniques through a T-tube tract or after endoscopic sphincterotomy; or fragmentation methods such as ultrasonography or electrohydraulic lithotripsy, lasers, and extracorporeal shock waves. Which, if any, of these methods will be appropriate for an individual patient depends on the type of stones, whether they are in the gallbladder or bile ducts, whether access to the biliary tree is available, the patient's age and general medical condition, and the availability of expert radiologists, endoscopists, and newer equipment. In the United States, the only available oral bile salt for cholesterol gallstone dissolution is chenodeoxycholate. Ursodeoxycholate, which is more rapid and less toxic, has not been approved by the Federal Drug Administration. These agents are most effective in thin women with small, floating, radiolucent cholesterol gallstones in a functioning gallbladder. Only about half of this small subset of patients, however, will experience partial or complete dissolution of stones in 6 to 12 months. Moreover, recurrence is very likely, and the potential toxicity of long-term therapy is unknown. Thus, for most patients, cholecystectomy remains the most cost-effective and, perhaps, safest option. Intragallbladder instillation of methyl tert-butyl ether and extracorporeal shock wave therapy are also likely to be applicable to only small subsets of patients and to be associated with high recurrence rates. In patients with retained ductal cholesterol stones and access to the biliary tree, mono-octanoin therapy is advantageous in that it can be begun as soon as cholangiography demonstrates no extravasation. In properly selected patients, a 90 percent success rate with mono-octanoin infusion can be expected within a week. Radiologic or endoscopic extraction techniques require maturation of a relatively straight T-tube tract but are not dependent on the type of stone. In the hands of experts, these techniques are highly successful. In postcholecystectomy patients without access to the biliary tree, endoscopic sphincterotomy has become the preferred method of management and can be expected to succeed in more than 90 percent of patients. At this point, the exact role for ultrasonic or electrohydraulic lithotripsy and lasers is unknown. However, these techniques may be applicable in the future in patients with retained bile duct stones in whom extraction and infusion techniques have failed.

Water retained in tall Cryptomeria japonica leaves as studied by infrared micro-spectroscopy.

PubMed

Azuma, Wakana; Nakashima, Satoru; Yamakita, Eri; Ishii, H Roaki; Kuroda, Keiko

2017-10-01

Recent studies in the tallest tree species suggest that physiological and anatomical traits of tree-top leaves are adapted to water-limited conditions. In order to examine water retention mechanism of leaves in a tall tree, infrared (IR) micro-spectroscopy was conducted on mature leaf cross-sections of tall Cryptomeria japonica D. Don from four different heights (51, 43, 31 and 19 m). We measured IR transmission spectra and mainly analyzed OH (3700-3000 cm-1) and C-O (1190-845 cm-1) absorption bands, indicating water molecules and sugar groups, respectively. The changes in IR spectra of leaf sections from different heights were compared with bulk-leaf hydraulics. Both average OH band area of the leaf sections and leaf water content were larger in the upper-crown, while osmotic potential at saturation did not vary with height, suggesting higher dissolved sugar contents of upper-crown leaves. As cell-wall is the main cellular structure of leaves, we inferred that larger average C-O band area of upper-crown leaves reflected higher content of structural polysaccharides such as cellulose, hemicellulose and pectin. Infrared micro-spectroscopic imaging showed that the OH and C-O band areas are large in the vascular bundle, transfusion tissue and epidermis. Infrared spectra of individual tissue showed that much more water is retained in vascular bundle and transfusion tissue than mesophyll. These results demonstrate that IR micro-spectroscopy is a powerful tool for visualizing detailed, quantitative information on the spatial distribution of chemical substances within plant tissues, which cannot be done using conventional methods like histochemical staining. The OH band could be well reproduced by four Gaussian OH components around 3530 (free water: long H bond), 3410 (pectin-like OH species), 3310 (cellulose-like OH species) and 3210 (bound water: short H bond) cm-1, and all of these OH components were higher in the upper crown while their relative proportions did not vary with height. Based on the spectral analyses, we inferred that polysaccharides play a key role in biomolecular retention of water in leaves of tall C. japonica. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Ecosystem Nitrogen Retention Following Severe Bark Beetle and Salvage Logging Disturbance in Lodgepole Pine Forests: a 15N Enrichment Study

NASA Astrophysics Data System (ADS)

Avera, B.; Rhoades, C.; Paul, E. A.; Cotrufo, M. F.

2017-12-01

In recent decades, bark beetle outbreaks have caused high levels of tree mortality in lodgepole pine (Pinus contorta) dominated forests across western North America. Previous work has found increased soil mineral nitrogen (N) with tree mortality in beetle infested stands, but surprisingly little change in stream N export. These findings suggest an important role of residual live vegetation and altered soil microbial response for retaining surplus N and mitigating N losses from disturbed lodgepole forests. Post outbreak salvage of merchantable timber reduces fuel levels and promotes tree regeneration; however, the implications of the combined bark beetle and harvesting disturbances on ecosystem N retention and productivity are uncertain. To advance understanding of post-disturbance N retention we compare unlogged beetle-infested forests and salvage logged stands with post-harvest woody residue retention or removal. We applied 15N-labeled (2 atom%) and natural abundance ammonium sulfate to eight year old lodgepole pine seedlings in three replicate plots of the three forest management treatments. This approach allows us to quantify the relative contributions of N retention in soil, microbial biomass, and plant tissue. Our study targets gaps in understanding of the processes that regulate N utilization and transfer between soil and vegetation that result in effective N retention in lodgepole pine ecosystems. These findings will also help guide forest harvest and woody residue management practices in order to maintain soil productivity.

Interpreting the deposition and vertical migration characteristics of 137Cs in forest soil after the Fukushima Dai-ichi Nuclear Power Plant accident.

PubMed

Kang, Seongjoo; Yoneda, Minoru; Shimada, Yoko; Satta, Naoya; Fujita, Yasutaka; Shin, In Hwan

2017-08-01

We investigated the deposition and depth distributions of radiocesium in the Takizawa Research Forest, Iwate Prefecture, in order to understand the behavior of radionuclides released from the Fukushima Dai-ichi Nuclear Power Plant. The deposition distribution and vertical depth distribution of radiocesium in the soil were compared between topographically distinct parts of the forest where two different tree species grow. The results for all investigated locations show that almost 85% of the radiocesium has accumulated in the region of soil from the topmost organic layer to a soil depth of 0-4 cm. However, no activity was detected at depths greater than 20 cm. Analysis of the radiocesium deposition patterns in forest locations dominated by either coniferous or deciduous tree species suggests that radiocesium was sequestered and retained in higher concentrations in coniferous areas. The deposition data showed large spatial variability, reflecting the differences in tree species and topography. The variations in the measured 137 Cs concentrations reflected the variability in the characteristics of the forest floor environment and the heterogeneity of the initial ground-deposition of the Fukushima fallout. Sequential extraction experiments showed that most of the 137 Cs was present in an un-exchangeable form with weak mobility. Nevertheless, the post-vertical distribution of 137 Cs is expected to be governed by the percentage of exchangeable 137 Cs in the organic layer and the organic-rich upper soil horizons.

Habitat features and predictive habitat modeling for the Colorado chipmunk in southern New Mexico

USGS Publications Warehouse

Rivieccio, M.; Thompson, B.C.; Gould, W.R.; Boykin, K.G.

2003-01-01

Two subspecies of Colorado chipmunk (state threatened and federal species of concern) occur in southern New Mexico: Tamias quadrivittatus australis in the Organ Mountains and T. q. oscuraensis in the Oscura Mountains. We developed a GIS model of potentially suitable habitat based on vegetation and elevation features, evaluated site classifications of the GIS model, and determined vegetation and terrain features associated with chipmunk occurrence. We compared GIS model classifications with actual vegetation and elevation features measured at 37 sites. At 60 sites we measured 18 habitat variables regarding slope, aspect, tree species, shrub species, and ground cover. We used logistic regression to analyze habitat variables associated with chipmunk presence/absence. All (100%) 37 sample sites (28 predicted suitable, 9 predicted unsuitable) were classified correctly by the GIS model regarding elevation and vegetation. For 28 sites predicted suitable by the GIS model, 18 sites (64%) appeared visually suitable based on habitat variables selected from logistic regression analyses, of which 10 sites (36%) were specifically predicted as suitable habitat via logistic regression. We detected chipmunks at 70% of sites deemed suitable via the logistic regression models. Shrub cover, tree density, plant proximity, presence of logs, and presence of rock outcrop were retained in the logistic model for the Oscura Mountains; litter, shrub cover, and grass cover were retained in the logistic model for the Organ Mountains. Evaluation of predictive models illustrates the need for multi-stage analyses to best judge performance. Microhabitat analyses indicate prospective needs for different management strategies between the subspecies. Sensitivities of each population of the Colorado chipmunk to natural and prescribed fire suggest that partial burnings of areas inhabited by Colorado chipmunks in southern New Mexico may be beneficial. These partial burnings may later help avoid a fire that could substantially reduce habitat of chipmunks over a mountain range.

Improving winter leaf area index estimation in evergreen coniferous forests and its significance in carbon and water fluxes modeling

NASA Astrophysics Data System (ADS)

Wang, R.; Chen, J. M.; Luo, X.

2016-12-01

Modeling of carbon and water fluxes at the continental and global scales requires remotely sensed LAI as inputs. For evergreen coniferous forests (ENF), severely underestimated winter LAI has been one of the issues for mostly available remote sensing products, which could cause negative bias in the modeling of Gross Primary Productivity (GPP) and evapotranspiration (ET). Unlike deciduous trees which shed all the leaves in winter, conifers retains part of their needles and the proportion of the retained needles depends on the needle longevity. In this work, the Boreal Ecosystem Productivity Simulator (BEPS) was used to model GPP and ET at eight FLUXNET Canada ENF sites. Two sets of LAI were used as the model inputs: the 250m 10-day University of Toronto (U of T) LAI product Version 2 and the corrected LAI based on the U of T LAI product and the needle longevity of the corresponding tree species at individual sites. Validating model daily GPP (gC/m2) against site measurements, the mean RMSE over eight sites decreases from 1.85 to 1.15, and the bias changes from -0.99 to -0.19. For daily ET (mm), mean RMSE decreases from 0.63 to 0.33, and the bias changes from -0.31 to -0.16. Most of the improvements occur in the beginning and at the end of the growing season when there is large correction of LAI and meanwhile temperature is still suitable for photosynthesis and transpiration. For the dormant season, the improvement in ET simulation mostly comes from the increased interception of precipitation brought by the elevated LAI during that time. The results indicate that model performance can be improved by the application the corrected LAI. Improving the winter RS LAI can make a large impact on land surface carbon and energy budget.

Rhizosphere Competitiveness of Trichloroethylene-Degrading, Poplar-Colonizing Recombinant Bacteria

PubMed Central

Shim, Hojae; Chauhan, Sadhana; Ryoo, Doohyun; Bowers, Kally; Thomas, Stuart M.; Canada, Keith A.; Burken, Joel G.; Wood, Thomas K.

2000-01-01

Indigenous bacteria from poplar tree (Populus canadensis var. eugenei ‘Imperial Carolina’) and southern California shrub rhizospheres, as well as two tree-colonizing Rhizobium strains (ATCC 10320 and ATCC 35645), were engineered to express constitutively and stably toluene o-monooxygenase (TOM) from Burkholderia cepacia G4 by integrating the tom locus into the chromosome. The poplar and Rhizobium recombinant bacteria degraded trichloroethylene at a rate of 0.8 to 2.1 nmol/min/mg of protein and were competitive against the unengineered hosts in wheat and barley rhizospheres for 1 month (colonization occurred at a level of 1.0 × 105 to 23 × 105 CFU/cm of root). In addition, six of these recombinants colonized poplar roots stably and competitively with populations as large as 79% ± 12% of all rhizosphere bacteria after 28 days (0.2 × 105 to 31 × 105 CFU/cm of root). Furthermore, five of the most competitive poplar recombinants (e.g., Pb3-1 and Pb5-1, which were identified as Pseudomonas sp. strain PsK recombinants) retained the ability to express TOM for 29 days as 100% ± 0% of the recombinants detected in the poplar rhizosphere expressed TOM constitutively. PMID:11055909

Physical and chemical characterization of biochars derived from different agricultural residues

NASA Astrophysics Data System (ADS)

Jindo, K.; Mizumoto, H.; Sawada, Y.; Sanchez-Monedero, M. A.; Sonoki, T.

2014-12-01

Biochar is widely recognized as an efficient tool for carbon sequestration and soil fertility. The understanding of its chemical and physical properties, which are strongly related to the type of the initial material used and pyrolysis conditions, is crucial to identify the most suitable application of biochar in soil. A selection of organic wastes with different characteristics (e.g., rice husk (RH), rice straw (RS), wood chips of apple tree (Malus pumila) (AB), and oak tree (Quercus serrata) (OB)) were pyrolyzed at different temperatures (400, 500, 600, 700, and 800 °C) in order to optimize the physicochemical properties of biochar as a soil amendment. Low-temperature pyrolysis produced high biochar yields; in contrast, high-temperature pyrolysis led to biochars with a high C content, large surface area, and high adsorption characteristics. Biochar obtained at 600 °C leads to a high recalcitrant character, whereas that obtained at 400 °C retains volatile and easily labile compounds. The biochar obtained from rice materials (RH and RS) showed a high yield and unique chemical properties because of the incorporation of silica elements into its chemical structure. The biochar obtained from wood materials (AB and OB) showed high carbon content and a high absorption character.

Environmental predictors of pre-European deforestation on Pacific islands.

PubMed

Rolett, Barry; Diamond, Jared

2004-09-23

Some Pacific island societies, such as those of Easter Island and Mangareva, inadvertently contributed to their own collapse by causing massive deforestation. Others retained forest cover and survived. How can those fateful differences be explained? Although the answers undoubtedly involve both different cultural responses of peoples and different susceptibilities of environments, how can one determine which environmental factors predispose towards deforestation and which towards replacement of native trees with useful introduced tree species? Here we code European-contact conditions and nine environmental variables for 81 sites on 69 Pacific islands from Yap in the west to Easter in the east, and from Hawaii in the north to New Zealand in the south. We thereby detect statistical decreases in deforestation and/or forest replacement with island rainfall, elevation, area, volcanic ash fallout, Asian dust transport and makatea terrain (uplifted reef), and increases with latitude, age and isolation. Comparative analyses of deforestation therefore lend themselves to much more detailed interpretations than previously possible. These results might be relevant to similar deforestation-associated collapses (for example, Fertile Crescent, Maya and Anasazi) or the lack thereof (Japan and highland New Guinea) elsewhere in the world.

Variability in the carbon isotope composition of individual amino acids in plant proteins from different sources: 1 Leaves.

PubMed

Lynch, Anthony H; Kruger, Nicholas J; Hedges, Robert E M; McCullagh, James S O

2016-05-01

The natural carbon isotope composition of individual amino acids from plant leaf proteins has been measured to establish potential sources of variability. The plant leaves studied, taken from a range of plant groups (forbs, trees, grasses, and freshwater aquatic plants), showed no significant influence of either season or environment (water and light availability) on their Δδ(13)C values. Plant groups did, however, differ in carbon isotope composition, although no consistent differences were identified at the species level. A discriminant analysis model was constructed which allowed leaves from (1) nettles, (2) Pooideae, (3) other Poales, (4) trees and (5) freshwater higher plants to be distinguished from each other on the basis of their natural abundance (13)C/(12)C ratios of individual amino acids. Differences in carbon isotope composition are known to be retained, to some extent, in the tissues of their consumers, and hence an understanding of compound-specific variation in (13)C/(12)C fractional abundance in plants has the potential to provide dietary insights of value in archaeological and ecological studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Improved analyses of human mtDNA sequences support a recent African origin for Homo sapiens.

PubMed

Penny, D; Steel, M; Waddell, P J; Hendy, M D

1995-09-01

New quantitative methods are applied to the 135 human mitochondrial sequences from the Vigilant et al. data set. General problems in analyzing large numbers of short sequences are discussed, and an improved strategy is suggested. A key feature is to focus not on individual trees but on the general "landscape" of trees. Over 1,000 searches were made from random starting trees with only one tree (a local optimum) being retained each time, thereby ensuring optima were found independently. A new tree comparison metric was developed that is unaffected by rearrangements of trees around many very short internal edges. Use of this metric showed that downweighting hypervariable sites revealed more evolutionary structure than studies that weighted all sites equally. Our results are consistent with convergence toward a global optimum. Crucial features are that the best optima show very strong regional differentiation, a common group of 49 African sequences is found in all the best optima, and the best optima contain the 16 !Kung sequences in a separate group of San people. The other 86 sequences form a heterogeneous mixture of Africans, Europeans, Australopapuans, and Asians. Thus all major human lineages occur in Africa, but only a subset occurs in the rest of the world. The existence of these African-only groups strongly contradicts multiregional theories for the origin of Homo sapiens that require widespread migration and interbreeding over the entire range of H. erectus. Only when the multiregional model is rejected is it appropriate to consider the root, based on a single locus, to be the center of origin of a population (otherwise different loci could give alternative geographic positions for the root). For this data, several methods locate the root within the group of 49 African sequences and are thus consistent with the recent African origin of H. sapiens. We demonstrate that the time of the last common ancestor cannot be the time of major expansion in human numbers, and our results are thus also consistent with recent models that differentiate between the last common ancestor, expansion out of Africa, and the major expansion in human populations. Such a two-phase model is consistent with a wide range of molecular and archeological evidence.

Tree-ring growth of Scots pine, Common beech and Pedunculate oak under future climate in northeastern Germany

NASA Astrophysics Data System (ADS)

Jurasinski, Gerald; Scharnweber, Tobias; Schröder, Christian; Lennartz, Bernd; Bauwe, Andreas

2017-04-01

Tree growth depends, among other factors, largely on the prevailing climatic conditions. Therefore, tree growth patterns are to be expected under climate change. Here, we analyze the tree-ring growth response of three major European tree species to projected future climate across a climatic (mostly precipitation) gradient in northeastern Germany. We used monthly data for temperature, precipitation, and the standardized precipitation evapotranspiration index (SPEI) over multiple time scales (1, 3, 6, 12, and 24 months) to construct models of tree-ring growth for Scots pine (Pinus syl- vestris L.) at three pure stands, and for Common beech (Fagus sylvatica L.) and Pedunculate oak (Quercus robur L.) at three mature mixed stands. The regression models were derived using a two-step approach based on partial least squares regression (PLSR) to extract potentially well explaining variables followed by ordinary least squares regression (OLSR) to consolidate the models to the least number of variables while retaining high explanatory power. The stability of the models was tested with a comprehensive calibration-verification scheme. All models were successfully verified with R2s ranging from 0.21 for the western pine stand to 0.62 for the beech stand in the east. For growth prediction, climate data forecasted until 2100 by the regional climate model WETTREG2010 based on the A1B Intergovernmental Panel on Climate Change (IPCC) emission scenario was used. For beech and oak, growth rates will likely decrease until the end of the 21st century. For pine, modeled growth trends vary and range from a slight growth increase to a weak decrease in growth rates depending on the position along the climatic gradient. The climatic gradient across the study area will possibly affect the future growth of oak with larger growth reductions towards the drier east. For beech, site-specific adaptations seem to override the influence of the climatic gradient. We conclude that in Northeastern Germany Scots pine has great potential to remain resilient to projected climate change without any greater impairment, whereas Common beech and Pedunculate oak will likely face lesser growth under the expected warmer and dryer climate conditions. The results call for an adaptation of forest management to mitigate the negative effects of climate change for beech and oak in the region.

Characterization of post-fire surface cover, soils, and burn severity at the Cerro Grande Fire, New Mexico, using hyperspectral and multispectral remote sensing

USGS Publications Warehouse

Kokaly, R.F.; Rockwell, B.W.; Haire, S.L.; King, T.V.V.

2007-01-01

Forest fires leave behind a changed ecosystem with a patchwork of surface cover that includes ash, charred organic matter, soils and soil minerals, and dead, damaged, and living vegetation. The distributions of these materials affect post-fire processes of erosion, nutrient cycling, and vegetation regrowth. We analyzed high spatial resolution (2.4??m pixel size) Airborne Visible and Infrared Imaging Spectrometer (AVIRIS) data collected over the Cerro Grande fire, to map post-fire surface cover into 10 classes, including ash, soil minerals, scorched conifer trees, and green vegetation. The Cerro Grande fire occurred near Los Alamos, New Mexico, in May 2000. The AVIRIS data were collected September 3, 2000. The surface cover map revealed complex patterns of ash, iron oxide minerals, and clay minerals in areas of complete combustion. Scorched conifer trees, which retained dry needles heated by the fire but not fully combusted by the flames, were found to cover much of the post-fire landscape. These scorched trees were found in narrow zones at the edges of completely burned areas. A surface cover map was also made using Landsat Enhanced Thematic Mapper plus (ETM+) data, collected September 5, 2000, and a maximum likelihood, supervised classification. When compared to AVIRIS, the Landsat classification grossly overestimated cover by dry conifer and ash classes and severely underestimated soil and green vegetation cover. In a comparison of AVIRIS surface cover to the Burned Area Emergency Rehabilitation (BAER) map of burn severity, the BAER high burn severity areas did not capture the variable patterns of post-fire surface cover by ash, soil, and scorched conifer trees seen in the AVIRIS map. The BAER map, derived from air photos, also did not capture the distribution of scorched trees that were observed in the AVIRIS map. Similarly, the moderate severity class of Landsat-derived burn severity maps generated from the differenced Normalized Burn Ratio (dNBR) calculation had low agreement with the AVIRIS classes of scorched conifer trees. Burn severity and surface cover images were found to contain complementary information, with the dNBR map presenting an image of degree of change caused by fire and the AVIRIS-derived map showing specific surface cover resulting from fire.

Trees as bioindicators of industrial air pollution during implementation of pro-environmental policy in Silesia region (Poland).

NASA Astrophysics Data System (ADS)

Sensuła, Barbara; Wilczyński, Slawomir; Opała, Magdalena; Pawełczyk, Sławomira; Piotrowska, Natalia

2015-04-01

The aim of research conducted within the project entitled "Trees as bioindicators of industrial air pollutants during the implementation of pro-environmental policies in the area of Silesia" (acronym BIOPOL) is the reconstruction of climate changes and anthropogenic effects and monitoring of the influence of human activities related to industrial development and the introduction of pro-environmental policy. The analysis will concern the climatic and anthropogenic signals recorded in annual tree rings width of Scots pine and in the isotopic composition of wood and its compenents (such as alpha-cellulose and glucose). Only a few studies made a complex multiproxies analysis of the influence of industrial air pollutants on changes in the tree rings width and their isotopic composition in any selected region. In addition, research is usually for a period of industrial development, is a lack of analysis for the period of implementation of EU law and standards on air quality to Polish law. The research area are the forests close to 3 different industrial plants (chemical- nitrogen plants, steel mills, power plants), in Silesia, where operating companies have strategic importance for the region and country. By analyzing the structure of land in Silesia noted a significant advantage of forest land and agricultural land. A large percentage of forest land providing protection for residents in case of failure in any of the plants. A cloud of noxious fumes is possible in large part retained in the trees. Waste generated by the chemical industry, metallurgy and energy represent the largest proportion of waste generated in the region. Already in the beginning of 21stcentury, the Waste Management Plans for various cities in Silesia are set out various strategic objectives to 2015, including in the economic sector: the implementation of non-waste technology and less and the best available techniques (BAT), the introduction of the principles of "cleaner production". The BIOPOL innovation is: a) multiproxy spatio-temporal analysis of the effects of climate changes and emission of air industrial pollution on trees during the development of industry and the implementation of pro-environmental policies in Silesia: - Analysis of the width of annual tree rings (since 1975) - Analysis of underestimation of the 14C concentration during the implementation of European standards (since 2000) - Analysis of the recorded signals of environmental changes in the composition of stable isotopes in annual tree rings - wood and its components b) modeling of the influence of pollutants emitted into the atmosphere on the width of annual growth of trees and C,O,N stable isotopes and radiocarbon - Spatio-temporal model of environmental change in the tree rings width and their isotopic composition close to each of the selected plants - comparison to the impact of climate change and industrial pollution for 3 different industries (steel mills, power plants, nitrogen plants) in the period from 1975 to present - Space model of environmental changes in the isotopic composition of trees near each of the selected plants (at varying distances from the chosen site) based on analysis of isotopic composition of annual shoots of pine trees in three consecutive years: from 2012 to 2014) - Estimation of emission components originating from industrial pollution for individual plants This project was funded by the National Science Centre allocated on the basis of the decision number DEC-2011/03/D/ST10/05251

Tree-ring-based drought reconstruction in the Iberian Range (east of Spain) since 1694

NASA Astrophysics Data System (ADS)

Tejedor, Ernesto; de Luis, Martín; Cuadrat, José María; Esper, Jan; Saz, Miguel Ángel

2016-03-01

Droughts are a recurrent phenomenon in the Mediterranean basin with negative consequences for society, economic activities, and natural systems. Nevertheless, the study of drought recurrence and severity in Spain has been limited so far due to the relatively short instrumental period. In this work, we present a reconstruction of the standardized precipitation index (SPI) for the Iberian Range. Growth variations and climatic signals within the network are assessed developing a correlation matrix and the data combined to a single chronology integrating 336 samples from 169 trees of five different pine species distributed throughout the province of Teruel. The new chronology, calibrated against regional instrumental climatic data, shows a high and stable correlation with the July SPI integrating moisture conditions over 12 months forming the basis for a 318-year drought reconstruction. The climate signal contained in this reconstruction is highly significant ( p < 0.05) and spatially robust over the interior areas of Spain located above 1000 meters above sea level (masl). According to our SPI reconstruction, seven substantially dry and five wet periods are identified since the late seventeenth century considering ≥±1.76 standard deviations. Besides these, 36 drought and 28 pluvial years were identified. Some of these years, such as 1725, 1741, 1803, and 1879, are also revealed in other drought reconstructions in Romania and Turkey, suggesting that coherent larger-scale synoptic patterns drove these extreme deviations. Since regional drought deviations are also retained in historical documents, the tree-ring-based reconstruction presented here will allow us to cross-validate drought frequency and magnitude in a highly vulnerable region.

Impacts of a spring heat wave on canopy processes in a northern hardwood forest.

PubMed

Filewod, Ben; Thomas, Sean C

2014-02-01

Heat wave frequency, duration, and intensity are predicted to increase with global warming, but the potential impacts of short-term high temperature events on forest functioning remain virtually unstudied. We examined canopy processes in a forest in Central Ontario following 3 days of record-setting high temperatures (31–33 °C) that coincided with the peak in leaf expansion of dominant trees in late May 2010. Leaf area dynamics, leaf morphology, and leaf-level gas-exchange were compared to data from prior years of sampling (2002–2008) at the same site, focusing on Acer saccharum Marsh., the dominant tree in the region. Extensive shedding of partially expanded leaves was observed immediately following high temperature days, with A. saccharum losing ca. 25% of total leaf production but subsequently producing an unusual second flush of neoformed leaves. Both leaf losses and subsequent reflushing were highest in the upper canopy; however, retained preformed leaves and neoformed leaves showed reduced size, resulting in an overall decline in end-of-season leaf area index of 64% in A. saccharum, and 16% in the entire forest. Saplings showed lower leaf losses, but also a lower capacity to reflush relative to mature trees. Both surviving preformed and neoformed leaves had severely depressed photosynthetic capacity early in the summer of 2010, but largely regained photosynthetic competence by the end of the growing season. These results indicate that even short-term heat waves can have severe impacts in northern forests, and suggest a particular vulnerability to high temperatures during the spring period of leaf expansion in temperate deciduous forests.

Tree-ring-based drought reconstruction in the Iberian Range (east of Spain) since 1694.

PubMed

Tejedor, Ernesto; de Luis, Martín; Cuadrat, José María; Esper, Jan; Saz, Miguel Ángel

2016-03-01

Droughts are a recurrent phenomenon in the Mediterranean basin with negative consequences for society, economic activities, and natural systems. Nevertheless, the study of drought recurrence and severity in Spain has been limited so far due to the relatively short instrumental period. In this work, we present a reconstruction of the standardized precipitation index (SPI) for the Iberian Range. Growth variations and climatic signals within the network are assessed developing a correlation matrix and the data combined to a single chronology integrating 336 samples from 169 trees of five different pine species distributed throughout the province of Teruel. The new chronology, calibrated against regional instrumental climatic data, shows a high and stable correlation with the July SPI integrating moisture conditions over 12 months forming the basis for a 318-year drought reconstruction. The climate signal contained in this reconstruction is highly significant (p < 0.05) and spatially robust over the interior areas of Spain located above 1000 meters above sea level (masl). According to our SPI reconstruction, seven substantially dry and five wet periods are identified since the late seventeenth century considering ≥±1.76 standard deviations. Besides these, 36 drought and 28 pluvial years were identified. Some of these years, such as 1725, 1741, 1803, and 1879, are also revealed in other drought reconstructions in Romania and Turkey, suggesting that coherent larger-scale synoptic patterns drove these extreme deviations. Since regional drought deviations are also retained in historical documents, the tree-ring-based reconstruction presented here will allow us to cross-validate drought frequency and magnitude in a highly vulnerable region.

Significant effect of topographic normalization of airborne LiDAR data on the retrieval of plant area index profile in mountainous forests

NASA Astrophysics Data System (ADS)

Liu, Jing; Skidmore, Andrew K.; Heurich, Marco; Wang, Tiejun

2017-10-01

As an important metric for describing vertical forest structure, the plant area index (PAI) profile is used for many applications including biomass estimation and wildlife habitat assessment. PAI profiles can be estimated with the vertically resolved gap fraction from airborne LiDAR data. Most research utilizes a height normalization algorithm to retrieve local or relative height by assuming the terrain to be flat. However, for many forests this assumption is not valid. In this research, the effect of topographic normalization of airborne LiDAR data on the retrieval of PAI profile was studied in a mountainous forest area in Germany. Results show that, although individual tree height may be retained after topographic normalization, the spatial arrangement of trees is changed. Specifically, topographic normalization vertically condenses and distorts the PAI profile, which consequently alters the distribution pattern of plant area density in space. This effect becomes more evident as the slope increases. Furthermore, topographic normalization may also undermine the complexity (i.e., canopy layer number and entropy) of the PAI profile. The decrease in PAI profile complexity is not solely determined by local topography, but is determined by the interaction between local topography and the spatial distribution of each tree. This research demonstrates that when calculating the PAI profile from airborne LiDAR data, local topography needs to be taken into account. We therefore suggest that for ecological applications, such as vertical forest structure analysis and modeling of biodiversity, topographic normalization should not be applied in non-flat areas when using LiDAR data.

Phase synchronization based minimum spanning trees for analysis of financial time series with nonlinear correlations

NASA Astrophysics Data System (ADS)

Radhakrishnan, Srinivasan; Duvvuru, Arjun; Sultornsanee, Sivarit; Kamarthi, Sagar

2016-02-01

The cross correlation coefficient has been widely applied in financial time series analysis, in specific, for understanding chaotic behaviour in terms of stock price and index movements during crisis periods. To better understand time series correlation dynamics, the cross correlation matrices are represented as networks, in which a node stands for an individual time series and a link indicates cross correlation between a pair of nodes. These networks are converted into simpler trees using different schemes. In this context, Minimum Spanning Trees (MST) are the most favoured tree structures because of their ability to preserve all the nodes and thereby retain essential information imbued in the network. Although cross correlations underlying MSTs capture essential information, they do not faithfully capture dynamic behaviour embedded in the time series data of financial systems because cross correlation is a reliable measure only if the relationship between the time series is linear. To address the issue, this work investigates a new measure called phase synchronization (PS) for establishing correlations among different time series which relate to one another, linearly or nonlinearly. In this approach the strength of a link between a pair of time series (nodes) is determined by the level of phase synchronization between them. We compare the performance of phase synchronization based MST with cross correlation based MST along selected network measures across temporal frame that includes economically good and crisis periods. We observe agreement in the directionality of the results across these two methods. They show similar trends, upward or downward, when comparing selected network measures. Though both the methods give similar trends, the phase synchronization based MST is a more reliable representation of the dynamic behaviour of financial systems than the cross correlation based MST because of the former's ability to quantify nonlinear relationships among time series or relations among phase shifted time series.

Effects of prolonged drought stress on Scots pine seedling carbon allocation.

PubMed

Aaltonen, Heidi; Lindén, Aki; Heinonsalo, Jussi; Biasi, Christina; Pumpanen, Jukka

2017-04-01

As the number of drought occurrences has been predicted to increase with increasing temperatures, it is believed that boreal forests will become particularly vulnerable to decreased growth and increased tree mortality caused by the hydraulic failure, carbon starvation and vulnerability to pests following these. Although drought-affected trees are known to have stunted growth, as well as increased allocation of carbon to roots, still not enough is known about the ways in which trees can acclimate to drought. We studied how drought stress affects belowground and aboveground carbon dynamics, as well as nitrogen uptake, in Scots pine (Pinus sylvestris L.) seedlings exposed to prolonged drought. Overall 40 Scots pine seedlings were divided into control and drought treatments over two growing seasons. Seedlings were pulse-labelled with 13CO2 and litter bags containing 15N-labelled root biomass, and these were used to follow nutrient uptake of trees. We determined photosynthesis, biomass distribution, root and rhizosphere respiration, water potential, leaf osmolalities and carbon and nitrogen assimilation patterns in both treatments. The photosynthetic rate of the drought-induced seedlings did not decrease compared to the control group, the maximum leaf specific photosynthetic rate being 0.058 and 0.045 µmol g-1 s-1 for the drought and control treatments, respectively. The effects of drought were, however, observed as lower water potentials, increased osmolalities as well as decreased growth and greater fine root-to-shoot ratio in the drought-treated seedlings. We also observed improved uptake of labelled nitrogen from soil to needles in the drought-treated seedlings. The results indicate acclimation of seedlings to long-term drought by aiming to retain sufficient water uptake with adequate allocation to roots and root-associated mycorrhizal fungi. The plants seem to control water potential with osmolysis, for which sufficient photosynthetic capability is needed. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Predicting breeding bird occurrence by stand- and microhabitat-scale features in even-aged stands in the Central Appalachians

USGS Publications Warehouse

McDermott, M.E.; Wood, P.B.; Miller, G.W.; Simpson, B.T.

2011-01-01

Spatial scale is an important consideration when managing forest wildlife habitat, and models can be used to improve our understanding of these habitats at relevant scales. Our objectives were to determine whether stand- or microhabitat-scale variables better predicted bird metrics (diversity, species presence, and abundance) and to examine breeding bird response to clearcut size and age in a highly forested landscape. In 2004-2007, vegetation data were collected from 62 even-aged stands that were 3.6-34.6. ha in size and harvested in 1963-1990 on the Monongahela National Forest, WV, USA. In 2005-2007, we also surveyed birds at vegetation plots. We used classification and regression trees to model breeding bird habitat use with a suite of stand and microhabitat variables. Among stand variables, elevation, stand age, and stand size were most commonly retained as important variables in guild and species models. Among microhabitat variables, medium-sized tree density and tree species diversity most commonly predicted bird presence or abundance. Early successional and generalist bird presence, abundance, and diversity were better predicted by microhabitat variables than stand variables. Thus, more intensive field sampling may be required to predict habitat use for these species, and management may be needed at a finer scale. Conversely, stand-level variables had greater utility in predicting late-successional species occurrence and abundance; thus management decisions and modeling at this scale may be suitable in areas with a uniform landscape, such as our study area. Our study suggests that late-successional breeding bird diversity can be maximized long-term by including harvests >10. ha in size into our study area and by increasing tree diversity. Some harvesting will need to be incorporated regularly, because after 15 years, the study stands did not provide habitat for most early successional breeding specialists. ?? 2010 Elsevier B.V.

Avian Species Richness in Relation to Intensive Forest Management Practices in Early Seral Tree Plantations

PubMed Central

Jones, Jay E.; Kroll, Andrew J.; Giovanini, Jack; Duke, Steven D.; Ellis, Tana M.; Betts, Matthew G.

2012-01-01

Background Managers of landscapes dedicated to forest commodity production require information about how practices influence biological diversity. Individual species and communities may be threatened if management practices truncate or simplify forest age classes that are essential for reproduction and survival. For instance, the degradation and loss of complex diverse forest in young age classes have been associated with declines in forest-associated Neotropical migrant bird populations in the Pacific Northwest, USA. These declines may be exacerbated by intensive forest management practices that reduce hardwood and broadleaf shrub cover in order to promote growth of economically valuable tree species in plantations. Methodology and Principal Findings We used a Bayesian hierarchical model to evaluate relationships between avian species richness and vegetation variables that reflect stand management intensity (primarily via herbicide application) on 212 tree plantations in the Coast Range, Oregon, USA. Specifically, we estimated the influence of broadleaf hardwood vegetation cover, which is reduced through herbicide applications, on bird species richness and individual species occupancy. Our model accounted for imperfect detection. We used average predictive comparisons to quantify the degree of association between vegetation variables and species richness. Both conifer and hardwood cover were positively associated with total species richness, suggesting that these components of forest stand composition may be important predictors of alpha diversity. Estimates of species richness were 35–80% lower when imperfect detection was ignored (depending on covariate values), a result that has critical implications for previous efforts that have examined relationships between forest composition and species richness. Conclusion and Significance Our results revealed that individual and community responses were positively associated with both conifer and hardwood cover. In our system, patterns of bird community assembly appear to be associated with stand management strategies that retain or increase hardwood vegetation while simultaneously regenerating the conifer cover in commercial tree plantations. PMID:22905249

Metrics for comparing neuronal tree shapes based on persistent homology.

PubMed

Li, Yanjie; Wang, Dingkang; Ascoli, Giorgio A; Mitra, Partha; Wang, Yusu

2017-01-01

As more and more neuroanatomical data are made available through efforts such as NeuroMorpho.Org and FlyCircuit.org, the need to develop computational tools to facilitate automatic knowledge discovery from such large datasets becomes more urgent. One fundamental question is how best to compare neuron structures, for instance to organize and classify large collection of neurons. We aim to develop a flexible yet powerful framework to support comparison and classification of large collection of neuron structures efficiently. Specifically we propose to use a topological persistence-based feature vectorization framework. Existing methods to vectorize a neuron (i.e, convert a neuron to a feature vector so as to support efficient comparison and/or searching) typically rely on statistics or summaries of morphometric information, such as the average or maximum local torque angle or partition asymmetry. These simple summaries have limited power in encoding global tree structures. Based on the concept of topological persistence recently developed in the field of computational topology, we vectorize each neuron structure into a simple yet informative summary. In particular, each type of information of interest can be represented as a descriptor function defined on the neuron tree, which is then mapped to a simple persistence-signature. Our framework can encode both local and global tree structure, as well as other information of interest (electrophysiological or dynamical measures), by considering multiple descriptor functions on the neuron. The resulting persistence-based signature is potentially more informative than simple statistical summaries (such as average/mean/max) of morphometric quantities-Indeed, we show that using a certain descriptor function will give a persistence-based signature containing strictly more information than the classical Sholl analysis. At the same time, our framework retains the efficiency associated with treating neurons as points in a simple Euclidean feature space, which would be important for constructing efficient searching or indexing structures over them. We present preliminary experimental results to demonstrate the effectiveness of our persistence-based neuronal feature vectorization framework.

Metrics for comparing neuronal tree shapes based on persistent homology

PubMed Central

Li, Yanjie; Wang, Dingkang; Ascoli, Giorgio A.; Mitra, Partha

2017-01-01

As more and more neuroanatomical data are made available through efforts such as NeuroMorpho.Org and FlyCircuit.org, the need to develop computational tools to facilitate automatic knowledge discovery from such large datasets becomes more urgent. One fundamental question is how best to compare neuron structures, for instance to organize and classify large collection of neurons. We aim to develop a flexible yet powerful framework to support comparison and classification of large collection of neuron structures efficiently. Specifically we propose to use a topological persistence-based feature vectorization framework. Existing methods to vectorize a neuron (i.e, convert a neuron to a feature vector so as to support efficient comparison and/or searching) typically rely on statistics or summaries of morphometric information, such as the average or maximum local torque angle or partition asymmetry. These simple summaries have limited power in encoding global tree structures. Based on the concept of topological persistence recently developed in the field of computational topology, we vectorize each neuron structure into a simple yet informative summary. In particular, each type of information of interest can be represented as a descriptor function defined on the neuron tree, which is then mapped to a simple persistence-signature. Our framework can encode both local and global tree structure, as well as other information of interest (electrophysiological or dynamical measures), by considering multiple descriptor functions on the neuron. The resulting persistence-based signature is potentially more informative than simple statistical summaries (such as average/mean/max) of morphometric quantities—Indeed, we show that using a certain descriptor function will give a persistence-based signature containing strictly more information than the classical Sholl analysis. At the same time, our framework retains the efficiency associated with treating neurons as points in a simple Euclidean feature space, which would be important for constructing efficient searching or indexing structures over them. We present preliminary experimental results to demonstrate the effectiveness of our persistence-based neuronal feature vectorization framework. PMID:28809960

Introduced and invasive species in novel rangeland ecosystems: friends or foes?

USGS Publications Warehouse

Belnap, Jayne; Ludwig, John A.; Wilcox, Bradford P.; Betancourt, Julio L.; Dean, W. Richard J.; Hoffmann, Benjamin D.; Milton, Sue J.

2012-01-01

Globally, new combinations of introduced and native plant and animal species have changed rangelands into novel ecosystems. Whereas many rangeland stakeholders (people who use or have an interest in rangelands) view intentional species introductions to improve forage and control erosion as beneficial, others focus on unintended costs, such as increased fire risk, loss of rangeland biodiversity, and threats to conservation efforts, specifically in nature reserves and parks. These conflicting views challenge all rangeland stakeholders, especially those making decisions on how best to manage novel ecosystems. To formulate a conceptual framework for decision making, we examined a wide range of novel ecosystems, created by intentional and unintentional introductions of nonnative species and land-use–facilitated spread of native ones. This framework simply divides decision making into two types: 1) straightforward–certain, and 2) complex–uncertain. We argue that management decisions to retain novel ecosystems are certain when goods and services provided by the system far outweigh the costs of restoration, for example in the case of intensively managed Cenchrus pastures. Decisions to return novel ecosystems to natural systems are also certain when the value of the system is low and restoration is easy and inexpensive as in the case of biocontrol of Opuntia infestations. In contrast, decisions whether to retain or restore novel ecosystems become complex and uncertain in cases where benefits are low and costs of control are high as, for example, in the case of stopping the expansion of Prosopis and Juniperus into semiarid rangelands. Decisions to retain or restore novel ecosystems are also complex and uncertain when, for example, nonnative Eucalyptus trees expand along natural streams, negatively affecting biodiversity, but also providing timber and honey. When decision making is complex and uncertain, we suggest that rangeland managers utilize cost–benefit analyses and hold stakeholder workshops to resolve conflicts.

Topology-guided deformable registration with local importance preservation for biomedical images

NASA Astrophysics Data System (ADS)

Zheng, Chaojie; Wang, Xiuying; Zeng, Shan; Zhou, Jianlong; Yin, Yong; Feng, Dagan; Fulham, Michael

2018-01-01

The demons registration (DR) model is well recognized for its deformation capability. However, it might lead to misregistration due to erroneous diffusion direction when there are no overlaps between corresponding regions. We propose a novel registration energy function, introducing topology energy, and incorporating a local energy function into the DR in a progressive registration scheme, to address these shortcomings. The topology energy that is derived from the topological information of the images serves as a direction inference to guide diffusion transformation to retain the merits of DR. The local energy constrains the deformation disparity of neighbouring pixels to maintain important local texture and density features. The energy function is minimized in a progressive scheme steered by a topology tree graph and we refer to it as topology-guided deformable registration (TDR). We validated our TDR on 20 pairs of synthetic images with Gaussian noise, 20 phantom PET images with artificial deformations and 12 pairs of clinical PET-CT studies. We compared it to three methods: (1) free-form deformation registration method, (2) energy-based DR and (3) multi-resolution DR. The experimental results show that our TDR outperformed the other three methods in regard to structural correspondence and preservation of the local important information including texture and density, while retaining global correspondence.

Tidal events and salt-marsh structure influence black mangrove (Avicennia germinans) recruitment across an ecotone.

PubMed

Peterson, Jennifer M; Bell, Susan S

2012-07-01

Field experiments were conducted at a black mangrove-salt-marsh ecotone in southwest Florida (U.S.A.) to investigate retention of propagules of the black mangrove, Avicennia germinans, by salt-marsh plants as a mechanism of facilitation operating on recruitment success at landward boundaries. Buoyant A. germinans propagules are dispersed by tides, and stranding is required for establishment; therefore, processes that enable stranding should facilitate mangrove recruitment. We expected the physical structure of salt-marsh vegetation to define propagule retention capacity, and we predicted that salt-marsh plants with distinct growth forms would differentially retain propagules. Experimental monoculture plots (1 m2) of salt-marsh plants with different growth forms (Sporobolus virginicus [grass], Sesuvium portulacastrum [succulent forb], and Batis maritima [succulent scrub]) were created, and A. germinans propagules were emplaced into these plots and monitored over time. For comparison, propagules were also placed into natural polyculture plots (1 m2). Polyculture plots contained at least two of the salt-marsh plant taxa selected for monoculture treatments, and S. virginicus was always present within these polyculture plots. Natural polyculture plots retained 59.3% +/- 11.0% (mean +/- SE) of emplaced propagules. Monocultures varied in their propagule retention capacities with plots of S. virginicus retaining on average 65.7% +/- 11.5% of transplanted propagules compared to 7.2% +/- 1.8% by B. maritima and 5.0% +/- 1.9% by S. portulacastrum. Plots containing S. virginicus retained a significantly greater percentage of emplaced propagules relative to the two succulent salt-marsh taxa. Furthermore, propagule entrapment, across all treatments, was strongly correlated with salt-marsh structure (r2 = 0.6253, P = 0.00001), which was estimated using an indirect quantitative metric (lateral obstruction) calculated from digital images of plots. Overall, our findings imply that entrapment of propagules by salt-marsh plants may be facilitative if propagules are dispersed beyond the established tree line by spring or storm tides, and that facilitation may be sustained over time. We conclude that salt-marsh ecotone permeability may modulate landward encroachment by A. germinans, and that interactions among the early life history stages of black mangroves and neighboring plants may direct community responses to climate change.

The equivalence of two phylogenetic biodiversity measures: the Shapley value and Fair Proportion index.

PubMed

Hartmann, Klaas

2013-11-01

Most biodiversity conservation programs are forced to prioritise species in order to allocate their funding. This paper contains a mathematical proof that provides biological support for one common approach based on phylogenetic indices. Phylogenetic trees describe the evolutionary relationships between a group of taxa. Two indices for computing the distinctiveness of each taxon in a phylogenetic tree are considered here-the Shapley value and the Fair Proportion index. These indices provide a measure of the importance of each taxon for overall biodiversity and have been used to prioritise taxa for conservation. The Shapley value is the biodiversity contribution a taxon is expected to make if all taxa are equally likely to become extinct. This interpretation makes it appealing to use the Shapley value in biodiversity conservation applications. The Fair Proportion index lacks a convenient interpretation, however it is significantly easier to calculate and understand. It has been empirically observed that there is a high correlation between the two indices. This paper shows the mathematical basis for this correlation and proves that as the number of taxa increases, the indices become equivalent. Consequently in biodiversity prioritisation the simpler Fair Proportion index can be used whilst retaining the appealing interpretation of the Shapley value.

Ultraconserved words point to deep language ancestry across Eurasia.

PubMed

Pagel, Mark; Atkinson, Quentin D; S Calude, Andreea; Meade, Andrew

2013-05-21

The search for ever deeper relationships among the World's languages is bedeviled by the fact that most words evolve too rapidly to preserve evidence of their ancestry beyond 5,000 to 9,000 y. On the other hand, quantitative modeling indicates that some "ultraconserved" words exist that might be used to find evidence for deep linguistic relationships beyond that time barrier. Here we use a statistical model, which takes into account the frequency with which words are used in common everyday speech, to predict the existence of a set of such highly conserved words among seven language families of Eurasia postulated to form a linguistic superfamily that evolved from a common ancestor around 15,000 y ago. We derive a dated phylogenetic tree of this proposed superfamily with a time-depth of ~14,450 y, implying that some frequently used words have been retained in related forms since the end of the last ice age. Words used more than once per 1,000 in everyday speech were 7- to 10-times more likely to show deep ancestry on this tree. Our results suggest a remarkable fidelity in the transmission of some words and give theoretical justification to the search for features of language that might be preserved across wide spans of time and geography.

Megagardeners of the forest - the role of elephants in seed dispersal

NASA Astrophysics Data System (ADS)

Campos-Arceiz, Ahimsa; Blake, Steve

2011-11-01

As the largest frugivores on Earth, elephants have unique ecological properties. Found in deserts, savannahs, and forests, they are the last remnants of a diverse lineage. Among the three currently recognized forms, African forest elephants are the most frugivorous, followed by Asian and African savannah elephants, although their role as seed dispersers is variable and context-dependent. African forest elephants may consume more seeds from more species than any other taxon of large vertebrate dispersers, defecating them over long distances in viable conditions into nutrient-rich and protective dung. In short, elephants are forest gardeners. The signature of elephant dispersal is evident in the spatial distribution of trees suggesting that elephants maintain tree diversity and retain low redundancy in seed dispersal systems. Large numbers of forest elephants ranging over large areas may be essential for ecosystem function. The loss of elephants will have important negative consequences for the ecological trajectories of some plant species and whole ecological communities, yet the conservation status of forest elephants is catastrophic in Asia and rapidly becoming so in Africa due to hunting and other conflicts with people. In this paper we review the current knowledge of elephants as seed dispersers, discuss the ecological consequences of their decline, and suggest priority areas for research and conservation action.

Ultraconserved words point to deep language ancestry across Eurasia

PubMed Central

Pagel, Mark; Atkinson, Quentin D.; S. Calude, Andreea; Meade, Andrew

2013-01-01

The search for ever deeper relationships among the World’s languages is bedeviled by the fact that most words evolve too rapidly to preserve evidence of their ancestry beyond 5,000 to 9,000 y. On the other hand, quantitative modeling indicates that some “ultraconserved” words exist that might be used to find evidence for deep linguistic relationships beyond that time barrier. Here we use a statistical model, which takes into account the frequency with which words are used in common everyday speech, to predict the existence of a set of such highly conserved words among seven language families of Eurasia postulated to form a linguistic superfamily that evolved from a common ancestor around 15,000 y ago. We derive a dated phylogenetic tree of this proposed superfamily with a time-depth of ∼14,450 y, implying that some frequently used words have been retained in related forms since the end of the last ice age. Words used more than once per 1,000 in everyday speech were 7- to 10-times more likely to show deep ancestry on this tree. Our results suggest a remarkable fidelity in the transmission of some words and give theoretical justification to the search for features of language that might be preserved across wide spans of time and geography. PMID:23650390

A new species of Euprox (Cervidae, Artiodactyla) from the upper Miocene of the Linxia Basin, Gansu Province, China, with interpretation of its paleoenvironment.

PubMed

Hou, Sukuan

2015-01-16

The Linxia Basin, Gansu Province, China, is known for its abundant and well preserved fossils. Here a new species, Euprox grandis sp. nov., is established based on a skull and antlers collected from the upper Miocene Liushu Formation of the Linxia Basin. The new species is distinguishable from other Euprox species by its large body size, notably long pedicle and weak burr. The main beam and the brow tine are slightly curved both medially and backwards, and the apex of the main beam turns, curving slightly laterally. The upper cheek teeth are brachydont, with a clear central fold on the premolars and internal postprotocrista and metaconule fold on M1-M2. The cingulum is almost absent, only occasionally weakly developed at the anterior and lingual surface of the teeth. Cladistic analysis was carried out using the TNT software, and two most parsimonious trees were retained. As the strict consensus tree shows E. grandis appears to be an advanced muntiacine form, which may have a close relationship with the genus Muntiacus. The presence of E. grandis in the Linxia Basin adds new evidence to support a warm and humid environment during the late Miocene in the basin. 

Mediterranean fruit fly on Mimusops zeyheri indigenous to South Africa: a threat to the horticulture industry.

PubMed

Dube, Zakheleni P; Mashela, Phatu W; Mathabatha, Raesibe V

2016-08-01

Claims abound that the Transvaal red milkwood, Mimusops zeyheri, indigenous to areas with tropical and subtropical commercial fruit trees and fruiting vegetables in South Africa, is relatively pest free owing to its copious concentrations of latex in the above-ground organs. On account of observed fruit fly damage symptoms, a study was conducted to determine whether M. zeyheri was a host to the notorious quarantined Mediterranean fruit fly (Ceratitis capitata). Fruit samples were kept for 16-21 days in plastic pots containing moist steam-pasteurised growing medium with tops covered with a mesh sheath capable of retaining emerging flies. Microscopic diagnosis of the trapped flies suggested that the morphological characteristics were congruent with those of C. capitata, which was confirmed through cytochrome c oxidase I (COI) gene sequence alignment with a 100% bootstrap value and 99% confidence probability when compared with those from the National Centre for Biotechnology Information database. This study demonstrated that M. zeyheri is a host of C. capitata. Therefore, C. capitata from infestation reservoirs of M. zeyheri fruit trees could be a major threat to the tropical and subtropical fruit industries in South Africa owing to the fruit-bearing nature of the new host. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

Irrigating poplar energy crops with landfill leachate negatively affects soil micro- and meso-fauna.

PubMed

Coyle, David R; Zalesny, Jill A; Zalesny, Ronald S; Wiese, Adam H

2011-10-01

Increased municipal solid waste generated worldwide combined with substantial demand for renewable energy has prompted testing and deployment of woody feedstock production systems that reuse and recycle wastewaters as irrigation and fertilization. Populus selections are ideal for such systems given their fast growth, extensive root systems, and high water usage rates. Maintaining ecological sustainability (i.e., the capacity for an ecosystem to maintain its function and retain its biodiversity over time) during tree establishment and development is an important component of plantation success, especially for belowground faunal populations. To determine the impact of solid waste leachate on soil micro- and meso-fauna, we compared soilfrom eight different Populus clones receiving municipal solid waste landfill leachate irrigation with clones receiving fertilized (N, P K) well water irrigation. Microfauna (i.e., nematodes) communities were more diverse in control soils. Mesofauna (i.e., insects) were associated with all clones; however, they were four times more abundant around trees found within the control plot than those that received leachate treatments. Nematode and insect abundance varied among Populus clones yet insect diversity was greater in the leachate-treated soils. Phytotechnologies must allow for soil faunal sustainability, as upsetting this balance could lead to great reductions in phytotechnology efficacy.

Efficient cost-sensitive human-machine collaboration for offline signature verification

NASA Astrophysics Data System (ADS)

Coetzer, Johannes; Swanepoel, Jacques; Sabourin, Robert

2012-01-01

We propose a novel strategy for the optimal combination of human and machine decisions in a cost-sensitive environment. The proposed algorithm should be especially beneficial to financial institutions where off-line signatures, each associated with a specific transaction value, require authentication. When presented with a collection of genuine and fraudulent training signatures, produced by so-called guinea pig writers, the proficiency of a workforce of human employees and a score-generating machine can be estimated and represented in receiver operating characteristic (ROC) space. Using a set of Boolean fusion functions, the majority vote decision of the human workforce is combined with each threshold-specific machine-generated decision. The performance of the candidate ensembles is estimated and represented in ROC space, after which only the optimal ensembles and associated decision trees are retained. When presented with a questioned signature linked to an arbitrary writer, the system first uses the ROC-based cost gradient associated with the transaction value to select the ensemble that minimises the expected cost, and then uses the corresponding decision tree to authenticate the signature in question. We show that, when utilising the entire human workforce, the incorporation of a machine streamlines the authentication process and decreases the expected cost for all operating conditions.

Sources of variation in concentrations of nickel and copper in mountain birch foliage near a nickel-copper smelter at Monchegorsk, north-western Russia: results of long-term monitoring.

PubMed

Kozlov, Mikhail V

2005-05-01

Concentrations of nickel and copper, two principal metal pollutants of the 'Severonikel' smelter at Monchegorsk, NW Russia, were measured in unwashed leaves of mountain birch, Betula pubescens subsp. czerepanovii, collected in eight study sites along the pollution gradient during 1991-2003. In spite of significant decline in metal emissions, concentrations of foliar metals in most of the study sites did not decrease, indicating that soil contamination remains extremely high. Multiyear mean values peaked at 6.6 km S of the smelter, where they were 20-25 times higher than in the most distant study site. Concentrations of both metals demonstrated pronounced annual variation, which was explained by the meteorological conditions of early summer: higher precipitation in May increased foliar concentrations of both metals, whereas higher precipitation in June resulted in lower foliar concentrations of nickel. These data suggest that ecotoxicological situation in metal-contaminated areas can be modified by the expected climate change. In heavily polluted sites individual birch trees generally retained their ranks in terms of metal contamination during 1995-2003, demonstrating that the use of the same set of trees can significantly increase the accuracy of the monitoring data.

Phytostabilization of a Pb-contaminated mine tailing by various tree species in pot and field trial experiments.

PubMed

Meeinkuirt, Weeradej; Pokethitiyook, Prayad; Kruatrachue, Maleeya; Tanhan, Phanwimol; Chaiyarat, Rattanawat

2012-10-01

The potential of 6 tree species (Leucaena leucocephala, Acacia mangium, Peltophorum pterocarpum, Pterocarpus macrocarpus, Lagerstroemia floribunda, Eucalyptus camaldulensis) for phytoremediation of Pb in sand tailings (total Pb >9850 mg kg(-1)) from KEMCO Pb mine in Kanchanaburi province, Thailand, were investigated employing a pot experiment (3 months) and field trial experiment (12 months). In pot study E. camaldulensis treated with Osmocote fertilizer attained the highest total biomass (15.3 g plant(-1)) followed by P. pterocarpum (12.6 g plant(-1)) and A. mangium (10.8 g plant(-1)) both treated with cow manure. Cow manure application resulted in the highest root Pb accumulation (>10000 mg kg(-1)) in L. floribunda and P. macrocarpus. These two species also exhibited the highest Pb uptake (85-88 mg plant(-1)). Results from field trial also showed that Osmocote promoted the best growth performance in E. camaldulensis (biomass 385.7 g plant(-1), height 141.7 cm) followed by A. mangium (biomass 215.9 g plant(-1), height 102.7 cm), and they also exhibited the highest Pb uptake (600-800 microg plant(-1)). A. mangium with the addition of organic fertilizer was the best option for phytostabilization of Pb-contaminated mine tailing because it retained higher Pb concentration in the roots.

Detailed characterization of Act d 12 and Act d 13 from kiwi seeds: implication in IgE cross-reactivity with peanut and tree nuts.

PubMed

Sirvent, S; Cantó, B; Gómez, F; Blanca, N; Cuesta-Herranz, J; Canto, G; Blanca, M; Rodríguez, R; Villalba, M; Palomares, O

2014-11-01

Act d 12 (11S globulin) and Act d 13 (2S albumin) are two novel relevant allergens from kiwi seeds that might be useful to improve the diagnostic sensitivity and the management of kiwifruit-allergic patients. To perform a comprehensive structural and immunological characterization of purified Act d 12 and Act d 13 from kiwi seeds. Sera from 55 well-defined kiwifruit-allergic patients were used. Act d 12 and Act d 13 were purified by chromatographic procedures. Circular dichroism, mass spectrometry, concanavalin A detection, immunoblotting, enzyme-linked immunosorbent assays, basophil activation tests, and IgE-inhibition experiments were used. Act d 12 and Act d 13 were purified from kiwi seeds to homogeneity by combining size-exclusion, ion-exchange, and RP-HPLC chromatographies. Both purified allergens preserve the structural integrity and display typical features of their homologous counterparts from the 11S globulin and 2S albumin protein families, respectively. These allergens are released from kiwi seeds after oral and gastric digestion of whole kiwifruit, demonstrating their bioavailability after ingestion. The allergens retain the capacity to bind serum IgE from kiwifruit-allergic patients, induce IgE cross-linking in effector-circulating basophils, and display in vitro IgE cross-reactivity with homologous counterparts from peanut and tree nuts. Purified Act d 12 and Act d 13 from kiwi seeds are well-defined molecules involved in in vitro IgE cross-reactivity with peanut and tree nuts. Their inclusion in component-resolved diagnosis of kiwifruit allergy might well contribute to improve the diagnostic sensitivity and the management of kiwifruit-allergic patients. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Evidence for substantial forestry canopy processing of nitrogen deposition using isotopic tracer experiments in low deposition conditions

NASA Astrophysics Data System (ADS)

Ferraretto, Daniele; Heal, Kate

2017-04-01

Temperate forest ecosystems are significant sinks for nitrogen deposition (Ndep) yielding benefits such as protection of waterbodies from eutrophication and enhanced sequestration of atmospheric CO2. Previous studies have shown evidence of biological nitrification and Ndep processing and retention in forest canopies. However, this was reported only at sites with high environmental or experimentally enhanced rates of Ndep (˜18 kg N ha-1 y-1) and has not yet been demonstrated in low Ndep environments. We have used bulk field hydrochemical measurements and labelled isotopic experiments to assess canopy processing in a lower Ndep environment (˜7 kg N ha-1 year-1) at a Sitka spruce plantation in Perthshire, Scotland, representing the dominant tree species (24%) in woodlands in Great Britain. Analysis of 4.5 years of measured N fluxes in rainfall (RF) and fogwater onto the canopy and throughfall (TF) and stemflow (SF) below the canopy suggests strong transformation and uptake of Ndep in the forest canopy. Annual canopy Ndep uptake was ˜4.7 kg N ha-1 year-1, representing 60-76% of annual Ndep. To validate these plot-scale results and track N uptake within the forest canopy in different seasons, double 15N-labelled NH4NO3 (98%) solution was sprayed in summer and winter onto the canopy of three trees at the measurement site. RF, TF and SF samples have been collected and analysed for 15NH4 and 15NO3. Comparing the amount of labelled N recovered under the sample trees with the measured δ15N signal is expected to provide further evidence of the role of forest canopies in actively processing and retaining atmospheric N deposition.

Chemometrics in biomonitoring: Distribution and correlation of trace elements in tree leaves.

PubMed

Deljanin, Isidora; Antanasijević, Davor; Bjelajac, Anđelika; Urošević, Mira Aničić; Nikolić, Miroslav; Perić-Grujić, Aleksandra; Ristić, Mirjana

2016-03-01

The concentrations of 15 elements were measured in the leaf samples of Aesculus hippocastanum, Tilia spp., Betula pendula and Acer platanoides collected in May and September of 2014 from four different locations in Belgrade, Serbia. The objective was to assess the chemical characterization of leaf surface and in-wax fractions, as well as the leaf tissue element content, by analyzing untreated, washed with water and washed with chloroform leaf samples, respectively. The combined approach of self-organizing networks (SON) and Preference Ranking Organization Method for Enrichment Evaluation (PROMETHEE) aided by Geometrical Analysis for Interactive Aid (GAIA) was used in the interpretation of multiple element loads on/in the tree leaves. The morphological characteristics of the leaf surfaces and the elemental composition of particulate matter (PM) deposited on tree leaves were studied by using scanning electron microscopy (SEM) with energy dispersive spectroscopy (EDS) detector. The results showed that the amounts of retained and accumulated element concentrations depend on several parameters, such as chemical properties of the element and morphological properties of the leaves. Among the studied species, Tilia spp. was found to be the most effective in the accumulation of elements in leaf tissue (70% of the total element concentration), while A. hippocastanum had the lowest accumulation (54%). After water and chloroform washing, the highest percentages of removal were observed for Al, V, Cr, Cu, Zn, As, Cd and Sb (>40%). The PROMETHEE/SON ranking/classifying results were in accordance with the results obtained from the GAIA clustering techniques. The combination of the techniques enabled extraction of additional information from datasets. Therefore, the use of both the ranking and clustering methods could be a useful tool to be applied in biomonitoring studies of trace elements. Copyright © 2015 Elsevier B.V. All rights reserved.

Post-breeding bird responses to canopy tree retention, stand size, and edge in regenerating Appalachian hardwood stands

USGS Publications Warehouse

McDermott, Molly E.; Wood, Petra B.

2011-01-01

Avian use of even-aged timber harvests is likely affected by stand attributes such as size, amount of edge, and retained basal area, all characteristics that can easily be manipulated in timber harvesting plans. However, few studies have examined their effects during the post-breeding period. We studied the impacts of clearcut, low-leave two-age, and high-leave two-age harvesting on post-breeding birds using transect sampling and mist-netting in north-central West Virginia. In our approach, we studied the effects of these harvest types as well as stand size and edge on species characteristic of both early-successional and mature forest habitats. In 2005–2006, 13 stands ranging from 4 to 10 years post-harvest and 4–21 ha in size were sampled from late June through mid-August. Capture rates and relative abundance were similar among treatments for generalist birds. Early-successional birds had the lowest capture rates and fewer species (∼30% lower), and late-successional birds reached their highest abundance and species totals (double the other treatments) in high-leave two-age stands. Area sensitivity was evident for all breeding habitat groups. Both generalist and late-successional bird captures were negatively related to stand size, but these groups showed no clear edge effects. Mean relative abundance decreased to nearly zero for the latter group in the largest stands. In contrast, early-successional species tended to use stand interiors more often and responded positively to stand size. Capture rates for this group tripled as stand size increased from 4 to 21 ha. Few birds in the forest periphery responded to harvest edge types despite within-stand edge effects evident for several species. To create suitable habitat for early-successional birds, large, non-linear openings with a low retained basal area are ideal, while smaller harvests and increased residual tree retention would provide habitat for more late-successional birds post-breeding. Although our study has identified habitat use patterns for different species in timber harvests, understanding habitat-specific bird survival is needed to help determine the quality of silvicultural harvests for post-breeding birds.

Comparison of breeding bird and vegetation communities in primary and secondary forests of Great Smoky Mountains National Park

USGS Publications Warehouse

Simons, Theodore R.; Shriner, Susan A.; Farnsworth, George L.

2006-01-01

We compared breeding bird communities and vegetation characteristics at paired point locations in primary (undisturbed) and mature secondary forest (70-100 years old) sites in Great Smoky Mountains National Park, USA to understand how sites logged prior to creation of the park compare to undisturbed sites following 70 years of protection from human disturbance. We found that bird and vegetation communities are currently similar, but retain some differences in species composition. Rank abundance curves for primary and secondary forest bird communities showed very similar patterns of species dominance. Species composition was also similar on the two sites which shared 24 of the 25 most frequently recorded species. Nonetheless, comparisons of density estimates derived from distance sampling showed three bird species were more abundant on primary forest sites and that one bird species was significantly more abundant on secondary forest sites. Notably, comparisons based on raw counts (unadjusted for potential differences in detectability) produced somewhat different results. Analyses of vegetation samples for the paired sites also showed relative similarity, but with some differences between primary and secondary forests. Primary forest sites had more large trees (trees greater than 50 cm diameter at breast height) and late successional species. Primary forest sites had a denser tall shrub layer while secondary forest sites had a denser canopy layer. Nonetheless, tree species richness, basal area of live trees and number of standing snags did not differ between primary and secondary forest sites. Results indicate that breeding bird communities on sites within the park that were logged commercially 70 years ago are currently quite similar to bird communities on sites with no history of human disturbance. Similarities between the bird communities on previously disturbed and undisturbed sites in Great Smoky Mountains National Park may exceed those on more fragmented landscapes because large patches of primary forest, adjacent to commercially logged sites, remained in the park when it was established in 1935. These patches of primary forest may have served as source areas for commercially logged sites.

Insights into recent and ancient trends in the co-evolution of Earth and life as revealed by microbial genomics

NASA Astrophysics Data System (ADS)

Anderson, R. E.; Huber, J. A.; Parsons, C.; Stüeken, E.

2017-12-01

Since the origin of life over 4 billion years ago, life has fundamentally altered the habitability of Earth. Similarly, the environment molds the evolutionary trajectory of life itself through natural selection. Microbial genomes retain a "memory" of the co-evolution of life and Earth and can be analyzed to better understand trends and events in both the recent and distant past. To examine evolutionary trends in the more recent past, we have used metagenomics analyses to investigate which environmental factors play the strongest role in driving the evolution of microbes in deep-sea hydrothermal vents, which are thought to have been important habitats in the earliest stages of life's evolution. We have shown that microbial populations in a deep, basalt-hosted system appear to be under stronger purifying selection than populations inhabiting a cooler serpentinizing system less than 20 km away, suggesting that environmental context and geochemistry have an important impact on evolutionary rates and trends. We also found evidence that viruses play an important role in driving evolution in these habitats. Changing environmental conditions may also effect long-term evolutionary trends in Earth's distant past, as revealed by comparative genomics. By reconciling phylogenetic trees for microbial species with trees of metabolic genes, we can determine approximately when crucial metabolic genes began to spread across the tree of life through horizontal gene transfer. Using these methods, we conducted an analysis of the relative timing of the spread of genes related to the nitrogen cycle. Our results indicate that the rate of horizontal gene transfer for important genes related to denitrification increased after the Great Oxidation Event, concurrent with geochemical evidence for increasing availability of nitrate, suggesting that the oxygenation of the atmosphere and surface ocean may have been an important determining factor for the spread of denitrification genes across the tree of life. In contrast, genes related to nitrogen fixation display much more consistent rates of horizontal gene transfer throughout Earth's history. Studies that couple genomics approaches with geochemistry have the potential to reveal insights into the co-evolution of life and Earth both in the recent and distant past.

Evolutionary analysis of the TPP-dependent enzyme family.

PubMed

Costelloe, Seán J; Ward, John M; Dalby, Paul A

2008-01-01

The evolutionary relationships of the thiamine pyrophosphate (TPP)-dependent family of enzymes was investigated by generation of a neighbor joining phylogenetic tree using sequences from the conserved pyrophosphate (PP) and pyrimidine (Pyr) binding domains of 17 TPP-dependent enzymes. This represents the most comprehensive analysis of TPP-dependent enzyme evolution to date. The phylogeny was shown to be robust by comparison with maximum likelihood trees generated for each individual enzyme and also broadly confirms the evolutionary history proposed recently from structural comparisons alone (Duggleby 2006). The phylogeny is most parsimonious with the TPP enzymes having arisen from a homotetramer which subsequently diverged into an alpha(2)beta(2) heterotetramer. The relationship between the PP- and Pyr-domains and the recruitment of additional protein domains was examined using the transketolase C-terminal (TKC)-domain as an example. This domain has been recruited by several members of the family and yet forms no part of the active site and has unknown function. Removal of the TKC-domain was found to increase activity toward beta-hydroxypyruvate and glycolaldehyde. Further truncations of the Pyr-domain yielded several variants with retained activity. This suggests that the influence of TKC-domain recruitment on the evolution of the mechanism and specificity of transketolase (TK) has been minor, and that the smallest functioning unit of TK comprises the PP- and Pyr-domains, whose evolutionary histories extend to all TPP-dependent enzymes.

Effects of tannin source and concentration from tree leaves on two species of tadpoles.

PubMed

Earl, Julia E; Semlitsch, Raymond D

2015-01-01

Vegetation in and around freshwater ecosystems can affect aquatic organisms through the production of secondary compounds, which are retained in leaves after senescence and are biologically active. Tannins can be toxic to tadpoles, but the plant source of tannins and tannin concentration have been confounded in experimental designs in previous studies. To examine the effects of the concentration and source of tannins (tree species), we examined the effects of 4 factors on tadpole survival, growth, and development: tannin source (red oak [Quercus rubra], white oak [Quercus alba], or sugar maple [Acer saccharum]); tannin concentration (including a control); diet protein level; and tadpole species (American toad [Anaxyrus americanus] and spring peepers [Pseudacris crucifer]). Tannin source and concentration affected spring peeper survival, but American toads had uniformly high survival. Spring peepers had a lower survival rate in high tannin concentrations of oak leachate but a high survival rate in both concentrations of sugar maple leachate. These differences in survival did not correspond with changes in dissolved oxygen, and no effect of dietary protein level on tadpole performance was observed. The presence of plant leachate resulted in increased tadpole growth in both species, but the mechanism for this finding is unclear. The results of the present study show that tannin concentration and source are important factors for tadpole performance, adding further evidence that plant chemistry can affect aquatic organisms. © 2014 SETAC.

Gene function prediction based on the Gene Ontology hierarchical structure.

PubMed

Cheng, Liangxi; Lin, Hongfei; Hu, Yuncui; Wang, Jian; Yang, Zhihao

2014-01-01

The information of the Gene Ontology annotation is helpful in the explanation of life science phenomena, and can provide great support for the research of the biomedical field. The use of the Gene Ontology is gradually affecting the way people store and understand bioinformatic data. To facilitate the prediction of gene functions with the aid of text mining methods and existing resources, we transform it into a multi-label top-down classification problem and develop a method that uses the hierarchical relationships in the Gene Ontology structure to relieve the quantitative imbalance of positive and negative training samples. Meanwhile the method enhances the discriminating ability of classifiers by retaining and highlighting the key training samples. Additionally, the top-down classifier based on a tree structure takes the relationship of target classes into consideration and thus solves the incompatibility between the classification results and the Gene Ontology structure. Our experiment on the Gene Ontology annotation corpus achieves an F-value performance of 50.7% (precision: 52.7% recall: 48.9%). The experimental results demonstrate that when the size of training set is small, it can be expanded via topological propagation of associated documents between the parent and child nodes in the tree structure. The top-down classification model applies to the set of texts in an ontology structure or with a hierarchical relationship.

Chemical element accumulation in tree bark grown in volcanic soils of Cape Verde-a first biomonitoring of Fogo Island.

PubMed

Marques, Rosa; Prudêncio, Maria Isabel; Freitas, Maria do Carmo; Dias, Maria Isabel; Rocha, Fernando

2017-05-01

Barks from Prosopis juliflora (acacia) were collected in 12 sites of different geological contexts over the volcanic Fogo Island (Cape Verde). Elemental contents of Ba, Br, Co, Cr, Fe, K, Na, Zn and some rare earth elements (REE)-La, Ce, Sm, Eu, Tb, Yb, and Lu, were obtained for biological samples and topsoils by using k 0 -standardized and comparative method of instrumental neutron activation analysis (INAA), aiming the evaluation of chemical elements uptake by acacia bark. This first biomonitoring study of Fogo Island showed that, in general, significant accumulations of trace elements present in high amounts in these soils occur. This can be partially explained by the semi-arid climate with a consequent bioavailability of chemical elements when rain drops fall in this non-polluted environment. REE enrichment factors (EFs) increase with the decrease of ionic radius. Heavy REE (HREE) are significantly enriched in bark, which agrees with their release after the primary minerals breakdown and the formation of more soluble compounds than the other REE, and uptake by plants. Among the potential harmful chemical elements, Cr appears to be partially retained in nanoparticles of iron oxides. The high EFs found in tree barks of Fogo Island are certainly of geogenic origin rather than anthropogenic input since industry and the use of fertilizers is scarce.

Facilitating normative judgments of conditional probability: frequency or nested sets?

PubMed

Yamagishi, Kimihiko

2003-01-01

Recent probability judgment research contrasts two opposing views. Some theorists have emphasized the role of frequency representations in facilitating probabilistic correctness; opponents have noted that visualizing the probabilistic structure of the task sufficiently facilitates normative reasoning. In the current experiment, the following conditional probability task, an isomorph of the "Problem of Three Prisoners" was tested. "A factory manufactures artificial gemstones. Each gemstone has a 1/3 chance of being blurred, a 1/3 chance of being cracked, and a 1/3 chance of being clear. An inspection machine removes all cracked gemstones, and retains all clear gemstones. However, the machine removes 1/2 of the blurred gemstones. What is the chance that a gemstone is blurred after the inspection?" A 2 x 2 design was administered. The first variable was the use of frequency instruction. The second manipulation was the use of a roulette-wheel diagram that illustrated a "nested-sets" relationship between the prior and the posterior probabilities. Results from two experiments showed that frequency alone had modest effects, while the nested-sets instruction achieved a superior facilitation of normative reasoning. The third experiment compared the roulette-wheel diagram to tree diagrams that also showed the nested-sets relationship. The roulette-wheel diagram outperformed the tree diagrams in facilitation of probabilistic reasoning. Implications for understanding the nature of intuitive probability judgments are discussed.

Diversity and decay ability of basidiomycetes isolated from lodgepole pines killed by the mountain pine beetle.

PubMed

Son, E; Kim, J-J; Lim, Y W; Au-Yeung, T T; Yang, C Y H; Breuil, C

2011-01-01

When lodgepole pines (Pinus contorta Douglas ex Louden var. latifolia Engelm. ex S. Watson) that are killed by the mountain pine beetle (Dendroctonus ponderosae) and its fungal associates are not harvested, fungal decay can affect wood and fibre properties. Ophiostomatoids stain sapwood but do not affect the structural properties of wood. In contrast, white or brown decay basidiomycetes degrade wood. We isolated both staining and decay fungi from 300 lodgepole pine trees killed by mountain pine beetle at green, red, and grey stages at 10 sites across British Columbia. We retained 224 basidiomycete isolates that we classified into 34 species using morphological and physiological characteristics and rDNA large subunit sequences. The number of basidiomycete species varied from 4 to 14 species per site. We assessed the ability of these fungi to degrade both pine sapwood and heartwood using the soil jar decay test. The highest wood mass losses for both sapwood and heartwood were measured for the brown rot species Fomitopsis pinicola and the white rot Metulodontia and Ganoderma species. The sap rot species Trichaptum abietinum was more damaging for sapwood than for heartwood. A number of species caused more than 50% wood mass losses after 12 weeks at room temperature, suggesting that beetle-killed trees can rapidly lose market value due to degradation of wood structural components.

40Ar/39Ar systematics and argon diffusion in amber: implications for ancient earth atmospheres

USGS Publications Warehouse

Landis, G.P.; Snee, L.W.

1991-01-01

Argon isotope data indicate retained argon in bulk amber (matrix gas) is radiogenic [40Ar/39Ar ???32o] than the much more abundant surface absorbed argon [40Ar/39Ar ???295.5]. Neutron-induced 39Ar is retained in amber during heating experiments to 150?? -250??C, with no evidence of recoiled 39Ar found after irradiation. A maximum permissible volume diffusion coefficient of argon in amber (at ambient temperature) D???1.5 x 10-17 cm2S-1 is calculated from 39Ar retention. 40Ar/39Ar age calculations indicate Dominican Republic amber is ??? 45 Ma and North Dakota amber is ??? 89 Ma, both at least reasonable ages for the amber based upon stratigraphic and paleontological constraints and upon the small amount of radiogenic 40Ar. To date, over 300 gas analyses of ambers and resins of Cretaceous to Recent age that are geographically distributed among fifteen noted world locations identify mixtures of gases in different sites within amber (Berner and Landis, 1988). The presence of multiple mixing trends between compositionally distinct end-members gases within the same sample and evidence for retained radiogenic argon within the amber argue persuasivley against rapid exchange by diffusion of amber-contained gases with moder air. Only gas in primary bubbles entrapped between successive flows of tree resin has been interpreted as original "ancient air", which is an O2-rich end-member gas with air-like N2/Ar ratios. Gas analyses of these primary bubbles indicate atmospheric O2 levels in the Late Cretaceous of ??? 35%, and that atmospheric O2 dropped by early Tertiary time to near a present atmospheric level of 21% O2. A very low argon diffusion coefficient in amber persuasively argues for a gas in primary bubbles trapped in amber being ancient air (possibly modified only by O2 reaction with amber). ?? 1991.

The development of episodic memory: items, contexts, and relations.

PubMed

Yim, Hyungwook; Dennis, Simon J; Sloutsky, Vladimir M

2013-11-01

Episodic memory involves the formation of relational structures that bind information about the stimuli people experience to the contexts in which they experience them. The ability to form and retain such structures may be at the core of the development of episodic memory. In the first experiment reported here, 4- and 7-year-olds were presented with paired-associate learning tasks requiring memory structures of different complexity. A multinomial-processing tree model was applied to estimate the use of different structures in the two age groups. The use of two-way list-context-to-target structures and three-way structures was found to increase between the ages of 4 and 7. Experiment 2 demonstrated that the ability to form increasingly complex relational memory structures develops between the ages of 4 and 7 years and that this development extends well into adulthood. These results have important implications for theories of memory development.

An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens

PubMed Central

Rensing, Stefan A; Ick, Julia; Fawcett, Jeffrey A; Lang, Daniel; Zimmer, Andreas; Van de Peer, Yves; Reski, Ralf

2007-01-01

Background: Analyses of complete genomes and large collections of gene transcripts have shown that most, if not all seed plants have undergone one or more genome duplications in their evolutionary past. Results: In this study, based on a large collection of EST sequences, we provide evidence that the haploid moss Physcomitrella patens is a paleopolyploid as well. Based on the construction of linearized phylogenetic trees we infer the genome duplication to have occurred between 30 and 60 million years ago. Gene Ontology and pathway association of the duplicated genes in P. patens reveal different biases of gene retention compared with seed plants. Conclusion: Metabolic genes seem to have been retained in excess following the genome duplication in P. patens. This might, at least partly, explain the versatility of metabolism, as described for P. patens and other mosses, in comparison to other land plants. PMID:17683536

Carbon and Nitrogen dynamics in deciduous and broad leaf trees under drought stress

NASA Astrophysics Data System (ADS)

Joseph, Jobin; Schaub, Marcus; Arend, Matthias; Saurer, Matthias; siegwolf, Rolf; Weiler, Markus; Gessler, Arthur

2017-04-01

Climate change is projected to lead to an increased frequency and duration of severe drought events in future. Already within the last twenty years, however, drought stress related forest mortality has been increasing across the globe. Tree and forest die off events have multiple adverse effects on ecosystem functioning and might convert previous carbon sinks to act as carbon sources instead and can thus intensify the effect of climate change and global warming. Current predictions of forest's functioning under drought and thus forest mortality under future climatic conditions are constrained by a still incomplete picture of the trees' physiological reactions that allows some trees to survive drought periods while others succumb. Concerning the effects of drought on the carbon balance and on tree hydraulics our picture is getting more complete, but still interactions between abiotic factors and pest and diseases as well as the interaction between carbon and nutrient balances as factors affecting drought induced mortality are not well understood. Reduced carbon allocation from shoots to roots might cause a lack of energy for root nutrient uptake and to a shortage of carbon skeletons for nitrogen assimilation and thus to an impaired nutrient status of trees. To tackle these points, we have performed a drought stress experiment with six different plant species, 3 broad leaf (maple, beech and oak) and 3 deciduous (pine, fir and spruce). Potted two-year-old seedlings were kept inside a greenhouse for 5 months and 3 levels of drought stress (no stress (control), intermediate and intensive drought stress) were applied by controlling water supply. Gas exchange measurements were performed periodically to monitor photosynthesis, transpiration, stomatal conductance. At the pinnacle of drought stress, we applied isotopic pulse labelling: On the one hand we exposed trees to 13CO2 to investigate on carbon dynamics and the allocation of new assimilates within the plant. Moreover, we labelled the soil with 15N nitrate by injecting nitrate solution into the soil without strongly changing the water content for investigating nitrogen uptake and distribution along different compartments of the plant soil continuum. We observed a distinct difference in the carbon and nitrogen dynamics and allocation pattern between broad leaf and conifer seedlings. Broad leaf species showed a lower reduction of CO2 assimilation under drought and still allocated significant amounts of the new assimilates to the roots. Especially in maple and oak the belowground transfer of assimilates was kept at high levels even under severe drought stress, while there was a reduction in assimilation transport in beech. Instead, only small amounts of 13C labelled new assimilates arrived in the roots of conifers in the drought treatments. In the deciduous species 15N taken up the roots was more intensively allocated to aboveground tissues compared to conifers under control conditions, which retained the largest amounts within the fine roots. 15N uptake was reduced in the drought treatments in all species assessed. There was, however, no clear relation of this reduction to changes in 13C allocation to the roots. We thus cannot conclude that the reduction of nitrogen uptake is due to reduced transport of new assimilates belowground. We thus need to assume that carbon storage is sufficient to provide energy and carbon for nitrogen uptake and assimilation at least over the short-term. During longer drought periods, however, depletion of carbon stores might adversely affect the nutrient uptake and balance of trees.

Biochar as a biosecurity tool for the management of invasive and/or infected plants.

NASA Astrophysics Data System (ADS)

Harries, Philip J. E.; Fielding, J. James; Alayne Street-Perrott, F.; Doerr, Stefan H.; Brackenbury, Sion

2014-05-01

Control of invasive alien/native plants and diseased trees is often achieved using labour-intensive mechanical methods, incurring high costs and significant carbon debt. Disposal of cleared biomass may be heavily regulated. The commonly used method, burning, wastes a potentially valuable resource. Biochar may offer a safe, cost-effective solution to the problem of disposal. Large areas of Wales are covered by bracken (Pteridium aquilinum) (37x103 ha) or invasive Rhododendron ponticum (area not yet quantified). Clearance of these plants is often necessary for agriculture or maintenance of biodiversity (bracken), or to curb the rapid dispersal of the fungus-like pathogen Phytophthora ramorum from rhododendron (the principal host) into commercial timber stands, notably Japanese larch (Larix kaempferi). In addition, ash dieback (the fungal disease Hymenoscyphus pseudoalbidus aka Chalara fraxinea) is now spreading aggressively in common ash trees (Fraxinus excelsior) in the UK. Pilot-scale experiments are being conducted using a BiGchar 1000 mobile, fast pyrolysis -gasification unit, focussing on chipped rhododendron, Japanese larch and common ash feedstocks. Preliminary results of these experiments will be presented. The biochars produced are being subjected to a range of physical and chemical analyses. Levels of micro- and macro-nutrients retained from the original feedstocks are being evaluated. Organic and inorganic contaminants are also being compared with those in the respective feedstocks. Biochar produced from R. ponticum comprised C 63.7-85.9%, H 0.4-0.8%, N 0.4-0.8%, S 0.27-1.79% and O 4.1-27.4%, with most of the mineral nutrients being retained from the original feedstock, especially Mn. Larch biochar comprised C 84.1-91.7%, H 1.8-3.1%, N 0.3-0.8%, S 0.42-0.69% and O 4.1-10.7%. Heavy-metal concentrations were below recommended limits (International Biochar Initiative, 2012), although R. ponticum growing on highly acidified soils showed some tendency to bio-accumulate Fe, Al and Cu. Life-Cycle Analyses of the pyrolysis unit and production process will be used to estimate the amount of carbon offset achievable during the operational lifetime of the unit. In addition, both gaseous and particulate emissions are being monitored in order to determine the environmental impact of the production process and ensure compliance with emissions regulations.

Effects of band selection on endmember extraction for forestry applications

NASA Astrophysics Data System (ADS)

Karathanassi, Vassilia; Andreou, Charoula; Andronis, Vassilis; Kolokoussis, Polychronis

2014-10-01

In spectral unmixing theory, data reduction techniques play an important role as hyperspectral imagery contains an immense amount of data, posing many challenging problems such as data storage, computational efficiency, and the so called "curse of dimensionality". Feature extraction and feature selection are the two main approaches for dimensionality reduction. Feature extraction techniques are used for reducing the dimensionality of the hyperspectral data by applying transforms on hyperspectral data. Feature selection techniques retain the physical meaning of the data by selecting a set of bands from the input hyperspectral dataset, which mainly contain the information needed for spectral unmixing. Although feature selection techniques are well-known for their dimensionality reduction potentials they are rarely used in the unmixing process. The majority of the existing state-of-the-art dimensionality reduction methods set criteria to the spectral information, which is derived by the whole wavelength, in order to define the optimum spectral subspace. These criteria are not associated with any particular application but with the data statistics, such as correlation and entropy values. However, each application is associated with specific land c over materials, whose spectral characteristics present variations in specific wavelengths. In forestry for example, many applications focus on tree leaves, in which specific pigments such as chlorophyll, xanthophyll, etc. determine the wavelengths where tree species, diseases, etc., can be detected. For such applications, when the unmixing process is applied, the tree species, diseases, etc., are considered as the endmembers of interest. This paper focuses on investigating the effects of band selection on the endmember extraction by exploiting the information of the vegetation absorbance spectral zones. More precisely, it is explored whether endmember extraction can be optimized when specific sets of initial bands related to leaf spectral characteristics are selected. Experiments comprise application of well-known signal subspace estimation and endmember extraction methods on a hyperspectral imagery that presents a forest area. Evaluation of the extracted endmembers showed that more forest species can be extracted as endmembers using selected bands.

δ13C values of soil organic matter in semiarid grassland with mesquite (Prosopis) encroachment in southeastern Arizona

USGS Publications Warehouse

Biggs, Thomas H.; Quade, Jay; Webb, Robert H.

2002-01-01

Over the past century, C3 woody plants and trees have increased in abundance in many semiarid ecosystems, displacing native C4 grasses. Livestock grazing, climatic fluctuations, and fire suppression are several reasons proposed for this shift. Soil carbon isotopic signatures are an ideal technique to evaluate carbon turnover rates in such ecosystems. On the gunnery ranges of Fort Huachuca in southeastern Arizona, study sites were established on homogeneous granitic alluvium to investigate the effects of fire frequency on δ13C values in surface soil organic matter (SOM). These ranges have had no livestock grazing for 50 years and a well-documented history of fires. Prosopis velutina Woot. (mesquite) trees have altered SOM δ13C pools by the concentration of plant nutrients and the addition of isotopically light litter. These soil carbon changes do not extend beyond canopy margins. Elevated total organic carbon (TOC), plant nutrient (N and P) concentrations, and depleted SOM δ13C values are associated with C3Prosopis on an unburned plot, which enables recognition of former Prosopis-occupied sites on plots with recent fire histories. Elevated nutrient concentrations associated with former Prosopis are retained in SOM for many decades. Surface SOM δ13C values indicate the estimated minimum turnover time of C4-derived carbon beneath large mature Prosopis is about 100–300 years. In contrast, complete turnover of original C3 carbon to C4 carbon under grasslands is estimated to take a minimum of 150–500 years. Our study confirms that C4 grass cover has declined over the past 100 years, although isolated C3 trees or shrubs were not uncommon on the historic C4-dominated grasslands. We find evidence in surface soil layers for a modern C3 plant expansion reflected in the substantial shift of SOM δ13C values from C4 grasses to C3 shrublands.

Forest structure and light regimes following moderate wind storms: implications for multi-cohort management.

PubMed

Hanson, Jacob J; Lorimer, Craig G

2007-07-01

Moderate-severity disturbances appear to be common throughout much of North America, but they have received relatively little detailed study compared to catastrophic disturbances and small gap dynamics. In this study, we examined the immediate impact of moderate-intensity wind storms on stand structure, opening sizes, and light regimes in three hemlock-hardwood forests of northeastern Wisconsin. These were compared to three stands managed by single-tree and group selection, the predominant forest management system for northern hardwoods in the region. Wind storms removed an average of 41% of the stand basal area, compared to 27% removed by uneven-aged harvests, but both disturbances removed trees from a wide range of size classes. The removal of nearly half of the large trees by wind in two old-growth stands caused partial retrogression to mature forest structure, which has been hypothesized to be a major disturbance pathway in the region. Wind storms resulted in residual stand conditions that were much more heterogeneous than in managed stands. Gap sizes ranged from less than 10 m2 up to 5000 m2 in wind-disturbed stands, whereas the largest opening observed in managed stands was only 200 m2. Wind-disturbed stands had, on average, double the available solar radiation at the forest floor compared to managed stands. Solar radiation levels were also more heterogeneous in wind-disturbed stands, with six times more variability at small scales (0.1225 ha) and 15 times more variability at the whole-stand level. Modification of uneven-aged management regimes to include occasional harvests of variable intensity and spatial pattern may help avoid the decline in species diversity that tends to occur after many decades of conventional uneven-aged management. At the same time, a multi-cohort system with these properties would retain a high degree of average crown cover, promote structural heterogeneity typical of old-growth forests, and maintain dominance by late-successional species.

Assessing herbivore foraging behavior with GPS collars in a semiarid grassland.

PubMed

Augustine, David J; Derner, Justin D

2013-03-15

Advances in global positioning system (GPS) technology have dramatically enhanced the ability to track and study distributions of free-ranging livestock. Understanding factors controlling the distribution of free-ranging livestock requires the ability to assess when and where they are foraging. For four years (2008-2011), we periodically collected GPS and activity sensor data together with direct observations of collared cattle grazing semiarid rangeland in eastern Colorado. From these data, we developed classification tree models that allowed us to discriminate between grazing and non-grazing activities. We evaluated: (1) which activity sensor measurements from the GPS collars were most valuable in predicting cattle foraging behavior, (2) the accuracy of binary (grazing, non-grazing) activity models vs. models with multiple activity categories (grazing, resting, traveling, mixed), and (3) the accuracy of models that are robust across years vs. models specific to a given year. A binary classification tree correctly removed 86.5% of the non-grazing locations, while correctly retaining 87.8% of the locations where the animal was grazing, for an overall misclassification rate of 12.9%. A classification tree that separated activity into four different categories yielded a greater misclassification rate of 16.0%. Distance travelled in a 5 minute interval and the proportion of the interval with the sensor indicating a head down position were the two most important variables predicting grazing activity. Fitting annual models of cattle foraging activity did not improve model accuracy compared to a single model based on all four years combined. This suggests that increased sample size was more valuable than accounting for interannual variation in foraging behavior associated with variation in forage production. Our models differ from previous assessments in semiarid rangeland of Israel and mesic pastures in the United States in terms of the value of different activity sensor measurements for identifying grazing activity, suggesting that the use of GPS collars to classify cattle grazing behavior will require calibrations specific to the environment and vegetation being studied.

Status of whitebarkpine in the Greater Yellowstone Ecosystem: A step-trend analysis comparing 2004-2007 to 2008-2011

USGS Publications Warehouse

Shanahan, Erin; Irvine, Kathryn M.; Roberts, Dave; Litt, Andrea R.; Legg, Kristin; Daley, Rob; Chambers, Nina

2014-01-01

Whitebark pine (Pinus albicaulis) is a foundation and keystone species in upper subalpine environments of the northern Rocky Mountains that strongly influences the biodiversity and productivity of high-elevation ecosystems (Tomback et al. 2001, Ellison et al. 2005). Throughout its historic range, whitebark pine has decreased significantly as a major component of high-elevation forests. As a result, it is critical to understand the challenges to whitebark pine—not only at the tree and stand level, but also as these factors influence the distribution of whitebark pine across the Greater Yellowstone Ecosystem (GYE). In 2003, the National Park Service (NPS) Greater Yellowstone Inventory & Monitoring Network identified whitebark pine as one of twelve significant natural resource indicators or vital signs to monitor (Jean et al. 2005, Fancy et al. 2009) and initiated a long-term, collaborative monitoring program. Partners in this effort include the U.S. Geological Survey, U.S. Forest Service, and Montana State University with representatives from each comprising the Greater Yellowstone Whitebark Pine Monitoring Working Group. The objectives of the monitoring program are to assess trends in (1) the proportion of live, whitebark pine trees (>1.4-m tall) infected with white pine blister rust (blister rust); (2) to document blister rust infection severity by the occurrence and location of persisting and new infections; (3) to determine mortality of whitebark pine trees and describe potential factors contributing to the death of trees; and (4) to assess the multiple components of the recruitment of understory whitebark pine into the reproductive population. In this report we summarize the past eight years (2004-2011) of whitebark pine status and trend monitoring in the GYE. Our study area encompasses six national forests (NF), two national parks (NP), as well as state and private lands in portions of Wyoming, Montana, and Idaho; this area is collectively described as the GYE here and in other studies. The sampling design is a probabilistic, twostage cluster design with stands of whitebark pine as the primary units and 10x50 m belt transects as the secondary units. Primary sampling units (stands) were selected randomly from a sample frame of approximately 10,770 mapped pure and mixed whitebark pine stands ≥2.0 hectares in the GYE (Dixon 1997, Landenburger 2012). From 2004 through 2007 (monitoring transect establishment or initial time-step), we established 176 permanent belt transects (secondary sampling units=176) in 150 whitebark pine stands and permanently marked approximately 4,740 individual trees >1.4 m tall to monitor long-term changes in blister rust infection and survival rates. Between 2008 and 2011 (revisit time-step), these same 176 transects were surveyed and again all previously tagged trees were observed for changes in blister rust infection and survival status. Objective 1. Using a combined ratio estimator, we estimated the proportion of live trees infected in the GYE in the initial time-step (2004-2007) to be 0.22 (0.031 SE). Following the completion of all surveys in the revisit time-step (2008-2011), we estimated the proportion of live trees infected with white pine blister rust as 0.23 (0.028 SE; Table 2). We detected no significant change in the proportion of trees infected in the GYE between the two time-steps. Objective 2. We documented blister rust canker locations as occurring in the canopy or bole. We compared changes in canker position between the initial time-step (2004-2007) and the revisit time-step (2008-2011) in order to assess changes in infection severity. This analysis included the 3,795 trees tagged during the initial time-step that were located and documented as alive at the end of the revisit time-step. At the end of the revisit time-step, we found 1,217 trees infected with blister rust. This includes the 287 newly tagged trees in the revisit time step of which 14 had documented infections. Of these 1,217 trees, 780 trees were infected with blister rust in both time steps. Trees with only canopy cankers made up approximately 43% (519 trees) of the total number of trees infected with blister rust at the end of the revisit time-step, while trees with only bole cankers comprised 20% (252 trees), and those with both canopy and bole cankers included 37% (446 trees) of the infected sample. A bole infection is considered to be more consequential than a canopy canker, as it compromises not only the overall longevity of the tree, but its functional capacity for reproductive output as well (Kendall and Arno 1990, Campbell and Antos 2000, McDonald and Hoff 2001, Schwandt and Kegley 2004). In addition to infection location, we also documented infection transition between the canopy and bole. Of the 780 live trees that were infected with blister rust in both time-steps, approximately 31% (242) maintained canopy cankers and 36% (281) retained bole infections at the end of the revisit time-step. Infection transition from canopy to bole occurred in 30% (234) of the revisit time-step trees while 3% (23) transitioned from bole to canopy infections during this period. Objective 3. To determine whitebark pine mortality, we resurveyed all belt transects to reassess the life status of permanently tagged trees >1.4 m tall. We compared the total number of live tagged trees recorded during monitoring transect establishment to the total number of resurveyed dead tagged trees recorded during the revisit time-step and identified all potential mortality-influencing conditions (blister rust, mountain pine beetle, fire and other). By the end of the revisit time-step, we observed a total of 975 dead tagged whitebark pine trees; using a ratio estimator, this represents a loss of approximately 20% (SE=4.35%) of the original live tagged tree population (GYWPMWG 2012). Objective 4. To investigate the proportion of live, reproducing tagged trees, we divided the total number of positively identified cone-bearing trees by the total number of live trees in the tagged tree sample at the end of the revisit time-step. To approximate the average density of recruitment trees per stand, trees ≤1.4 m tall were summed by stand (within the 500 m² transect area) and divided by the total number of stands. Reproducing trees made up approximately 24% (996 trees) of the total live tagged population at the end of the revisit time-step. Differentiating between whitebark pine and limber pine seedlings or saplings is problematic given the absence of cones or cone scars. Therefore, understory summaries as presented in this report may include individuals of both species when they are sympatric in a stand. The average density of small trees ≤1.4 m tall was 53 understory trees per 500 m². Raw counts of these understory individuals ranged from 0-635 small trees per belt transect. In addition, a total of 287 trees were added to the tagged tree population by the end of 2011. These newly tagged trees were individuals that upon subsequent revisits had reached a height of >1.4 m tall and subsequently added to the sample. Throughout the past decade in the GYE, monitoring has helped document shifts in whitebark pine forests; whitebark pine stands have been impacted by insect, pathogen, wildland fire, and other disturbance events. Blister rust infection is ubiquitous throughout the ecosystem and infection proportions are variable across the region. And while we have documented mortality of whitebark pine, we have also recorded considerable recruitment. We provide this first step-trend report as a quantifiable baseline for understanding the state of whitebark pine in the GYE. Many aspects of whitebark pine health are highly variable across the range of its distribution in the GYE. Through sustained implementation of the monitoring program, we will continue efforts to document and quantify whitebark pine forest dynamics as they arise under periodic upsurges in insect, pathogen, fire episodes, and climatic events in the GYE. Since its inception, this monitoring program perseveres as one of the only sustained longterm efforts conducted in the GYE with a singular purpose to track the health and status of this prominent keystone species.

Heard but not seen: Comparing bat assemblages and study methods in a mosaic landscape in the Western Ghats of India.

PubMed

Wordley, Claire F R; Sankaran, Mahesh; Mudappa, Divya; Altringham, John D

2018-04-01

We used capture (mist-netting) and acoustic methods to compare the species richness, abundance, and composition of a bat assemblage in different habitats in the Western Ghats of India. In the tropics, catching bats has been more commonly used as a survey method than acoustic recordings. In our study, acoustic methods based on recording echolocation calls detected greater bat activity and more species than mist-netting. However, some species were detected more frequently or exclusively by capture. Ideally, the two methods should be used together to compensate for the biases in each. Using combined capture and acoustic data, we found that protected forests, forest fragments, and shade coffee plantations hosted similar and diverse species assemblages, although some species were recorded more frequently in protected forests. Tea plantations contained very few species from the overall bat assemblage. In riparian habitats, a strip of forested habitat on the river bank improved the habitat for bats compared to rivers with tea planted up to each bank. Our results show that shade coffee plantations are better bat habitat than tea plantations in biodiversity hotspots. However, if tea is to be the dominant land use, forest fragments and riparian corridors can improve the landscape considerably for bats. We encourage coffee growers to retain traditional plantations with mature native trees, rather than reverting to sun grown coffee or coffee shaded by a few species of timber trees.

Sampling algorithms for validation of supervised learning models for Ising-like systems

NASA Astrophysics Data System (ADS)

Portman, Nataliya; Tamblyn, Isaac

2017-12-01

In this paper, we build and explore supervised learning models of ferromagnetic system behavior, using Monte-Carlo sampling of the spin configuration space generated by the 2D Ising model. Given the enormous size of the space of all possible Ising model realizations, the question arises as to how to choose a reasonable number of samples that will form physically meaningful and non-intersecting training and testing datasets. Here, we propose a sampling technique called ;ID-MH; that uses the Metropolis-Hastings algorithm creating Markov process across energy levels within the predefined configuration subspace. We show that application of this method retains phase transitions in both training and testing datasets and serves the purpose of validation of a machine learning algorithm. For larger lattice dimensions, ID-MH is not feasible as it requires knowledge of the complete configuration space. As such, we develop a new ;block-ID; sampling strategy: it decomposes the given structure into square blocks with lattice dimension N ≤ 5 and uses ID-MH sampling of candidate blocks. Further comparison of the performance of commonly used machine learning methods such as random forests, decision trees, k nearest neighbors and artificial neural networks shows that the PCA-based Decision Tree regressor is the most accurate predictor of magnetizations of the Ising model. For energies, however, the accuracy of prediction is not satisfactory, highlighting the need to consider more algorithmically complex methods (e.g., deep learning).

Specificity of extrafloral nectar induction by herbivores differs among native and invasive populations of tallow tree.

PubMed

Wang, Yi; Carrillo, Juli; Siemann, Evan; Wheeler, Gregory S; Zhu, Lin; Gu, Xue; Ding, Jianqing

2013-08-01

Invasive plants can be released from specialist herbivores and encounter novel generalists in their introduced ranges, leading to variation in defence among native and invasive populations. However, few studies have examined how constitutive and induced indirect defences change during plant invasion, especially during the juvenile stage. Constitutive extrafloral nectar (EFN) production of native and invasive populations of juvenile tallow tree (Triadica sebifera) were compared, and leaf clipping, and damage by a native specialist (Noctuid) and two native generalist caterpillars (Noctuid and Limacodid) were used to examine inducible EFN production. Plants from introduced populations had more leaves producing constitutive EFN than did native populations, but the content of soluble solids of EFN did not differ. Herbivores induced EFN production more than simulated herbivory. The specialist (Noctuid) induced more EFN than either generalist for native populations. The content of soluble solids in EFN was higher (2·1 times), with the specialist vs. the generalists causing the stronger response for native populations, but the specialist response was always comparable with the generalist responses for invasive populations. These results suggest that constitutive and induced indirect defences are retained in juvenile plants of invasive populations even during plant establishment, perhaps due to generalist herbivory in the introduced range. However, responses specific to a specialist herbivore may be reduced in the introduced range where specialists are absent. This decreased defence may benefit specialist insects that are introduced for classical biological control of invasive plants.

The value of crossdating to retain high-frequency variability, climate signals, and extreme events in environmental proxies.

PubMed

Black, Bryan A; Griffin, Daniel; van der Sleen, Peter; Wanamaker, Alan D; Speer, James H; Frank, David C; Stahle, David W; Pederson, Neil; Copenheaver, Carolyn A; Trouet, Valerie; Griffin, Shelly; Gillanders, Bronwyn M

2016-07-01

High-resolution biogenic and geologic proxies in which one increment or layer is formed per year are crucial to describing natural ranges of environmental variability in Earth's physical and biological systems. However, dating controls are necessary to ensure temporal precision and accuracy; simple counts cannot ensure that all layers are placed correctly in time. Originally developed for tree-ring data, crossdating is the only such procedure that ensures all increments have been assigned the correct calendar year of formation. Here, we use growth-increment data from two tree species, two marine bivalve species, and a marine fish species to illustrate sensitivity of environmental signals to modest dating error rates. When falsely added or missed increments are induced at one and five percent rates, errors propagate back through time and eliminate high-frequency variability, climate signals, and evidence of extreme events while incorrectly dating and distorting major disturbances or other low-frequency processes. Our consecutive Monte Carlo experiments show that inaccuracies begin to accumulate in as little as two decades and can remove all but decadal-scale processes after as little as two centuries. Real-world scenarios may have even greater consequence in the absence of crossdating. Given this sensitivity to signal loss, the fundamental tenets of crossdating must be applied to fully resolve environmental signals, a point we underscore as the frontiers of growth-increment analysis continue to expand into tropical, freshwater, and marine environments. © 2016 John Wiley & Sons Ltd.

Sediment retention in a bottomland hardwood wetland in Eastern Arkansas

USGS Publications Warehouse

Kleiss, B.A.

1996-01-01

One of the often-stated functions of wetlands is their ability to remove sediments and other particulates from water, thus improving water quality in the adjacent aquatic system. However, actual rates of suspended sediment removal have rarely been measured in freshwater wetland systems. To address this issue, suspended sediment dynamics were measured in a 85-km2 bottomland hardwood (BLH) wetland adjacent to the highly turbid Cache River in eastern Arkansas during the 1988-1990 water years. A suspended sediment mass balance was calculated using depth-integrated, flow-weighted daily measurements at wetland inflow and outflow points. Over the three-year period, suspended sediment load decreased an average of 14% between upstream and downstream sampling points. To test the idea that the suspended sediments were retained by the adjacent wetland and to determine what portion of the BLH forest was most responsible for retaining the suspended sediments, concurrent measurements of sediment accretion were made at 30 sites in the wetland using feldspar clay marker horizons, sedimentation disks, the 137cesium method, and dendrogeomorphic techniques. Sedimentation rates exceeding 1 cm/yr were measured in frequently flooded areas dominated by Nyssa aquatica and Taxodium distichum. Maximum sedimentation rates did not occur on the natural levee, as would be predicted by classical fluvial geomorphology, but in the "first bottom," where retention time of the water reached a maximum. Multiple regression was used to relate sedimentation rates with several physical and biological factors. A combination of distance from the river, flood duration, and tree basal area accounted for nearly 90% of the variation in sedimentation rates.

Wooden Foreign Body in the Skull Base: How Did We Miss It?

PubMed

Jusué-Torres, Ignacio; Burks, S Shelby; Levine, Corinna G; Bhatia, Rita G; Casiano, Roy; Bullock, Ross

2016-08-01

Timely detection of intraorbital and skull base wooden foreign bodies is crucial. Wooden foreign bodies are difficult to detect on imaging. The radiologist may fail to identify wooden foreign bodies on two thirds of initial scans and can miss them in almost one third of total cases. A 66-year-old woman sustained a penetrating injury through the left upper eyelid with a small tree branch. The branch was immediately removed in the field, and she was provided with prompt medical care at a local hospital. Initial computed tomography (CT) scan diagnosis was "posttraumatic sinusitis," and this was treated empirically with vancomycin and piperacillin/tazobactam. On the eighth day after injury, she developed progressive swelling and pain of her eyelid with left trigeminal/supraorbital numbness and complete left ophthalmoplegia. A new CT scan showed an open "track" from the region of the left upper orbit/superior rectus to the contralateral sphenoid sinus, which raised suspicion for a retained foreign body. Further imaging confirmed the suspicion. Endoscopic sinus surgery was performed with extraction of the wooden object and evacuation of the left orbital infection. This case indicates that intraorbital and skull base wooden foreign bodies are elusive, demanding a high index of suspicion from both clinicians and radiologists to identify retained material in the setting of ocular or sinus trauma. For better identification of wooden foreign bodies, bone windows on CT should have a width of -1000 Hounsfield units with a soft tissue window level of -500 Hounsfield units. Published by Elsevier Inc.

Tracing photosynthetic carbon in leaves with nanoSIMS after 13CO2 labelling

NASA Astrophysics Data System (ADS)

Dannoura, Masako; Takeuchi, Miyuki; Kominami, Yuji; Takanashi, Satoru; Kenichi, Yoshimura; Ataka, Mioko

2015-04-01

To understand the carbon allocation of the tree and forest ecosystem, it is important to consider the residence time of carbon in different pools at suitable time scales. For example the carbon used for respiration will stay a few minutes to a few days in the tree, the carbon used for storage or structure of leaves will stay months to years, and the carbon used for wood structure, it will stay over the whole lifespan of the tree. The leaves are the entrance of carbon in trees where it can be used for foliage growth and maintenance or exported to the other organs or the other forest ecosystem compartments. Tracing carbon isotope using NanoSIMS technique is one of useful methods to estimate where and how long the carbon stay in the tree organs. In this study, 13CO2 pulse labelling were conducted and 13C was measured by IRMS to see the amount of C remaining in the leaves with time.NanoSIMS was used to localize where the labelled C remained within the leaf tissue. Twice labelling were done on branches of Quercus serrata at FFPRI(Forest and Forest Products research Institute) in Kyoto, Japan. The first labelling was in 30 April 2012 when the leaves start flushing and the second one was in 29 May 2012 when the leaves were completely deployed. For both labelling experiment, one branch was selected and covered with transparent plastic bag. CO2 concentration was recorded with IRGA and air temperature inside the chamber was monitored. Then 13CO2 was injected into the bag, and after 1 hour, the bag was removed and the branch was again exposed to ambient air. Leaves were collected before and 10-12 times after labelling and their isotope compositions were measured by IRMS. The leaf collected just after labelling and 6 days after labelling were used for NanoSIMS observation. Samples for nanoSIMS were preserved in glutaraldehyde and then embed in epoxy resin. The sliced sample were placed on the silicon wafer and observed by NanoSIMS 50L(Cameca, France). The 13C was highest just after labelling and decreased with the time. Half life time of delta 13C was longer in April-labelling than May-labelling that indicates that more carbon was retained in structural growth and less exported non-assimilatory organs in April than in May. The NanoSIMS observation showed 13C in starch grains was shown only in May in leaves sampled 6 days after -labelling. This suggests that the usage of carbon differ depending on the stage of leaf formation.

Floating nut retention system

NASA Technical Reports Server (NTRS)

Charles, J. F.; Theakston, H. A. (Inventor)

1980-01-01

A floating nut retention system includes a nut with a central aperture. An inner retainer plate has an opening which is fixedly aligned with the nut aperture. An outer retainer member is formed of a base plate having an opening and a surface adjacent to a surface of the inner retainer plate. The outer retainer member includes a securing mechanism for retaining the inner retainer plate adjacent to the outer retainer member. The securing mechanism enables the inner retainer plate to float with respect to the outer retainer number, while simultaneously forming a bearing surface for inner retainer plate.

Fabrication of Multscale Fractal-Like Structures by Controlling Fluid Interface Instability

PubMed Central

Islam, Tanveer ul; Gandhi, Prasanna S.

2016-01-01

Nature, in quest for the best designs has shaped its vital systems into fractal geometries. Effectual way of spontaneous fabrication of scalable, ordered fractal-like structures by controlling Saffman-Taylor instability in a lifted Hele-Shaw cell is deployed here. In lifted Hele-Shaw cell uncontrolled penetration of low-viscosity fluid into its high-viscosity counterpart is known to develop irregular, non-repeatable, normally short-lived, branched patterns. We propose and characterize experimentally anisotropies in a form of spatially distributed pits on the cell plates to control initiation and further penetration of non-splitting fingers. The proposed control over shielding mechanism yields recipes for fabrication of families of ordered fractal-like patterns of multiple generations. As an example, we demonstrate and characterize fabrication of a Cayley tree fractal-like pattern. The patterns, in addition, are retained permanently by employing UV/thermally curable fluids. The proposed technique thus establishes solid foundation for bio-mimicking natural structures spanning multiple-scales for scientific and engineering use. PMID:27849003

Fabrication of Multscale Fractal-Like Structures by Controlling Fluid Interface Instability

NASA Astrophysics Data System (ADS)

Islam, Tanveer Ul; Gandhi, Prasanna S.

2016-11-01

Nature, in quest for the best designs has shaped its vital systems into fractal geometries. Effectual way of spontaneous fabrication of scalable, ordered fractal-like structures by controlling Saffman-Taylor instability in a lifted Hele-Shaw cell is deployed here. In lifted Hele-Shaw cell uncontrolled penetration of low-viscosity fluid into its high-viscosity counterpart is known to develop irregular, non-repeatable, normally short-lived, branched patterns. We propose and characterize experimentally anisotropies in a form of spatially distributed pits on the cell plates to control initiation and further penetration of non-splitting fingers. The proposed control over shielding mechanism yields recipes for fabrication of families of ordered fractal-like patterns of multiple generations. As an example, we demonstrate and characterize fabrication of a Cayley tree fractal-like pattern. The patterns, in addition, are retained permanently by employing UV/thermally curable fluids. The proposed technique thus establishes solid foundation for bio-mimicking natural structures spanning multiple-scales for scientific and engineering use.

Maintenance of Ecosystem Nitrogen Limitation by Ephemeral Forest Disturbance: An Assessment using MODIS, Hyperion, and Landsat ETM+

NASA Technical Reports Server (NTRS)

McNeil, Brenden E.; deBeurs, Kirsten M.; Eshleman, Keith N.; Foster, Jane R.; Townsend, Philip A.

2007-01-01

Ephemeral disturbances, such as non-lethal insect defoliations and crown damage from meteorological events, can significantly affect the delivery of ecosystem services by helping maintain nitrogen (N) limitation in temperate forest ecosystems. However, the impacts of these disturbances are difficult to observe across the broad-scales at which they affect ecosystem function. Using remotely sensed measures and field data, we find support for the hypothesis that ephemeral disturbances help maintain landscape-wide ecosystem N limitation. Specifically, a phenology-based defoliation index derived from daily MODIS satellite imagery predicts three ecosystem responses from oak-dominated forested watersheds: elevated stream water N export (R(exp 2) = 0.48), decreased foliar N (R(exp 2) = 0.69, assessed with Hyperion imagery), and reduced vegetation growth vigor (R(exp 2) = 0.49, assessed with Landsat ETM+ imagery). The results indicate that ephemeral disturbances and other forest stressors may sustain N limitation by reducing the ability of trees to compete for--and retain--soil available N.

Green trees for greenhouse gases: a fair trade-off?

PubMed

Schmidt, C W

2001-03-01

While forests retain carbon in plants, detritus, and soils, utility companies spew it into the air as carbon dioxide, the main greenhouse gas behind global warming. Industrial carbon dioxide emissions aren't currently regulated by federal law, but a number of companies are trying to address the problem voluntarily by launching carbon sequestration programs in heavily forested countries, where carbon is contained in so-called sinks. But the November 2000 meeting of the Kyoto Protocol delegates in The Hague collapsed over the issue of the acceptability of carbon sinks as a source of carbon pollution credits, delivering what many see as a deathblow to the concept. At issue are a host of ecological and statistical questions, differing local land use practices, cultural factors, issues of verifiability, and even disagreement over definitions of basic terms such as "forest" Kyoto negotiators are gearing up for another round of discussions in Bonn in May 2001, and it is likely that the continuing debate over carbon sinks will dominate the agenda.

Winners and losers in the competition for space in tropical forest canopies.

PubMed

Kellner, James R; Asner, Gregory P

2014-05-01

Trees compete for space in the canopy, but where and how individuals or their component parts win or lose is poorly understood. We developed a stochastic model of three-dimensional dynamics in canopies using a hierarchical Bayesian framework, and analysed 267,533 positive height changes from 1.25 m pixels using data from airborne LiDAR within 43 ha on the windward flank of Mauna Kea. Model selection indicates a strong resident's advantage, with 97.9% of positions in the canopy retained by their occupants over 2 years. The remaining 2.1% were lost to a neighbouring contender. Absolute height was a poor predictor of success, but short stature greatly raised the risk of being overtopped. Growth in the canopy was exponentially distributed with a scaling parameter of 0.518. These findings show how size and spatial proximity influence the outcome of competition for space, and provide a general framework for the analysis of canopy dynamics. © 2014 John Wiley & Sons Ltd/CNRS.

Fast and Robust STEM Reconstruction in Complex Environments Using Terrestrial Laser Scanning

NASA Astrophysics Data System (ADS)

Wang, D.; Hollaus, M.; Puttonen, E.; Pfeifer, N.

2016-06-01

Terrestrial Laser Scanning (TLS) is an effective tool in forest research and management. However, accurate estimation of tree parameters still remains challenging in complex forests. In this paper, we present a novel algorithm for stem modeling in complex environments. This method does not require accurate delineation of stem points from the original point cloud. The stem reconstruction features a self-adaptive cylinder growing scheme. This algorithm is tested for a landslide region in the federal state of Vorarlberg, Austria. The algorithm results are compared with field reference data, which show that our algorithm is able to accurately retrieve the diameter at breast height (DBH) with a root mean square error (RMSE) of ~1.9 cm. This algorithm is further facilitated by applying an advanced sampling technique. Different sampling rates are applied and tested. It is found that a sampling rate of 7.5% is already able to retain the stem fitting quality and simultaneously reduce the computation time significantly by ~88%.

Physical and chemical characterizations of biochars derived from different agricultural residues

NASA Astrophysics Data System (ADS)

Jindo, K.; Mizumoto, H.; Sawada, Y.; Sanchez-Monedero, M. A.; Sonoki, T.

2014-08-01

Biochar has received large attention as a strategy to tackle against carbon emission. Not only carbon fixation has been carried out but also other merits for agricultural application due to unique physical and chemical character such as absorption of contaminated compounds in soil, trapping ammonia and methane emission from compost, and enhancement of fertilizer quality. In our study, different local waste feed stocks (rice husk, rice straw, wood chips of apple tree (Malus Pumila) and oak tree (Quercus serrata)), in Aomori, Japan, were utilized for creating biochar with different temperature (400-800 °C). Concerning to the biochar production, the pyrolysis of lower temperature had more biochar yield than higher temperature pyrolysis process. On the contrary, surface areas and adsorption characters have been increased as increasing temperature. The proportions of carbon content in the biochars also increased together with increased temperatures. Infrared-Fourier spectra (FT-IR) and 13C-NMR were used to understand carbon chemical compositions in our biochars, and it was observed that the numbers of the shoulders representing aromatic groups, considered as stable carbon structure appeared as the temperature came closer to 600 °C, as well as in FT-IR. In rice materials, the peak assigned to SiO2, was observed in all biochars (400-800 °C) in FT-IR. We suppose that the pyrolysis at 600 °C creates the most recalcitrant character for carbon sequestration, meanwhile the pyrolysis at 400 °C produces the superior properties as a fertilizer by retaining volatile and easily labile compounds which promotes soil microbial activities.

Genetic and Ecological Outcomes of Inga vera Subsp. affinis (Leguminosae) Tree Plantations in a Fragmented Tropical Landscape

PubMed Central

Cruz Neto, Oswaldo; Aguiar, Antonio V.; Twyford, Alex D.; Neaves, Linda E.; Pennington, R. Toby; Lopes, Ariadna V.

2014-01-01

Planting of native trees for habitat restoration is a widespread practice, but the consequences for the retention and transmission of genetic diversity in planted and natural populations are unclear. Using Inga vera subsp. affinis as a model species, we genotyped five natural and five planted populations in the Atlantic forest of northeastern Brazil at polymorphic microsatellite loci. We studied the breeding system and population structure to test how much genetic diversity is retained in planted relative to natural populations. We then genotyped seedlings from these populations to test whether genetic diversity in planted populations is restored by outcrossing to natural populations of I. vera. The breeding system of natural I. vera populations was confirmed to be highly outcrossing (t = 0.92; FIS = −0.061, P = 0.04), with populations showing weak population substructure (FST = 0.028). Genetic diversity in planted populations was 50% less than that of natural populations (planted: AR = 14.9, HO = 0.865 and natural: AR = 30.8, HO = 0.655). However, seedlings from planted populations showed a 30% higher allelic richness relative to their parents (seedlings AR = 10.5, parents AR = 7.6). Understanding the processes and interactions that shape this system are necessary to provide ecologically sensible goals and successfully restore hyper-fragmented habitats. Future restoration plans for I. vera must consider the genetic diversity of planted populations and the potential for gene flow between natural populations in the landscape, in order to preserve ecological interactions (i.e. pollination), and promote opportunities for outcrossing. PMID:24932729

Genetic and ecological outcomes of Inga vera subsp. affinis (Leguminosae) tree plantations in a fragmented tropical landscape.

PubMed

Cruz Neto, Oswaldo; Aguiar, Antonio V; Twyford, Alex D; Neaves, Linda E; Pennington, R Toby; Lopes, Ariadna V

2014-01-01

Planting of native trees for habitat restoration is a widespread practice, but the consequences for the retention and transmission of genetic diversity in planted and natural populations are unclear. Using Inga vera subsp. affinis as a model species, we genotyped five natural and five planted populations in the Atlantic forest of northeastern Brazil at polymorphic microsatellite loci. We studied the breeding system and population structure to test how much genetic diversity is retained in planted relative to natural populations. We then genotyped seedlings from these populations to test whether genetic diversity in planted populations is restored by outcrossing to natural populations of I. vera. The breeding system of natural I. vera populations was confirmed to be highly outcrossing (t = 0.92; FIS = -0.061, P = 0.04), with populations showing weak population substructure (FST = 0.028). Genetic diversity in planted populations was 50% less than that of natural populations (planted: AR = 14.9, HO = 0.865 and natural: AR = 30.8, HO = 0.655). However, seedlings from planted populations showed a 30% higher allelic richness relative to their parents (seedlings AR = 10.5, parents AR = 7.6). Understanding the processes and interactions that shape this system are necessary to provide ecologically sensible goals and successfully restore hyper-fragmented habitats. Future restoration plans for I. vera must consider the genetic diversity of planted populations and the potential for gene flow between natural populations in the landscape, in order to preserve ecological interactions (i.e. pollination), and promote opportunities for outcrossing.

Foreign bodies in tracheobronchial tree in children: a review of cases over a twenty-year period.

PubMed

Yeh, L C; Li, H Y; Huang, T S

1998-03-01

Foreign body inhalation into the tracheobronchial tree of children is rather rare but serious problem. It may be hazardous and even cause fatal sequelae in the children if misdiagnosed and not managed promptly. We retrospectively reviewed the records of 81 patients with foreign bodies inhaled into the larynx, trachea and bronchi. The children were all treated during the 20-year period from July 1976 through June 1996 at Chang Gung Memorial Hospital. Of these patients, 82% were 36 months of age or younger. The male to female ratio was 3:1. All of the patients initially received flexible fiberoptic bronchoscopy to identify the foreign objects. The foreign bodies were removed by jet ventilation bronchoscopy with apneic techniques under general anesthesia. Peanuts were found to be the most common causative foreign body agent which occurred in 53 instances (65%). The most common manifestation was coughing, with subsequent dyspnea and audible wheezing. The foreign bodies were lodged in the left bronchus more than in the right. The most obvious radiologic evidence observed in aspirated children were emphysematous changes at same side of the foreign bodies caused by "expansile check-valve" phenomenon. Four patients showed radio-opaque objects on chest roentgenograms. Six patients required second extraction procedures due to the retained foreign bodies. Neither serious complications nor deaths occurred in these patients due to the foreign body inhalation. Early diagnosis and management is essential in children with foreign bodies in the airways to prevent morbidity or death. Small materials or food bits should be kept far away from young child.

Specificity of extrafloral nectar induction by herbivores differs among native and invasive populations of tallow tree

PubMed Central

Wang, Yi; Carrillo, Juli; Siemann, Evan; Wheeler, Gregory S.; Zhu, Lin; Gu, Xue; Ding, Jianqing

2013-01-01

Background and Aims Invasive plants can be released from specialist herbivores and encounter novel generalists in their introduced ranges, leading to variation in defence among native and invasive populations. However, few studies have examined how constitutive and induced indirect defences change during plant invasion, especially during the juvenile stage. Methods Constitutive extrafloral nectar (EFN) production of native and invasive populations of juvenile tallow tree (Triadica sebifera) were compared, and leaf clipping, and damage by a native specialist (Noctuid) and two native generalist caterpillars (Noctuid and Limacodid) were used to examine inducible EFN production. Key results Plants from introduced populations had more leaves producing constitutive EFN than did native populations, but the content of soluble solids of EFN did not differ. Herbivores induced EFN production more than simulated herbivory. The specialist (Noctuid) induced more EFN than either generalist for native populations. The content of soluble solids in EFN was higher (2·1 times), with the specialist vs. the generalists causing the stronger response for native populations, but the specialist response was always comparable with the generalist responses for invasive populations. Conclusions These results suggest that constitutive and induced indirect defences are retained in juvenile plants of invasive populations even during plant establishment, perhaps due to generalist herbivory in the introduced range. However, responses specific to a specialist herbivore may be reduced in the introduced range where specialists are absent. This decreased defence may benefit specialist insects that are introduced for classical biological control of invasive plants. PMID:23761685

Multi-Proxy Reconstructions of Northeast Pacific Decadal Variability from Bivalve Mollusks and Trees

NASA Astrophysics Data System (ADS)

Black, B.; Griffin, D.

2017-12-01

Decadal-scale climate variability in the Northeast Pacific Ocean profoundly influences fisheries production, forest growth, wildfire, drought, and snowpack in western North America. However, there remains considerable and long-standing uncertainly in its behavior prior to AD 1900 and the extent to which 20th century dynamics are atypical in a multi-centennial context. Here, we target the leading EOF of SST in the northeastern Pacific (ARCSST) as an index of Pacific Decadal Variability, which has been dynamically linked to sea level pressure and unlike the Pacific Decadal Oscillation Index, retains a linear warming trend. The ARCSST reconstruction is generated from a broad network of target-sensitive North American tree-ring data standardized using signal-free detrending to preserve lower frequency signals common to the original data. In a preliminary analysis, the mean of the approximately 50 chronologies that significantly (p < 0.01) correlate to the target variable explain 60% of the variance in cool-season ARCSST. Reconstruction skill is independently verified by three marine bivalve (Pacific geoduck; Panopea generosa) chronologies, the mean of which accounts for over 50% of the reconstruction variance over the common 1870-1900 interval. The nested reconstruction spans over 500 years and indicates that i) PDV is dominated by pentadecadal cycles, ii) century-long quiescent periods can occur, iii) 20th century regime shifts are typical, but iv) late 20th century warming is atypical in the longer-term context. Moreover, the reconstruction closely tracks paleofisheries datasets, particularly northern anchovy (Engraulis mordax) abundance inferred from scale deposition rates in the Santa Barbara Basin.

Fuel treatment impacts on estimated wildfire carbon loss from forests in Montana, Oregon, California, and Arizona

USGS Publications Warehouse

Stephens, Scott L.; Boerner, Ralph E.J.; Maghaddas, Jason J.; Maghaddas, Emily E.Y.; Collins, Brandon M.; Dow, Christopher B.; Edminster, Carl; Fiedler, Carl E.; Fry, Danny L.; Hartsough, Bruce R.; Keeley, Jon E.; Knapp, Eric E.; McIver, James D.; Skinner, Carl N.; Youngblood, Andrew P.

2012-01-01

Using forests to sequester carbon in response to anthropogenically induced climate change is being considered across the globe. A recent U.S. executive order mandated that all federal agencies account for sequestration and emissions of greenhouse gases, highlighting the importance of understanding how forest carbon stocks are influenced by wildfire. This paper reports the effects of the most common forest fuel reduction treatments on carbon pools composed of live and dead biomass as well as potential wildfire emissions from six different sites in four western U.S. states. Additionally, we predict the median forest product life spans and uses of materials removed during mechanical treatments. Carbon loss from modeled wildfire-induced tree mortality was lowest in the mechanical plus prescribed fire treatments, followed by the prescribed fire-only treatments. Wildfire emissions varied from 10–80 Mg/ha and were lowest in the prescribed fire and mechanical followed by prescribed fire treatments at most sites. Mean biomass removals per site ranged from approximately 30–60 dry Mg/ha; the median lives of products in first use varied considerably (from <10 to >50 years). Our research suggests most of the benefits of increased fire resistance can be achieved with relatively small reductions in current carbon stocks. Retaining or growing larger trees also reduced the vulnerability of carbon loss from wildfire. In addition, modeled vulnerabilities to carbon losses and median forest product life spans varied considerably across our study sites, which could be used to help prioritize treatment implementation.

Vegetation composition, nutrient, and sediment dynamics along a floodplain landscape

USGS Publications Warehouse

Rybicki, Nancy B.; Noe, Gregory; Hupp, Cliff R.; Robinson, Myles

2015-01-01

Forested floodplains are important landscape features for retaining river nutrients and sediment loads but there is uncertainty in how vegetation influences nutrient and sediment retention. In order to understand the role of vegetation in nutrient and sediment trapping, we quantified species composition and the uptake of nutrients in plant material relative to landscape position and ecosystem attributes in an urban, Piedmont watershed in Virginia, USA. We investigated in situ interactions among vegetative composition, abundance, carbon (C), nitrogen (N) and phosphorus (P) fluxes and ecosystem attributes such as water level, shading, soil nutrient mineralization, and sediment deposition. This study revealed strong associations between vegetation and nutrient and sediment cycling processes at the plot scale and in the longitudinal dimension, but there were few strong patterns between these aspects at the scale of geomorphic features (levee, backswamp, and toe-slope). Patterns reflected the nature of the valley setting rather than a simple downstream continuum. Plant nutrient uptake and sediment trapping were greatest at downstream sites with the widest floodplain and lowest gradient where the hydrologic connection between the floodplain and stream is greater. Sediment trapping increased in association with higher herbaceous plant coverage and lower tree canopy density that, in turn, was associated with a more water tolerant tree community found in the lower watershed but not at the most downstream site in the watershed. Despite urbanization effects on the hydrology, this floodplain functioned as an efficient nutrient trap. N and P flux rates of herbaceous biomass and total litterfall more than accounted for the N and P mineralization flux rate, indicating that vegetation incorporated nearly all mineralized nutrients into biomass.

7 CFR 1767.25 - Retained earnings.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 12 2010-01-01 2010-01-01 false Retained earnings. 1767.25 Section 1767.25....25 Retained earnings. The retained earnings accounts identified in this section shall be used by all RUS borrowers. Retained Earnings 433-439 [Reserved] Retained Earnings 433-439 [Reserved] ...

Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes

PubMed Central

Richardson, Dale N; Simmons, Mark P; Reddy, Anireddy SN

2006-01-01

Background Kinesins, a superfamily of molecular motors, use microtubules as tracks and transport diverse cellular cargoes. All kinesins contain a highly conserved ~350 amino acid motor domain. Previous analysis of the completed genome sequence of one flowering plant (Arabidopsis) has resulted in identification of 61 kinesins. The recent completion of genome sequencing of several photosynthetic and non-photosynthetic eukaryotes that belong to divergent lineages offers a unique opportunity to conduct a comprehensive comparative analysis of kinesins in plant and non-plant systems and infer their evolutionary relationships. Results We used the kinesin motor domain to identify kinesins in the completed genome sequences of 19 species, including 13 newly sequenced genomes. Among the newly analyzed genomes, six represent photosynthetic eukaryotes. A total of 529 kinesins was used to perform comprehensive analysis of kinesins and to construct gene trees using the Bayesian and parsimony approaches. The previously recognized 14 families of kinesins are resolved as distinct lineages in our inferred gene tree. At least three of the 14 kinesin families are not represented in flowering plants. Chlamydomonas, a green alga that is part of the lineage that includes land plants, has at least nine of the 14 known kinesin families. Seven of ten families present in flowering plants are represented in Chlamydomonas, indicating that these families were retained in both the flowering-plant and green algae lineages. Conclusion The increase in the number of kinesins in flowering plants is due to vast expansion of the Kinesin-14 and Kinesin-7 families. The Kinesin-14 family, which typically contains a C-terminal motor, has many plant kinesins that have the motor domain at the N terminus, in the middle, or the C terminus. Several domains in kinesins are present exclusively either in plant or animal lineages. Addition of novel domains to kinesins in lineage-specific groups contributed to the functional diversification of kinesins. Results from our gene-tree analyses indicate that there was tremendous lineage-specific duplication and diversification of kinesins in eukaryotes. Since the functions of only a few plant kinesins are reported in the literature, this comprehensive comparative analysis will be useful in designing functional studies with photosynthetic eukaryotes. PMID:16448571

Use of isotopic and hydrometric monitoring methods to partition hydrologic contributions to forested wetlands in the Upper Peninsula of Michigan

NASA Astrophysics Data System (ADS)

Van Grinsven, M. J.; Pypker, T. G.; Kolka, R. K.

2012-12-01

As a result of their landscape position and physical soil properties, northern forested wetlands are capable of retaining springtime snowmelt, rain and near surface groundwater inputs into the growing season. Hydrological conditions such as source water chemistry, duration of inundation, and magnitude of water table fluctuations are affected by the relative contribution of snow, rain, and groundwater sources, and in turn these hydrological conditions strongly influence the structure and function of northern forested wetlands. Black ash (Fraxinus nigra) is a facultative wet tree species, and is known to occur in 23 U.S. states and 7 Canadian provinces in northeastern North America. Black ash trees have ecological, economic, and cultural significance, and are currently threatened by the rapid expansion of the exotic emerald ash borer (Burprestidae: Agrilus planipennis). Since its initial detection in 2002 near Detroit, MI, the emerald ash borer has killed millions of ash trees in 15 U.S. states and 2 Canadian provinces. There is very little known about black ash wetland hydrology and ecology, and as a result of the looming infestation, there is a critical need to gain a better understanding of the hydrology in undisturbed ecosystems. The main objective of this study is to partition source water contributions in black ash wetlands in the western Upper Peninsula of Michigan. We hypothesize that snowmelt and near surface groundwater supply the majority of water to these wetlands annually, and summer rain is readily removed from the system through the evapotranspiration pathway. Hydrometric monitoring methods were used in conjunction with isotopic analysis using a linear mixing model to characterize source water contributions in nine black ash wetlands. The results suggest a connection with near surface groundwater during spring and early summer, and a short residence time for rain water following summer storm events. The outcome of this research aims to inform land managers in northeastern North America about the natural hydrologic condition of black ash wetlands, and provide baseline data that underscores potential water and forest resource impacts of current and future emerald ash borer infestations.

Fire treatment effects on vegetation structure, fuels, and potential fire severity in western U.S. forests

USGS Publications Warehouse

Stephens, S.L.; Moghaddas, J.J.; Edminster, C.; Fiedler, C.E.; Haase, S.; Harrington, M.; Keeley, J.E.; Knapp, E.E.; Mciver, J.D.; Metlen, K.; Skinner, C.N.; Youngblood, A.

2009-01-01

Abstract. Forest structure and species composition in many western U.S. coniferous forests have been altered through fire exclusion, past and ongoing harvesting practices, and livestock grazing over the 20th century. The effects of these activities have been most pronounced in seasonally dry, low and mid-elevation coniferous forests that once experienced frequent, low to moderate intensity, fire regimes. In this paper, we report the effects of Fire and Fire Surrogate (FFS) forest stand treatments on fuel load profiles, potential fire behavior, and fire severity under three weather scenarios from six western U.S. FFS sites. This replicated, multisite experiment provides a framework for drawing broad generalizations about the effectiveness of prescribed fire and mechanical treatments on surface fuel loads, forest structure, and potential fire severity. Mechanical treatments without fire resulted in combined 1-, 10-, and 100-hour surface fuel loads that were significantly greater than controls at three of five FFS sites. Canopy cover was significantly lower than controls at three of five FFS sites with mechanical-only treatments and at all five FFS sites with the mechanical plus burning treatment; fire-only treatments reduced canopy cover at only one site. For the combined treatment of mechanical plus fire, all five FFS sites with this treatment had a substantially lower likelihood of passive crown fire as indicated by the very high torching indices. FFS sites that experienced significant increases in 1-, 10-, and 100-hour combined surface fuel loads utilized harvest systems that left all activity fuels within experimental units. When mechanical treatments were followed by prescribed burning or pile burning, they were the most effective treatment for reducing crown fire potential and predicted tree mortality because of low surface fuel loads and increased vertical and horizontal canopy separation. Results indicate that mechanical plus fire, fire-only, and mechanical-only treatments using whole-tree harvest systems were all effective at reducing potential fire severity under severe fire weather conditions. Retaining the largest trees within stands also increased fire resistance. ?? 2009 by the Ecological Society of America.

Naturally Elevated Monomethylmercury and Mercury Concentrations of Redwood Trees of Coastal California

NASA Astrophysics Data System (ADS)

Rytuba, J. J.

2014-12-01

Redwood trees (Sequoia sempervirens) of coastal California acquire up to a third of their annual water through direct foliar uptake from summer coastal fog. Coastal fog contains elevated concentrations of monomethylmercury (MMeHg) up to 9.8 ng/L (Weiss-Penzias et al., Geophys Res Letters, 39). MMeHg introduced by fog is concentrated in old growth redwood trees throughout their distribution along the California coast. High concentrations of MMeHg occur in living redwood needles (0.20 to 3.76 ng/g dry weight basis, dwb) and are about 2 orders of magnitude greater than typical in evergreen needles that do not receive coastal fog water. MMeHg concentration in living redwood needles changes seasonally reaching a maximum at the end of the fog season (October) and a minimum at the beginning of the fog season (March). Hg concentrations in living redwood needles range from 21.7 to 80.5 ng/g (dwb), comparable to reported values for evergreen needles from non-coastal trees. Redwoods planted in the suburban landscape inland from the coastal fog belt have considerably lower MMeHg concentrations (<0.20 ng/g) but similar Hg concentrations to redwoods in their natural coastal environment. Redwood needles die after 3 years and contain comparable concentrations of MMeHg to those in living needles from the same old growth redwoods but Hg concentrations are much higher (up to 142 ng/g) since Hg accumulates throughout the life of the needle. Stream waters in old growth redwood forests under low and high flow conditions have very low concentrations of MMeHg (<.02 ng/L). However, under high flow conditions Hg concentrations are elevated, up to 22 ng/L, compared to low flow conditions (1.3-3.15 ng/L) and in rainwater (5.4 ng/L). MMeHg concentrations in stream waters are not elevated because MMeHg is retained in redwood needles. Hg concentrations in high flow stream waters are elevated because soils developed under old growth redwoods have elevated concentrations of Hg, up to 280 ng/g (3 times background), resulting from decomposition of litter and transformation of MMeHg to Hg-humic acid complexes (79-91%), and HgS and Hgo (8-20%) as indicated by sequential selective chemical extractions. Because of the high biomass density and annual litter fall, 850 g of Hg and 23 g of MMeHg per ha are added to the redwood ecosystem over a 2000 year life span.

Breeding bird responses to three silvicultural treatments in the Oregon Coast Range

USGS Publications Warehouse

Chambers, C.L.; McComb, W.C.; Tappeiner, J. C.

1999-01-01

Silvicultural alternatives to clear-cutting have been suggested to promote development, retention, or creation of late-successional features such as large trees, multilayered canopies, snags, and logs. We assessed bird response to three silvicultural alternatives to clear-cutting that retained structural features found in old Douglas-fir (Pseudotsuga menziesii) forests and that imitated natural disturbance regimes more closely than did traditional clear-cutting: (1) small-patch group selection treatment representing a low-intensity disturbance; (2) two-story treatment, representing a moderate to high-intensity disturbance; and (3) modified clear-cut treatment, representing a high-intensity disturbance. We counted diurnal breeding birds 1 yr prior to and 2 yr after harvest to estimate effects of the silvicultural treatments on bird communities compared with uncut controls. The small-patch group selection treatment was most similar in species composition to control stands. The two-story treatment was more similar to the modified clear-cut treatment. Ten bird species remained abundant following the small-patch group selection treatment. They declined in abundance in modified clearcuts and two-story stands. These species included four neotropical migratory species and five species with restricted geographic ranges and habitat associations. Nine species increased in response to moderate and/or high-intensity disturbances. This group included a larger proportion of species that were habitat generalists. Silvicultural treatments imitating low-intensity disturbances were most effective in retaining bird communities associated with mature forest; high-intensity disturbances such as the two-story and modified clear-cut treatments greatly altered bird community composition. Bird responses to the silvicultural treatments that we studied indicate that a variety of stand types is needed to meet needs of all species.

Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching

PubMed Central

Filichkin, Sergei A.; Hamilton, Michael; Dharmawardhana, Palitha D.; Singh, Sunil K.; Sullivan, Christopher; Ben-Hur, Asa; Reddy, Anireddy S. N.; Jaiswal, Pankaj

2018-01-01

Abiotic stresses affect plant physiology, development, growth, and alter pre-mRNA splicing. Western poplar is a model woody tree and a potential bioenergy feedstock. To investigate the extent of stress-regulated alternative splicing (AS), we conducted an in-depth survey of leaf, root, and stem xylem transcriptomes under drought, salt, or temperature stress. Analysis of approximately one billion of genome-aligned RNA-Seq reads from tissue- or stress-specific libraries revealed over fifteen millions of novel splice junctions. Transcript models supported by both RNA-Seq and single molecule isoform sequencing (Iso-Seq) data revealed a broad array of novel stress- and/or tissue-specific isoforms. Analysis of Iso-Seq data also resulted in the discovery of 15,087 novel transcribed regions of which 164 show AS. Our findings demonstrate that abiotic stresses profoundly perturb transcript isoform profiles and trigger widespread intron retention (IR) events. Stress treatments often increased or decreased retention of specific introns – a phenomenon described here as differential intron retention (DIR). Many differentially retained introns were regulated in a stress- and/or tissue-specific manner. A subset of transcripts harboring super stress-responsive DIR events showed persisting fluctuations in the degree of IR across all treatments and tissue types. To investigate coordinated dynamics of intron-containing transcripts in the study we quantified absolute copy number of isoforms of two conserved transcription factors (TFs) using Droplet Digital PCR. This case study suggests that stress treatments can be associated with coordinated switches in relative ratios between fully spliced and intron-retaining isoforms and may play a role in adjusting transcriptome to abiotic stresses. PMID:29483921

Bio-Energy Retains Its Mitigation Potential Under Elevated CO2

PubMed Central

Bellassen, Valentin; Njakou Djomo, Sylvestre; Lukac, Martin; Calfapietra, Carlo; Janssens, Ivan A.; Hoosbeek, Marcel R.; Viovy, Nicolas; Churkina, Galina; Scarascia-Mugnozza, Giuseppe; Ceulemans, Reinhart

2010-01-01

Background If biofuels are to be a viable substitute for fossil fuels, it is essential that they retain their potential to mitigate climate change under future atmospheric conditions. Elevated atmospheric CO2 concentration [CO2] stimulates plant biomass production; however, the beneficial effects of increased production may be offset by higher energy costs in crop management. Methodology/Main Findings We maintained full size poplar short rotation coppice (SRC) systems under both current ambient and future elevated [CO2] (550 ppm) and estimated their net energy and greenhouse gas balance. We show that a poplar SRC system is energy efficient and produces more energy than required for coppice management. Even more, elevated [CO2] will increase the net energy production and greenhouse gas balance of a SRC system with 18%. Managing the trees in shorter rotation cycles (i.e., 2 year cycles instead of 3 year cycles) will further enhance the benefits from elevated [CO2] on both the net energy and greenhouse gas balance. Conclusions/Significance Adapting coppice management to the future atmospheric [CO2] is necessary to fully benefit from the climate mitigation potential of bio-energy systems. Further, a future increase in potential biomass production due to elevated [CO2] outweighs the increased production costs resulting in a northward extension of the area where SRC is greenhouse gas neutral. Currently, the main part of the European terrestrial carbon sink is found in forest biomass and attributed to harvesting less than the annual growth in wood. Because SRC is intensively managed, with a higher turnover in wood production than conventional forest, northward expansion of SRC is likely to erode the European terrestrial carbon sink. PMID:20657833

An Objective Approach to Select Climate Scenarios when Projecting Species Distribution under Climate Change

PubMed Central

Casajus, Nicolas; Périé, Catherine; Logan, Travis; Lambert, Marie-Claude; de Blois, Sylvie; Berteaux, Dominique

2016-01-01

An impressive number of new climate change scenarios have recently become available to assess the ecological impacts of climate change. Among these impacts, shifts in species range analyzed with species distribution models are the most widely studied. Whereas it is widely recognized that the uncertainty in future climatic conditions must be taken into account in impact studies, many assessments of species range shifts still rely on just a few climate change scenarios, often selected arbitrarily. We describe a method to select objectively a subset of climate change scenarios among a large ensemble of available ones. Our k-means clustering approach reduces the number of climate change scenarios needed to project species distributions, while retaining the coverage of uncertainty in future climate conditions. We first show, for three biologically-relevant climatic variables, that a reduced number of six climate change scenarios generates average climatic conditions very close to those obtained from a set of 27 scenarios available before reduction. A case study on potential gains and losses of habitat by three northeastern American tree species shows that potential future species distributions projected from the selected six climate change scenarios are very similar to those obtained from the full set of 27, although with some spatial discrepancies at the edges of species distributions. In contrast, projections based on just a few climate models vary strongly according to the initial choice of climate models. We give clear guidance on how to reduce the number of climate change scenarios while retaining the central tendencies and coverage of uncertainty in future climatic conditions. This should be particularly useful during future climate change impact studies as more than twice as many climate models were reported in the fifth assessment report of IPCC compared to the previous one. PMID:27015274

An Objective Approach to Select Climate Scenarios when Projecting Species Distribution under Climate Change.

PubMed

Casajus, Nicolas; Périé, Catherine; Logan, Travis; Lambert, Marie-Claude; de Blois, Sylvie; Berteaux, Dominique

2016-01-01

An impressive number of new climate change scenarios have recently become available to assess the ecological impacts of climate change. Among these impacts, shifts in species range analyzed with species distribution models are the most widely studied. Whereas it is widely recognized that the uncertainty in future climatic conditions must be taken into account in impact studies, many assessments of species range shifts still rely on just a few climate change scenarios, often selected arbitrarily. We describe a method to select objectively a subset of climate change scenarios among a large ensemble of available ones. Our k-means clustering approach reduces the number of climate change scenarios needed to project species distributions, while retaining the coverage of uncertainty in future climate conditions. We first show, for three biologically-relevant climatic variables, that a reduced number of six climate change scenarios generates average climatic conditions very close to those obtained from a set of 27 scenarios available before reduction. A case study on potential gains and losses of habitat by three northeastern American tree species shows that potential future species distributions projected from the selected six climate change scenarios are very similar to those obtained from the full set of 27, although with some spatial discrepancies at the edges of species distributions. In contrast, projections based on just a few climate models vary strongly according to the initial choice of climate models. We give clear guidance on how to reduce the number of climate change scenarios while retaining the central tendencies and coverage of uncertainty in future climatic conditions. This should be particularly useful during future climate change impact studies as more than twice as many climate models were reported in the fifth assessment report of IPCC compared to the previous one.

Element budgets of two contrasting catchments in the Black Forest (Federal Republic of Germany)

NASA Astrophysics Data System (ADS)

Feger, K. H.; Brahmer, G.; Zöttl, H. W.

1990-08-01

Rainfall and throughfall inputs of all major cations and anions, via open-field bulk precipitation and canopy throughfall, are compared with streamwater outputs in two forested catchments at higher altitudes of the Black Forest. The sites differ considerably in terms of bedrock geology, soil type, soilwater characteristics, topography, and forest management history. Deposition at both sites is almost equal and, in contrast to other forest areas in Central Europe, of a low-to-moderate level. Dry deposition does not seem to play an important role. Distinct differences in the elemental output emerge owing to the differing site conditions. At Villingen, deposited nitrogen is almost totally retained, whereas at Schluchsee, nitrogen output and input are of the same order of magnitude. This is consistent with the different nitrogen nutrition level of the stands, microbial turnover in the soil, and former management practices (change of tree species, excessive nutrient export). Sulphur is not retained in either of the catchments. At Schluchsee, sulphur export exceeds input from canopy throughfall by a factor of 2.5. The higher output rates, both of nitrogen and sulphur at Schluchsee, are due to the much higher microbial mineralization of organic matter as shown by previous incubation tests. Differences in cation and proton export are mainly caused by a different drainage pattern. In contrast to the Schluchsee catchment, where vertical water pathways prevail, the streamwater solute output at Villingen is dominated by a shallow subsurface runoff. Atmospheric deposition is a contributing, but not the dominant, factor in the biogeochemical cycling at these sites. Hence, a generally applicable quantitative definition of 'critical loads', especially for nitrogen, is illusory and the use of such numbers will be misleading.

Comparative evaluation of salivary bisphenol A levels in patients wearing vacuum-formed and Hawley retainers: An in-vivo study.

PubMed

Raghavan, Akila Srinivasan; Pottipalli Sathyanarayana, Haritha; Kailasam, Vignesh; Padmanabhan, Sridevi

2017-03-01

The aims of the study were to evaluate and compare the bisphenol A (BPA) levels in saliva in patients using vacuum-formed retainers or Hawley retainers. Forty-five patients who had completed their fixed orthodontic treatment and were entering the retention phase were randomly allocated into 1 of 3 groups: vacuum-formed retainer, Hawley retainer fabricated by heat cure, and Hawley retainer fabricated by chemical cure. Saliva samples were collected immediately before placement, within 1 hour after placement, 1 week and 1 month after placement. Statistical analyses were performed by using 2-way analysis of variance and post-hoc multiple-comparisons Tukey HSD tests. Statistically significant BPA levels in saliva were found for all groups (P ≤0.05). The highest levels were noted in the vacuum-formed retainer group, followed by Hawley retainers fabricated by chemical cure; the lowest levels were found with Hawley retainers fabricated by heat cure. With many options available for removable retainers, clinicians should consider the BPA release from these retainers; a Hawley retainer fabricated by heat cure is a favorable choice. Copyright © 2016 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

Preservation of kinematics with posterior cruciate-, bicruciate- and patient-specific bicruciate-retaining prostheses in total knee arthroplasty by using computational simulation with normal knee model

PubMed Central

Koh, Y-G.; Son, J.; Kwon, S-K.; Kim, H-J.; Kang, K-T.

2017-01-01

Objectives Preservation of both anterior and posterior cruciate ligaments in total knee arthroplasty (TKA) can lead to near-normal post-operative joint mechanics and improved knee function. We hypothesised that a patient-specific bicruciate-retaining prosthesis preserves near-normal kinematics better than standard off-the-shelf posterior cruciate-retaining and bicruciate-retaining prostheses in TKA. Methods We developed the validated models to evaluate the post-operative kinematics in patient-specific bicruciate-retaining, standard off-the-shelf bicruciate-retaining and posterior cruciate-retaining TKA under gait and deep knee bend loading conditions using numerical simulation. Results Tibial posterior translation and internal rotation in patient-specific bicruciate-retaining prostheses preserved near-normal kinematics better than other standard off-the-shelf prostheses under gait loading conditions. Differences from normal kinematics were minimised for femoral rollback and internal-external rotation in patient-specific bicruciate-retaining, followed by standard off-the-shelf bicruciate-retaining and posterior cruciate-retaining TKA under deep knee bend loading conditions. Moreover, the standard off-the-shelf posterior cruciate-retaining TKA in this study showed the most abnormal performance in kinematics under gait and deep knee bend loading conditions, whereas patient-specific bicruciate-retaining TKA led to near-normal kinematics. Conclusion This study showed that restoration of the normal geometry of the knee joint in patient-specific bicruciate-retaining TKA and preservation of the anterior cruciate ligament can lead to improvement in kinematics compared with the standard off-the-shelf posterior cruciate-retaining and bicruciate-retaining TKA. Cite this article: Y-G. Koh, J. Son, S-K. Kwon, H-J. Kim, O-R. Kwon, K-T. Kang. Preservation of kinematics with posterior cruciate-, bicruciate- and patient-specific bicruciate-retaining prostheses in total knee arthroplasty by using computational simulation with normal knee model. Bone Joint Res 2017;6:557–565. DOI: 10.1302/2046-3758.69.BJR-2016-0250.R1. PMID:28947604

Periodontal health and compliance: A comparison between Essix and Hawley retainers.

PubMed

Manzon, Licia; Fratto, Giovanni; Rossi, Eros; Buccheri, Alfio

2018-06-01

Many studies on removable retainers have focused on retention efficacy and characteristics. However, studies on plaque accumulation, periodontal health, breakages, and patient compliance are still lacking. Thus, in this study, we aimed at evaluating these parameters in 2 groups of young patients wearing Essix or Hawley retainers for a 6-month period. Seventy subjects were included. Periodontal health was investigated by measuring the plaque, gingival, calculus, and bleeding on probing indexes. Evaluations were performed at 1, 3, and 6 months of wearing. Accumulation of plaque on the retainers was also evaluated. Furthermore, compliance on wearing retainers and breakage data were collected by specific questionnaires. Subjects wearing Essix retainers had significantly higher levels of plaque, gingival, and calculus indexes and increased percentages of bleeding sites, compared with subjects wearing Hawley retainers. The Essix group also had increased accumulations of plaque and calculus on the retainers. Nonetheless, subjects of the Essix group had better overall experiences, self-perceptions, and comfort compared with those of the Hawley group. Essix retainers had higher incidences of little and serious breakages compared with Hawley retainers. Our results suggest that Essix retainers are well accepted by patients for their esthetic and oral comfort characteristics. However, Essix retainers may cause greater accumulations of plaque on both teeth and retainers, presumably because of inhibition of the cleaning effect of saliva caused by the thermoplastic material or the reduced opportunity for good hygiene on the retainer. Copyright © 2018 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

Patient compliance to wear orthodontic retainers during postretention may vary by age, gender, and time since braces were removed.

PubMed

Vig, Katherine W L

2012-09-01

During January to July 2008 a questionnaire was mailed to 1085 subjects who had completed comprehensive orthodontic fixed-appliance treatment from 6 months to 6 years following active tooth movement. This yielded 280 responses (25.8% response rate) after 2 mailings, 3 months apart. The respondents ranged in age from 8 to 72 years. Respondents were from various socioeconomic groups and urban or rural environments. Identifiers allowed respondents to be classified into subgroups. Predictors of compliance among patients/subjects who were provided with removable vacuum-formed retainers (VFRs) or Hawley retainers in the postretention phase of orthodontic treatment. The main outcome measure was self-reported compliance with different types of removable orthodontic retainers worn during the postretention phase of treatment. A logistic regression model identified probabilities of retainer wear, including a likelihood ratio to test the model parameters using chi-square statistics to identify significant variables. The model found age, gender, amount of time since braces were removed, type of retainer, and interpretation of compliance in retainer wear to be statistically significant variables. Time on retainer compliance revealed better compliance with VFR than Hawley retainers during the first 2 years after braces were removed, but then compliance increased with Hawley retainers and overall compliance was greater with Hawley retainers. Compliance with wearing removable retainers was initially better with VFRs but over time was greater with Hawley retainers, and esthetics was not a determinant. Several variables determined compliance, including age, gender, and type of retainer. Copyright © 2012. Published by Mosby, Inc. All rights reserved.

Two-stage recovery of amphibian assemblages following selective logging of tropical forests.

PubMed

Adum, Gilbert Baase; Eichhorn, Markus Peter; Oduro, William; Ofori-Boateng, Caleb; Rödel, Mark-Oliver

2013-04-01

There is a lack of quantitative information on the effectiveness of selective-logging practices in ameliorating effects of logging on faunal communities. We conducted a large-scale replicated field study in 3 selectively logged moist semideciduous forests in West Africa at varying times after timber extraction to assess post logging effects on amphibian assemblages. Specifically, we assessed whether the diversity, abundance, and assemblage composition of amphibians changed over time for forest-dependent species and those tolerant of forest disturbance. In 2009, we sampled amphibians in 3 forests (total of 48 study plots, each 2 ha) in southwestern Ghana. In each forest, we established plots in undisturbed forest, recently logged forest, and forest logged 10 and 20 years previously. Logging intensity was constant across sites with 3 trees/ha removed. Recently logged forests supported substantially more species than unlogged forests. This was due to an influx of disturbance-tolerant species after logging. Simultaneously Simpson's index decreased, with increased in dominance of a few species. As time since logging increased richness of disturbance-tolerant species decreased until 10 years after logging when their composition was indistinguishable from unlogged forests. Simpson's index increased with time since logging and was indistinguishable from unlogged forest 20 years after logging. Forest specialists decreased after logging and recovered slowly. However, after 20 years amphibian assemblages had returned to a state indistinguishable from that of undisturbed forest in both abundance and composition. These results demonstrate that even with low-intensity logging (≤3 trees/ha) a minimum 20-year rotation of logging is required for effective conservation of amphibian assemblages in moist semideciduous forests. Furthermore, remnant patches of intact forests retained in the landscape and the presence of permanent brooks may aid in the effective recovery of amphibian assemblages. © 2012 Society for Conservation Biology.

A methodological combined framework for roadmapping biosensor research: a fault tree analysis approach within a strategic technology evaluation frame.

PubMed

Siontorou, Christina G; Batzias, Fragiskos A

2014-03-01

Biosensor technology began in the 1960s to revolutionize instrumentation and measurement. Despite the glucose sensor market success that revolutionized medical diagnostics, and artificial pancreas promise currently the approval stage, the industry is reluctant to capitalize on other relevant university-produced knowledge and innovation. On the other hand, the scientific literature is extensive and persisting, while the number of university-hosted biosensor groups is growing. Considering the limited marketability of biosensors compared to the available research output, the biosensor field has been used by the present authors as a suitable paradigm for developing a methodological combined framework for "roadmapping" university research output in this discipline. This framework adopts the basic principles of the Analytic Hierarchy Process (AHP), replacing the lower level of technology alternatives with internal barriers (drawbacks, limitations, disadvantages), modeled through fault tree analysis (FTA) relying on fuzzy reasoning to count for uncertainty. The proposed methodology is validated retrospectively using ion selective field effect transistor (ISFET) - based biosensors as a case example, and then implemented prospectively membrane biosensors, putting an emphasis on the manufacturability issues. The analysis performed the trajectory of membrane platforms differently than the available market roadmaps that, considering the vast industrial experience in tailoring and handling crystallic forms, suggest the technology path of biomimetic and synthetic materials. The results presented herein indicate that future trajectories lie along with nanotechnology, and especially nanofabrication and nano-bioinformatics, and focused, more on the science-path, that is, on controlling the natural process of self-assembly and the thermodynamics of bioelement-lipid interaction. This retained the nature-derived sensitivity of the biosensor platform, pointing out the differences between the scope of academic research and the market viewpoint.

Comparative Transcriptomic Approaches Exploring Contamination Stress Tolerance in Salix sp. Reveal the Importance for a Metaorganismal de Novo Assembly Approach for Nonmodel Plants1[OPEN

PubMed Central

Brereton, Nicholas J. B.; Marleau, Julie; Nissim, Werther Guidi; Labrecque, Michel; Joly, Simon; Pitre, Frederic E.

2016-01-01

Metatranscriptomic study of nonmodel organisms requires strategies that retain the highly resolved genetic information generated from model organisms while allowing for identification of the unexpected. A real-world biological application of phytoremediation, the field growth of 10 Salix cultivars on polluted soils, was used as an exemplar nonmodel and multifaceted crop response well-disposed to the study of gene expression. Sequence reads were assembled de novo to create 10 independent transcriptomes, a global transcriptome, and were mapped against the Salix purpurea 94006 reference genome. Annotation of assembled contigs was performed without a priori assumption of the originating organism. Global transcriptome construction from 3.03 billion paired-end reads revealed 606,880 unique contigs annotated from 1588 species, often common in all 10 cultivars. Comparisons between transcriptomic and metatranscriptomic methodologies provide clear evidence that nonnative RNA can mistakenly map to reference genomes, especially to conserved regions of common housekeeping genes, such as actin, α/β-tubulin, and elongation factor 1-α. In Salix, Rubisco activase transcripts were down-regulated in contaminated trees across all 10 cultivars, whereas thiamine thizole synthase and CP12, a Calvin Cycle master regulator, were uniformly up-regulated. De novo assembly approaches, with unconstrained annotation, can improve data quality; care should be taken when exploring such plant genetics to reduce de facto data exclusion by mapping to a single reference genome alone. Salix gene expression patterns strongly suggest cultivar-wide alteration of specific photosynthetic apparatus and protection of the antenna complexes from oxidation damage in contaminated trees, providing an insight into common stress tolerance strategies in a real-world phytoremediation system. PMID:27002060

Distinctive Architecture of the Chloroplast Genome in the Chlorodendrophycean Green Algae Scherffelia dubia and Tetraselmis sp. CCMP 881.

PubMed

Turmel, Monique; de Cambiaire, Jean-Charles; Otis, Christian; Lemieux, Claude

2016-01-01

The Chlorodendrophyceae is a small class of green algae belonging to the core Chlorophyta, an assemblage that also comprises the Pedinophyceae, Trebouxiophyceae, Ulvophyceae and Chlorophyceae. Here we describe for the first time the chloroplast genomes of chlorodendrophycean algae (Scherffelia dubia, 137,161 bp; Tetraselmis sp. CCMP 881, 100,264 bp). Characterized by a very small single-copy (SSC) region devoid of any gene and an unusually large inverted repeat (IR), the quadripartite structures of the Scherffelia and Tetraselmis genomes are unique among all core chlorophytes examined thus far. The lack of genes in the SSC region is offset by the rich and atypical gene complement of the IR, which includes genes from the SSC and large single-copy regions of prasinophyte and streptophyte chloroplast genomes having retained an ancestral quadripartite structure. Remarkably, seven of the atypical IR-encoded genes have also been observed in the IRs of pedinophycean and trebouxiophycean chloroplast genomes, suggesting that they were already present in the IR of the common ancestor of all core chlorophytes. Considering that the relationships among the main lineages of the core Chlorophyta are still unresolved, we evaluated the impact of including the Chlorodendrophyceae in chloroplast phylogenomic analyses. The trees we inferred using data sets of 79 and 108 genes from 71 chlorophytes indicate that the Chlorodendrophyceae is a deep-diverging lineage of the core Chlorophyta, although the placement of this class relative to the Pedinophyceae remains ambiguous. Interestingly, some of our phylogenomic trees together with our comparative analysis of gene order data support the monophyly of the Trebouxiophyceae, thus offering further evidence that the previously observed affiliation between the Chlorellales and Pedinophyceae is the result of systematic errors in phylogenetic reconstruction.

Low offspring survival in mountain pine beetle infesting the resistant Great Basin bristlecone pine supports the preference-performance hypothesis.

PubMed

Eidson, Erika L; Mock, Karen E; Bentz, Barbara J

2018-01-01

The preference-performance hypothesis states that ovipositing phytophagous insects will select host plants that are well-suited for their offspring and avoid host plants that do not support offspring performance (survival, development and fitness). The mountain pine beetle (Dendroctonus ponderosae), a native insect herbivore in western North America, can successfully attack and reproduce in most species of Pinus throughout its native range. However, mountain pine beetles avoid attacking Great Basin bristlecone pine (Pinus longaeva), despite recent climate-driven increases in mountain pine beetle populations at the high elevations where Great Basin bristlecone pine grows. Low preference for a potential host plant species may not persist if the plant supports favorable insect offspring performance, and Great Basin bristlecone pine suitability for mountain pine beetle offspring performance is unclear. We infested cut bolts of Great Basin bristlecone pine and two susceptible host tree species, limber (P. flexilis) and lodgepole (P. contorta) pines with adult mountain pine beetles and compared offspring performance. To investigate the potential for variation in offspring performance among mountain pine beetles from different areas, we tested beetles from geographically-separated populations within and outside the current range of Great Basin bristlecone pine. Although mountain pine beetles constructed galleries and laid viable eggs in all three tree species, extremely few offspring emerged from Great Basin bristlecone pine, regardless of the beetle population. Our observed low offspring performance in Great Basin bristlecone pine corresponds with previously documented low mountain pine beetle attack preference. A low preference-low performance relationship suggests that Great Basin bristlecone pine resistance to mountain pine beetle is likely to be retained through climate-driven high-elevation mountain pine beetle outbreaks.

A Systematic Prediction of Drug-Target Interactions Using Molecular Fingerprints and Protein Sequences.

PubMed

Huang, Yu-An; You, Zhu-Hong; Chen, Xing

2018-01-01

Drug-Target Interactions (DTI) play a crucial role in discovering new drug candidates and finding new proteins to target for drug development. Although the number of detected DTI obtained by high-throughput techniques has been increasing, the number of known DTI is still limited. On the other hand, the experimental methods for detecting the interactions among drugs and proteins are costly and inefficient. Therefore, computational approaches for predicting DTI are drawing increasing attention in recent years. In this paper, we report a novel computational model for predicting the DTI using extremely randomized trees model and protein amino acids information. More specifically, the protein sequence is represented as a Pseudo Substitution Matrix Representation (Pseudo-SMR) descriptor in which the influence of biological evolutionary information is retained. For the representation of drug molecules, a novel fingerprint feature vector is utilized to describe its substructure information. Then the DTI pair is characterized by concatenating the two vector spaces of protein sequence and drug substructure. Finally, the proposed method is explored for predicting the DTI on four benchmark datasets: Enzyme, Ion Channel, GPCRs and Nuclear Receptor. The experimental results demonstrate that this method achieves promising prediction accuracies of 89.85%, 87.87%, 82.99% and 81.67%, respectively. For further evaluation, we compared the performance of Extremely Randomized Trees model with that of the state-of-the-art Support Vector Machine classifier. And we also compared the proposed model with existing computational models, and confirmed 15 potential drug-target interactions by looking for existing databases. The experiment results show that the proposed method is feasible and promising for predicting drug-target interactions for new drug candidate screening based on sizeable features. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Technical and institutional innovation in agroforestry for protected areas management in the Brazilian Amazon: opportunities and limitations.

PubMed

Schroth, Götz; da Mota, Maria do Socorro S

2013-08-01

Tropical forest countries are struggling with the partially conflicting policy objectives of socioeconomic development, forest conservation, and safeguarding the livelihoods of local forest-dependent people. We worked with communities in the lower Tapajós region of the central Brazilian Amazon for over 10 years to understand their traditional and present land use practices, the constraints, and decision making processes imposed by their biophysical, socioeconomic, and political environment, and to facilitate development trajectories to improve the livelihoods of forest communities while conserving the forest on the farms and in the larger landscape. The work focused on riverine communities initially in the Tapajós National Forest and then in the Tapajós-Arapiuns Extractive Reserve. These communities have a century-old tradition of planting rubber agroforests which despite their abandonment during the 1990s still widely characterize the vegetation of the river banks, especially in the two protected areas where they are safe from the recent expansion of mechanized rice and soybean agriculture. The project evolved from the capacity-building of communities in techniques to increase the productivity of the rubber agroforests without breaking their low-input and low-risk logic, to the establishment of a community enterprise that allowed reserve inhabitants to reforest their own land with tree species of their choice and sell reforestation (not carbon) credits to local timber companies while retaining the ownership of the trees. By making land use practices economically more viable and ecologically more appropriate for protected areas, the project shows ways to strengthen the system of extractive and sustainable development reserves that protects millions of hectares of Amazon forest with the consent of the communities that inhabit them.

Tropical forests are thermally buffered despite intensive selective logging.

PubMed

Senior, Rebecca A; Hill, Jane K; Benedick, Suzan; Edwards, David P

2018-03-01

Tropical rainforests are subject to extensive degradation by commercial selective logging. Despite pervasive changes to forest structure, selectively logged forests represent vital refugia for global biodiversity. The ability of these forests to buffer temperature-sensitive species from climate warming will be an important determinant of their future conservation value, although this topic remains largely unexplored. Thermal buffering potential is broadly determined by: (i) the difference between the "macroclimate" (climate at a local scale, m to ha) and the "microclimate" (climate at a fine-scale, mm to m, that is distinct from the macroclimate); (ii) thermal stability of microclimates (e.g. variation in daily temperatures); and (iii) the availability of microclimates to organisms. We compared these metrics in undisturbed primary forest and intensively logged forest on Borneo, using thermal images to capture cool microclimates on the surface of the forest floor, and information from dataloggers placed inside deadwood, tree holes and leaf litter. Although major differences in forest structure remained 9-12 years after repeated selective logging, we found that logging activity had very little effect on thermal buffering, in terms of macroclimate and microclimate temperatures, and the overall availability of microclimates. For 1°C warming in the macroclimate, temperature inside deadwood, tree holes and leaf litter warmed slightly more in primary forest than in logged forest, but the effect amounted to <0.1°C difference between forest types. We therefore conclude that selectively logged forests are similar to primary forests in their potential for thermal buffering, and subsequent ability to retain temperature-sensitive species under climate change. Selectively logged forests can play a crucial role in the long-term maintenance of global biodiversity. © 2017 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

Technical and Institutional Innovation in Agroforestry for Protected Areas Management in the Brazilian Amazon: Opportunities and Limitations

NASA Astrophysics Data System (ADS)

Schroth, Götz; da Mota, Maria do Socorro S.

2013-08-01

Tropical forest countries are struggling with the partially conflicting policy objectives of socioeconomic development, forest conservation, and safeguarding the livelihoods of local forest-dependent people. We worked with communities in the lower Tapajós region of the central Brazilian Amazon for over 10 years to understand their traditional and present land use practices, the constraints, and decision making processes imposed by their biophysical, socioeconomic, and political environment, and to facilitate development trajectories to improve the livelihoods of forest communities while conserving the forest on the farms and in the larger landscape. The work focused on riverine communities initially in the Tapajós National Forest and then in the Tapajós-Arapiuns Extractive Reserve. These communities have a century-old tradition of planting rubber agroforests which despite their abandonment during the 1990s still widely characterize the vegetation of the river banks, especially in the two protected areas where they are safe from the recent expansion of mechanized rice and soybean agriculture. The project evolved from the capacity-building of communities in techniques to increase the productivity of the rubber agroforests without breaking their low-input and low-risk logic, to the establishment of a community enterprise that allowed reserve inhabitants to reforest their own land with tree species of their choice and sell reforestation (not carbon) credits to local timber companies while retaining the ownership of the trees. By making land use practices economically more viable and ecologically more appropriate for protected areas, the project shows ways to strengthen the system of extractive and sustainable development reserves that protects millions of hectares of Amazon forest with the consent of the communities that inhabit them.

Low offspring survival in mountain pine beetle infesting the resistant Great Basin bristlecone pine supports the preference-performance hypothesis

PubMed Central

Mock, Karen E.; Bentz, Barbara J.

2018-01-01

The preference-performance hypothesis states that ovipositing phytophagous insects will select host plants that are well-suited for their offspring and avoid host plants that do not support offspring performance (survival, development and fitness). The mountain pine beetle (Dendroctonus ponderosae), a native insect herbivore in western North America, can successfully attack and reproduce in most species of Pinus throughout its native range. However, mountain pine beetles avoid attacking Great Basin bristlecone pine (Pinus longaeva), despite recent climate-driven increases in mountain pine beetle populations at the high elevations where Great Basin bristlecone pine grows. Low preference for a potential host plant species may not persist if the plant supports favorable insect offspring performance, and Great Basin bristlecone pine suitability for mountain pine beetle offspring performance is unclear. We infested cut bolts of Great Basin bristlecone pine and two susceptible host tree species, limber (P. flexilis) and lodgepole (P. contorta) pines with adult mountain pine beetles and compared offspring performance. To investigate the potential for variation in offspring performance among mountain pine beetles from different areas, we tested beetles from geographically-separated populations within and outside the current range of Great Basin bristlecone pine. Although mountain pine beetles constructed galleries and laid viable eggs in all three tree species, extremely few offspring emerged from Great Basin bristlecone pine, regardless of the beetle population. Our observed low offspring performance in Great Basin bristlecone pine corresponds with previously documented low mountain pine beetle attack preference. A low preference-low performance relationship suggests that Great Basin bristlecone pine resistance to mountain pine beetle is likely to be retained through climate-driven high-elevation mountain pine beetle outbreaks. PMID:29715269

18 CFR 367.4360 - Account 436, Appropriations of retained earnings.

Code of Federal Regulations, 2010 CFR

2010-04-01

..., Appropriations of retained earnings. 367.4360 Section 367.4360 Conservation of Power and Water Resources FEDERAL... NATURAL GAS ACT Retained Earnings Accounts § 367.4360 Account 436, Appropriations of retained earnings. This account must include appropriations of retained earnings as follows: (a) Appropriations required...

45 CFR 1611.9 - Retainer agreements.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 45 Public Welfare 4 2014-10-01 2014-10-01 false Retainer agreements. 1611.9 Section 1611.9 Public... ELIGIBILITY § 1611.9 Retainer agreements. (a) When a recipient provides extended service to a client, the recipient shall execute a written retainer agreement with the client. The retainer agreement shall be...

Accelerated aging effects on surface hardness and roughness of lingual retainer adhesives.

PubMed

Ramoglu, Sabri Ilhan; Usumez, Serdar; Buyukyilmaz, Tamer

2008-01-01

To test the null hypothesis that accelerated aging has no effect on the surface microhardness and roughness of two light-cured lingual retainer adhesives. Ten samples of light-cured materials, Transbond Lingual Retainer (3M Unitek) and Light Cure Retainer (Reliance) were cured with a halogen light for 40 seconds. Vickers hardness and surface roughness were measured before and after accelerated aging of 300 hours in a weathering tester. Differences between mean values were analyzed for statistical significance using a t-test. The level of statistical significance was set at P < .05. The mean Vickers hardness of Transbond Lingual Retainer was 62.8 +/- 3.5 and 79.6 +/- 4.9 before and after aging, respectively. The mean Vickers hardness of Light Cure Retainer was 40.3 +/- 2.6 and 58.3 +/- 4.3 before and after aging, respectively. Differences in both groups were statistically significant (P < .001). Following aging, mean surface roughness was changed from 0.039 microm to 0.121 microm and from 0.021 microm to 0.031 microm for Transbond Lingual Retainer and Light Cure Retainer, respectively. The roughening of Transbond Lingual Retainer with aging was statistically significant (P < .05), while the change in the surface roughness of Light Cure Retainer was not (P > .05). Accelerated aging significantly increased the surface microhardness of both light-cured retainer adhesives tested. It also significantly increased the surface roughness of the Transbond Lingual Retainer.

Carbon dioxide is a powerful inducer of monokaryotic hyphae and spore development in Cryptococcus gattii and carbonic anhydrase activity is dispensable in this dimorphic transition.

PubMed

Ren, Ping; Chaturvedi, Vishnu; Chaturvedi, Sudha

2014-01-01

Cryptococcus gattii is unique among human pathogenic fungi with specialized ecological niche on trees. Since leaves concentrate CO2, we investigated the role of this gaseous molecule in C. gattii biology and virulence. We focused on the genetic analyses of β-carbonic anhydrase (β-CA) encoded by C. gattii CAN1 and CAN2 as later is critical for CO2 sensing in a closely related pathogen C. neoformans. High CO2 conditions induced robust development of monokaryotic hyphae and spores in C. gattii. Conversely, high CO2 completely repressed hyphae development in sexual mating. Both CAN1 and CAN2 were dispensable for CO2 induced morphogenetic transitions. However, C. gattii CAN2 was essential for growth in ambient air similar to its reported role in C. neoformans. Both can1 and can2 mutants retained full pathogenic potential in vitro and in vivo. These results provide insight into C. gattii adaptation for arboreal growth and production of infectious propagules by β-CA independent mechanism(s).

Graph rigidity, cyclic belief propagation, and point pattern matching.

PubMed

McAuley, Julian J; Caetano, Tibério S; Barbosa, Marconi S

2008-11-01

A recent paper [1] proposed a provably optimal polynomial time method for performing near-isometric point pattern matching by means of exact probabilistic inference in a chordal graphical model. Its fundamental result is that the chordal graph in question is shown to be globally rigid, implying that exact inference provides the same matching solution as exact inference in a complete graphical model. This implies that the algorithm is optimal when there is no noise in the point patterns. In this paper, we present a new graph that is also globally rigid but has an advantage over the graph proposed in [1]: Its maximal clique size is smaller, rendering inference significantly more efficient. However, this graph is not chordal, and thus, standard Junction Tree algorithms cannot be directly applied. Nevertheless, we show that loopy belief propagation in such a graph converges to the optimal solution. This allows us to retain the optimality guarantee in the noiseless case, while substantially reducing both memory requirements and processing time. Our experimental results show that the accuracy of the proposed solution is indistinguishable from that in [1] when there is noise in the point patterns.

Environmental drivers on leaf phenology of ironstone outcrops species under seasonal climate.

PubMed

Garcia, Letícia C; Barros, Fernanda V; Lemos-Filho, José P

2017-01-01

Banded iron formations (BIF) have a particular vegetation type and provide a good model system for testing theories related to leaf phenology, due to unique stressful environmental conditions. As a consequence of the stressful conditions of BIF environment, we hypothesize that most species would retain at least some significant canopy cover, even at the end of the dry season, independently of growth form - trees, shrubs, and sub-shrubs. Considering the strong seasonality, we also hypothesize that photoperiod and rainfall act as triggers for leaf fall and leaf flushing in these environments. The majority of the fifteen studied species had a semi-deciduous behavior and shed their leaves mainly during the dry season, with a recovery at the end of this season. In general, leaf flushing increased around the spring equinox (end of the dry season and start of the rainy season). A trade-off between leaf loss and leaf maintenance is expected in a community in which most plants are naturally selected to be semi-deciduous. Our results suggest photoperiod as a dominant factor in predicting leaf phenology.

Carbon Dioxide is a Powerful Inducer of Monokaryotic Hyphae and Spore Development in Cryptococcus gattii and Carbonic Anhydrase Activity is Dispensable in This Dimorphic Transition

PubMed Central

Ren, Ping; Chaturvedi, Vishnu; Chaturvedi, Sudha

2014-01-01

Cryptococcus gattii is unique among human pathogenic fungi with specialized ecological niche on trees. Since leaves concentrate CO2, we investigated the role of this gaseous molecule in C. gattii biology and virulence. We focused on the genetic analyses of β-carbonic anhydrase (β-CA) encoded by C. gattii CAN1 and CAN2 as later is critical for CO2 sensing in a closely related pathogen C. neoformans. High CO2 conditions induced robust development of monokaryotic hyphae and spores in C. gattii. Conversely, high CO2 completely repressed hyphae development in sexual mating. Both CAN1 and CAN2 were dispensable for CO2 induced morphogenetic transitions. However, C. gattii CAN2 was essential for growth in ambient air similar to its reported role in C. neoformans. Both can1 and can2 mutants retained full pathogenic potential in vitro and in vivo. These results provide insight into C. gattii adaptation for arboreal growth and production of infectious propagules by β-CA independent mechanism(s). PMID:25478697

Phylogeny and Systematics of Leptomyxid Amoebae (Amoebozoa, Tubulinea, Leptomyxida).

PubMed

Smirnov, Alexey; Nassonova, Elena; Geisen, Stefan; Bonkowski, Michael; Kudryavtsev, Alexander; Berney, Cedric; Glotova, Anna; Bondarenko, Natalya; Dyková, Iva; Mrva, Martin; Fahrni, Jose; Pawlowski, Jan

2017-04-01

We describe four new species of Flabellula, Leptomyxa and Rhizamoeba and publish new SSU rRNA gene and actin gene sequences of leptomyxids. Using these data we provide the most comprehensive SSU phylogeny of leptomyxids to date. Based on the analyses of morphological data and results of the SSU rRNA gene phylogeny we suggest changes in the systematics of the order Leptomyxida (Amoebozoa: Lobosa: Tubulinea). We propose to merge the genera Flabellula and Paraflabellula (the genus Flabellula remains valid by priority rule). The genus Rhizamoeba is evidently polyphyletic in all phylogenetic trees; we suggest retaining the generic name Rhizamoeba for the group unifying R. saxonica, R.matisi n. sp. and R. polyura, the latter remains the type species of the genus Rhizamoeba. Based on molecular and morphological evidence we move all remaining Rhizamoeba species to the genus Leptomyxa. New family Rhizamoebidae is established here in order to avoid paraphyly of the family Leptomyxidae. With the suggested changes both molecular and morphological systems of the order Leptomyxida are now fully congruent to each other. Copyright © 2016 Elsevier GmbH. All rights reserved.

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

PubMed Central

2012-01-01

Background With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it. Results PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available. Conclusions PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net. PMID:22568821

A Biogeotechnical engineering approach to Combat Desertification

NASA Astrophysics Data System (ADS)

Chang, I.; Im, J.; Cho, G. C.; Lee, S. J.

2016-12-01

The acceleration of global warming is not only inducing rising sea levels and abnormal climate problems, but also geotechnical hazards such as desertification. Recently, 30% of Earth's dry land has been affected by desertification, and approximately 850 million people are suffering due to famine, poverty, and hygiene problems induced by desertification. Global warming and unsustainable land development are known to be major triggers promoting desertification. Numerous global agencies and companies are thus contributing to anti-desertification movements. However, tree planting alone is not an ideal solution given that it takes approximately 2 3 years for stabilization. It is thus imperative to develop innovative technology that can promote vegetation growth and improve soil erosion resistance. In this study, a unique soil treatment and anti-desertification method is developed using microbial biopolymers. Biopolymers can effectively strengthen soil and improve durability. In particular, anionic-hydrophilic biopolymers delay water evaporation, thereby retaining a higher soil moisture condition compared to non-treated soil. Results of this study show that microbial biopolymer treatment is highly effective in improving both vegetation growth (3 times faster) and soil erosion resistance (less than 2%), compared to untreated earth surfaces.

Assimilate partitioning in avocado, Persea americana

DOE Office of Scientific and Technical Information (OSTI.GOV)

Finazzo, S.; Davenport, T.L.

1986-04-01

Assimilate partitioning is being studied in avocado, Persea americana cv. Millborrow in relation to fruit set. Single leaves on girdled branches of 10 year old trees were radiolabeled for 1 hr with 13..mu..Ci of /sup 14/CO/sub 2/. The source leaves were sampled during the experiment to measure translocation rates. At harvest the sink tissues were dissected and the incorporated radioactivity was measured. The translocation of /sup 14/C-labelled compounds to other leaves was minimal. Incorporation of label into fruitlets varied with the tissue and the stage of development. Sink (fruitlets) nearest to the labelled leaf and sharing the same phyllotaxy incorporatedmore » the most /sup 14/C. Source leaves for single non-abscising fruitlets retained 3X more /sup 14/C-labelled compounds than did source leaves for 2 or more fruitlets at 31 hrs. post-labelling. Export of label decreased appreciably when fruitlets abscised. If fruitlets abscised within 4 days of labeling then the translocation pattern was similar to the pattern for single fruitlets. If the fruitlet abscised later, the translocation pattern was intermediate between the single and double fruitlet pattern.« less

Oxidative stress and inflammation in retained placenta: a pilot study of protein and gene expression of GPX1 and NFκB.

PubMed

Endler, Margit; Saltvedt, Sissel; Eweida, Mohamed; Åkerud, Helena

2016-12-06

Retained placenta is associated with severe postpartum hemorrhage. Its etiology is unknown and its biochemistry has not been studied. We aimed to assess whether levels of the antioxidative enzyme Glutathione Peroxidase 1 (GPX1) and the transcription factor Nuclear Factor κβ (NFκβ), as markers of oxidative stress and inflammation, were affected in retained placentas compared to spontaneously released placentas from otherwise normal full term pregnancies. In a pilot study we assessed concentrations of GPX1 by ELISA and gene (mRNA) expression of GPX1, NFκβ and its inhibitor Iκβα, by quantitative real-time-PCR in periumbilical and peripheral samples from retained (n = 29) and non-retained (n = 31) placental tissue. Median periumbilical GPX1 concentrations were 13.32 ng/ml in retained placentas and 17.96 ng/ml in non-retained placentas (p = 0.22), peripheral concentrations were 13.27 ng/ml and 19.09 ng/ml (p = 0.08). Retained placental tissue was more likely to have a low GPX1 protein concentration (OR 3.82, p = 0.02 for periumbilical and OR 3.95, p = 0.02 for peripheral samples). Median periumbilical GPX1 gene expressions were 1.13 for retained placentas and 0.88 for non-retained placentas (p = 0.08), peripheral expression was 1.32 and 1.18 (p = 0.46). Gene expressions of NFκβ and Iκβα were not significantly different between retained and non-retained placental tissue. Women with retained placenta were more likely to have a low level of GPX1 protein concentration in placental tissue compared to women without retained placenta and retained placental tissue showed a tendency of lower median concentrations of GPX1 protein expression. This may indicate decreased antioxidative capacity as a component in this disorder but requires a larger sample to corroborate results.

The inherited risk of retained placenta: a population based cohort study.

PubMed

Endler, M; Cnattingius, S; Granfors, M; Wikström, A-K

2018-05-01

To investigate whether retained placenta in the first generation is associated with an increased risk of retained placenta in the second generation. Population-based cohort study. Sweden. Using linked generational data from the Swedish Medical Birth Register 1973-2012, we identified 494 000 second-generation births with information on the birth of the mother (first-generation index birth). For 292 897 of these births there was information also on the birth of the father. Risk of retained placenta in the second generation was calculated as adjusted odds ratios (aOR) by unconditional logistic regression with 95% confidence intervals (95% CI) according to whether retained placenta occurred in a first generation birth or not. Retained placenta in the second generation. The risk of retained placenta in a second-generation birth was increased if retained placenta had occurred at the mother's own birth (aOR 1.66, 95% CI 1.52-1.82), at the birth of one of her siblings (aOR 1.58, 95% CI 1.43-1.76) or both (aOR 2.75, 95% CI 2.18-3.46). The risk was slightly increased if retained placenta had occurred at the birth of the father (aOR 1.23, 95% CI 1.07-1.41). For preterm births in both generations, the risk of retained placenta in the second generation was increased six-fold if retained placenta had occurred at the mother's birth (OR 6.55, 95% CI 2.68-16.02). There is an intergenerational recurrence of retained placenta on the maternal and most likely also on the paternal side. The recurrence risk seems strongest in preterm pregnancies. A population-based cohort study suggests that there is an intergenerational recurrence of retained placenta. © 2017 Royal College of Obstetricians and Gynaecologists.

Inadequacy, Impurity and Infidelity; Modifying the Modified Brendel Alpha-Cellulose Extraction Method for Resinous Woods in Stable Isotope Dendroclimatology

NASA Astrophysics Data System (ADS)

Brookman, T. H.; Whittaker, T. E.; King, P. L.; Horton, T. W.

2011-12-01

Stable isotope dendroclimatology is a burgeoning field in palaeoclimate science due to its unique potential to contribute (sub)annually resolved climate records, over millennial timescales, to the terrestrial palaeoclimate record. Until recently the time intensive methods precluded long-term climate reconstructions. Advances in continuous-flow mass spectrometry and isolation methods for α-cellulose (ideal for palaeoclimate studies as, unlike other wood components, it retains its initial isotopic composition) have made long-term, calendar dated palaeoclimate reconstructions a viable proposition. The Modified Brendel (mBrendel) α-cellulose extraction method is a fast, cost-effective way of preparing whole-wood samples for stable oxygen and carbon isotope analysis. However, resinous woods often yield incompletely processed α-cellulose using the standard mBrendel approach. As climate signals may be recorded by small (<1%) isotopic shifts it is important to investigate if incomplete processing affects the accuracy and precision of tree-ring isotopic records. In an effort to address this methodological issue, we investigated three highly resinous woods: kauri (Agathis australis), ponderosa pine (Pinus ponderosa) and huon pine (Lagarastrobus franklinii). Samples of each species were treated with 16 iterations of the mBrendel, varying reaction temperature, time and reagent volumes. Products were investigated using microscopic and bulk transmission Fourier Transform infrared spectroscopy (FITR) to reveal variations in the level of processing; poorly-digested fibres display a peak at 1520cm-1 suggesting residual lignin and a peak at ~1600cm-1 in some samples suggests retained resin. Despite the different levels of purity, replicate analyses of samples processed by high temperature digestion yielded consistent δ18O within and between experiments. All α-cellulose samples were 5-7% enriched compared to the whole-wood, suggesting that even incomplete processing at high temperature can provide acceptable δ18O analytical external precision. For kauri, short, lower temperature extractions produced α-cellulose with δ18O consistently ~1% lower than longer, higher temperature kauri experiments. These findings suggest that temperature and time are significant variables that influence the analytical precision of α-cellulose stable isotope analysis and that resinous hardwoods (e.g. kauri) may require longer and/or hotter digestions than softwoods. The effects of mBrendel variants on the carbon isotope ratio precision of α-cellulose extracts will also be presented. Our findings indicate that the standard mBrendel α-cellulose extraction method may not fully remove lignins and resins depending on the type of wood being analysed. Residual impurities can decrease analytical precision and accuracy. Fortunately, FTIR analysis prior to isotopic analysis is a relatively fast and cost effective way to determine α-cellulose extract purity, ultimately improving the data quality, accuracy and utility of tree-ring based stable isotopic climate records.

Polyurethane retainers for ball bearings

NASA Technical Reports Server (NTRS)

Christy, R. I.

1973-01-01

Evaluation of a new ball bearing retainer material is reported. A special composite polyurethane foam ball retainer has been developed that has virtually zero wear, is chemically inert to hydrocarbon lubricants, and stores up to 60 times as much lubricant per unit volume as the most commonly used retainer material, cotton phenolic. This new retainer concept shows promise of years of ball bearing operation without reoiling, based on life testing in high vacuum.

Reoccurrence of retained placenta at a subsequent delivery: an observational study.

PubMed

Alufi, Anat; Mizrachi, Yossi; Lurie, Samuel

2017-05-01

To test the generalizability of previously reported increased risk of reoccurrence of retained placenta in yet another setting. In this observational retrospective study we longitudinally followed women who had a vaginal delivery complicated by a partial or complete retained placenta at Edith Wolfson Medical Center between 1 January 2009 and 31 December 2012. The study group included parturient women who had a partial or complete retained placenta after a vaginal delivery (n = 90). The control group included parturient women who did not have a partial or complete retained placenta after a vaginal delivery from the same time period using the same inclusion criteria (n = 90). Retained partial or complete placenta at a previous delivery was found to be an independent risk factor for retained partial or complete placenta in a subsequent delivery (adjusted OR 9.8, 95%CI 1.2 to 80.6, p = 0.032) and for retained partial or complete placenta and/or postpartum hemorrhage in a subsequent delivery (adjusted OR 14.1, 95% CI 1.7 to 111.9, p = 0.012), after controlling for gestational age and induction of labor at previous delivery. Retained partial or complete placenta at an index delivery increases the risk of reoccurrence of retained partial or complete placenta in a subsequent delivery.

Academic retainer medicine: an innovative business model for cross-subsidizing primary care.

PubMed

Lucier, David J; Frisch, Nicholas B; Cohen, Brian J; Wagner, Michael; Salem, Deeb; Fairchild, David G

2010-06-01

Retainer-medicine primary care practices, commonly referred to as "luxury" or "concierge" practices, provide enhanced services to patients beyond those available in traditional practices for a yearly retainer fee. Adoption of retainer practices has been largely absent in academic health centers (AHCs). Reasons for this trend stem primarily from ethical concerns, such as the potential for patient abandonment when physicians downsize from larger, traditional practices to smaller, retainer-medicine practices.In 2004, the Department of Medicine at Tufts Medical Center developed an academic retainer-medicine primary care practice within the Division of General Medicine that not only generates financial support for the division but also incorporates a clinical and business model that is aligned with the mission and ethics of an academic institution.In contrast to private retainer-medicine practices, this unique business model addresses several of the ethical issues associated with traditional retainer practices-it does not restrict net access to care and it neutralizes concerns about patient abandonment. Addressing the growing primary care shortage, the model also presents the opportunity for a retainer practice to cross-subsidize the expansion of general medicine in an academic medical setting. The authors elucidate the benefits, as well as the inherent challenges, of embedding an academic retainer-medicine practice within an AHC.

[Effects of crop tree release on stand growth and stand structure of Cunninghamia lanceolata plantation].

PubMed

Wu, Jian-qiang; Wang, Yi-xiang; Yang, Yi; Zhu, Ting-ting; Zhu, Xu-dan

2015-02-01

Crop trees were selected in a 26-year-old even-aged Cunninghamia lanceolata plantation in Lin' an, and compared in plots that were released and unreleased to examine growth and structure responses for 3 years after thinning. Crop tree release significantly increased the mean increments of diameter and volume of individual tree by 1.30 and 1.25 times relative to trees in control stands, respectively. The increments of diameter and volume of crop trees were significantly higher than those of general trees in thinning plots, crop trees and general trees in control plots, which suggested that the responses from different tree types to crop tree release treatment were different. Crop tree release increased the average distances of crop trees to the nearest neighboring trees, reducing competition among crop trees by about 68.2%. 3-year stand volume increment for thinning stands had no significant difference with that of control stands although the number of trees was only 81.5% of the control. Crop trees in thinned plots with diameters over than 14 cm reached 18.0% over 3 years, compared with 12.0% for trees without thinning, suggesting that crop tree release benefited the larger individual trees. The pattern of tree locations in thinning plots tended to be random, complying with the rule that tree distribution pattern changes with growth. Crop tree release in C. lanceolata plantation not only promoted the stand growth, but also optimized the stand structure, benefiting crop trees sustained rapid growth and larger diameter trees production.

31 CFR 203.20 - Investment account requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... collector depositaries that accept term investments, investor depositaries, or retainer depositaries. Such... § 203.16(a) for an investor or retainer depositary processing tax deposits through PATAX. (2) EFTPS—(i... procedural instructions. (e) Balance limits—(1) Retainer and investor depositaries. A retainer or investor...

Reoccurrence of retained placenta at vaginal delivery: an observational study.

PubMed

Nikolajsen, Sys; Løkkegaard, Ellen Christine Leth; Bergholt, Thomas

2013-04-01

To estimate the prevalence and validate the diagnosis of retained placenta in nulliparous women and the risk of reoccurrence at subsequent vaginal delivery. Nested cohort study. Department of Gynecology and Obstetrics, university-affiliated teaching hospital. 10 334 nulliparous singleton pregnancies who delivered vaginally at the hospital during 2000-2009. Data from a computerized database information system were used to identify 287 women who had an ICD-10 diagnosis of retained placenta and 572 randomly selected controls matched by the date of first delivery. At chart review the diagnosis was confirmed by: (1) excessive bleeding <30 minutes after delivery without placental separation, (2) placenta not separated 30 minutes after delivery or (3) confirmation of retained placental tissue >2 hours postpartum. Confirmation of the diagnosis and prevalence of retained placenta. Risk of reoccurrence in a subsequent vaginal delivery. The prevalence of retained placenta increased from 2.8 to 7.0% after confirmation according to the set criteria. Of the selected women, 48.4% had a subsequent vaginal delivery. Of these women, 25.3% (23/91) with a previous retained placenta and 5.3% (11/206) without previously retained placenta, experienced retained placenta in subsequent delivery. This corresponds to an adjusted odds ratio of 5.5 (95% confidence interval 2.6-12.7) in the multivariate analysis for recurrence of retained placenta in a subsequent vaginal delivery. The use of the ICD-10 diagnosis of retained placenta underestimated the prevalence. The risk of reoccurrence of retained placenta is significantly increased in a subsequent vaginal delivery. © 2012 The Authors Acta Obstetricia et Gynecologica Scandinavica © 2012 Nordic Federation of Societies of Obstetrics and Gynecology.

Structural stability of posterior retainer design for resin-bonded prostheses: a 3D finite element study.

PubMed

Lin, Jie; Zheng, Zhiqiang; Shinya, Akikazu; Matinlinna, Jukka Pekka; Botelho, Michael George; Shinya, Akiyoshi

2015-09-01

The purpose of this in vitro study was to compare the stress distribution and natural frequency of different shape and thickness retainer designs for maxillary posterior resin-bonded prostheses using finite element (FE) method. A 3D FE model of a three unit posterior resin-bonded prosthesis analysis model was generated. Three different shaped retainer designs, viz. C-shaped (three axial surface wraparounds), D-shaped (three axial surface wraparounds with central groove) and O-shaped (360° wraparounds), and three different thicknesses, viz., 0.4, 0.8, and 1.2 mm, resin-bonded prostheses were used in this study. The resin-bonded prosthesis analysis model was imported into an FE analysis software (ANSYS 10.0, ANSYS, USA) and attribution of material properties. The nodes at the bottom surface of the roots were assigned fixed zero displacement in the three spatial dimensions. A simulated angle of 45° loading of a 100 N force was applied to the node of the pontic lingual cusp surface. The stress distributions and corresponding natural frequencies were analyzed and resolved. The C-shaped retainer for 0.4 mm thickness recorded the greatest von Mises stresses of 71.4 MPa for all three groups. C-shaped, D-shaped and O-shaped retainer presented natural frequencies 3,988, 7,754, and 10,494 Hz, respectively. D-shaped retainer and O-shaped retainer increased natural frequencies and structural rigidity over the traditional C-shaped retainer. The maximum von Mises stresses values of the remaining tooth and prosthesis decreased with greater retainer thickness. D-shaped retainer and O-shaped retainer increased natural frequencies and structural rigidity over the traditional C-shaped retainer.

Gbm.auto: A software tool to simplify spatial modelling and Marine Protected Area planning

PubMed Central

Officer, Rick; Clarke, Maurice; Reid, David G.; Brophy, Deirdre

2017-01-01

Boosted Regression Trees. Excellent for data-poor spatial management but hard to use Marine resource managers and scientists often advocate spatial approaches to manage data-poor species. Existing spatial prediction and management techniques are either insufficiently robust, struggle with sparse input data, or make suboptimal use of multiple explanatory variables. Boosted Regression Trees feature excellent performance and are well suited to modelling the distribution of data-limited species, but are extremely complicated and time-consuming to learn and use, hindering access for a wide potential user base and therefore limiting uptake and usage. BRTs automated and simplified for accessible general use with rich feature set We have built a software suite in R which integrates pre-existing functions with new tailor-made functions to automate the processing and predictive mapping of species abundance data: by automating and greatly simplifying Boosted Regression Tree spatial modelling, the gbm.auto R package suite makes this powerful statistical modelling technique more accessible to potential users in the ecological and modelling communities. The package and its documentation allow the user to generate maps of predicted abundance, visualise the representativeness of those abundance maps and to plot the relative influence of explanatory variables and their relationship to the response variables. Databases of the processed model objects and a report explaining all the steps taken within the model are also generated. The package includes a previously unavailable Decision Support Tool which combines estimated escapement biomass (the percentage of an exploited population which must be retained each year to conserve it) with the predicted abundance maps to generate maps showing the location and size of habitat that should be protected to conserve the target stocks (candidate MPAs), based on stakeholder priorities, such as the minimisation of fishing effort displacement. Gbm.auto for management in various settings By bridging the gap between advanced statistical methods for species distribution modelling and conservation science, management and policy, these tools can allow improved spatial abundance predictions, and therefore better management, decision-making, and conservation. Although this package was built to support spatial management of a data-limited marine elasmobranch fishery, it should be equally applicable to spatial abundance modelling, area protection, and stakeholder engagement in various scenarios. PMID:29216310

Biomagnetic monitoring of heavy metals contamination in deposited atmospheric dust, a case study from Isfahan, Iran.

PubMed

Norouzi, Samira; Khademi, Hossein; Cano, Angel Faz; Acosta, Jose A

2016-05-15

Tree leaves are considered as one of the best biogenic dust collectors due to their ability to trap and retain particulate matter on their surfaces. In this study, the magnetic susceptibility (MS) and the concentration of selected heavy metals of plane tree (Platanus orientalis L.) leaves and deposited atmospheric dust, sampled by an indirect and a direct method, respectively, were determined to investigate the relationships between leaf magnetic parameters and the concentration of heavy metals in deposited atmospheric dust. The objective was to develop a biomagnetic method as an alternative to the common ones used for determining atmospheric heavy metal contaminations. Plane tree leaves were monthly sampled on the 19th of May to November, 2012 (T1-T7), for seven months from 21 different sites in the city of Isfahan, central Iran. Deposited atmospheric dust samples were also collected using flat glass surfaces from the same sites on the same dates, except for T1. MS (χlf, χhf) values in washed (WL) and unwashed leaves (UL) as well as Cu, Fe, Mn, Ni, Pb, and Zn concentrations in UL and deposited atmospheric dust samples were determined. The results showed that the MS content with a biogenic source was low with almost no significant change during the sampling period, while an increasing trend was observed in the MS content of UL samples due to the deposition of heavy metals and magnetic particles on leaf surfaces throughout the plant growth. The latter type of MS content could be reduced through washing off by rain. Most heavy metals examined, as well as the Tomlinson pollution load index (PLI) in UL, showed statistically significant correlations with MS values. The correlation between heavy metals content in atmospheric dust deposited on glass surfaces and leaf MS values was significant for Cu, Fe, Pb, and Zn. Moreover, the similarity observed between the spatial distribution maps of leaf MS and deposited atmospheric dust PLI provided convincing evidence regarding the suitability of the biomagnetic approach as a relatively rapid and inexpensive method for identifying highly polluted urban areas with selected heavy metals, especially those subjected to anthropogenic and other traffic related sources. Copyright © 2016 Elsevier Ltd. All rights reserved.

Dosage and duration effects of nitrogen additions on ectomycorrhizal sporocarp production and functioning: an example from two N-limited boreal forests.

PubMed

Hasselquist, Niles J; Högberg, Peter

2014-08-01

Although it is well known that nitrogen (N) additions strongly affect ectomycorrhizal (EM) fungal community composition, less is known about how different N application rates and duration of N additions affect the functional role EM fungi play in the forest N cycle.We measured EM sporocarp abundance and species richness as well as determined the δ (15)N in EM sporocarps and tree foliage in two Pinus sylvestris forests characterized by short- and long-term N addition histories and multiple N addition treatments. After 20 and 39 years of N additions, two of the long-term N addition treatments were terminated, thereby providing a unique opportunity to examine the temporal recovery of EM sporocarps after cessation of high N loading.In general, increasing N availability significantly reduced EM sporocarp production, species richness, and the amount of N retained in EM sporocarps. However, these general responses were strongly dependent on the application rate and duration of N additions. The annual addition of 20 kg·N·ha(-1) for the past 6 years resulted in a slight increase in the production and retention of N in EM sporocarps, whereas the addition of 100 kg·N·ha(-1)·yr(-1) during the same period nearly eliminated EM sporocarps. In contrast, long-term additions of N at rates of ca. 35 or 70 kg·N·ha(-1)·yr(-1) for the past 40 years did not eliminate tree carbon allocation to EM sporocarps, although there was a decrease in the abundance and a shift in the dominant EM sporocarp taxa. Despite no immediate recovery, EM sporocarp abundance and species richness approached those of the control 20 years after terminating N additions in the most heavily fertilized treatment, suggesting a recovery of carbon allocation to EM sporocarps after cessation of high N loading.Our results provide evidence for a tight coupling between tree carbon allocation to and N retention in EM sporocarps and moreover highlight the potential use of δ (15)N in EM sporocarps as a relative index of EM fungal sink strength for N. However, nitrogen additions at high dosage rates or over long time periods appear to disrupt this feedback, which could have important ramifications on carbon and nitrogen dynamics in these forested ecosystems.

Chemotactic activity of cotyledons for mononuclear leukocytes related to occurrence of retained placenta in dexamethasone induced parturition in cattle.

PubMed

Benedictus, L; Jorritsma, R; Knijn, H M; Vos, P L A M; Koets, A P

2011-09-15

Induction of parturition with glucocorticosteroids in cattle is used for research purposes, in diseased or injured pregnant cows, and as a management tool to time parturition. A negative side effect of induction of parturition with glucocorticosteroids is the high incidence of retained placenta that occurs after these calvings. Reaction of the maternal immune system against the 'foreign' foetal membranes contributes to the breakdown of the foetal-maternal attachment. Several studies indicate that failure of this immune assisted detachment increases the occurrence of retained placenta. We hypothesized that retained placenta occurring after induction of parturition with glucocorticosteroids is caused by failure of immune assisted detachment of the foetal membranes. The chemotactic activity of cotyledons for mononuclear leukocytes was used as a parameter to see whether immune assisted detachment of the foetal membranes had occurred. Cotyledons were collected from spontaneously calving non-retained placenta cows and from dexamethasone induced non-retained placenta and retained placenta cows. The study showed that the chemotactic activity of cotyledons for mononuclear leukocytes was lower (P < 0.001) in cotyledons obtained from retained placenta cows in which parturition was induced with dexamethasone compared to the chemotactic activity of cotyledons obtained from spontaneously calving non-retained placenta cows, whereas the chemotactic activity of cotyledons obtained from induced non-retained placenta cows was not lower (P = 0.10) than the chemotactic activity of cotyledons obtained from spontaneously calving non-retained placenta cows. We concluded that induction of parturition with dexamethasone causes a failure of immune assisted detachment of the foetal membranes and the accompanying release of chemotactic factors. As a result, the chemotactic activity of cotyledons for mononuclear leukocytes is lower in induced retained placenta cows than in cotyledons from non-retained placenta cows in which successful immune assisted detachment of the foetal membranes occurs. Copyright © 2011 Elsevier Inc. All rights reserved.

[Application of single-retainer all-ceramic resin-bonded fixed partial denture in replacing single anterior tooth].

PubMed

Lili, Yang; Debiao, Du; Ruoyu, Ning; Deying, Chen; Junling, Wu

2017-08-01

Objective In this study, we aimed to evaluate the clinical effect of single-retainer all-ceramic resin-bonded fixed partial denture (RBFPD) on the single anterior tooth loss patients. Methods A total of 20 single-retainer all-ceramic RBFPD
were fabricated and evaluated in a two-year follow-up observation. The restorations were examined on the basis of the American Public Health Association (APHA) criteria. Results A total of 20 single-retainer all-ceramic RBFPD achieved class A evaluation after a six-month follow-up observation. One single-retainer all-ceramic RBFPD was classified as class B for secondary caries after a one-year follow-up observation. After a two-year follow-up observation, one single-retainer all-ceramic RBFPD was classified as class B because of secondary caries, and one single-retainer all-ceramic RBFPD was classified as class B because of fracture. Conclusion Single-retainer all-ceramic RBFPD is a promising and optional method in replacing single anterior tooth.

Correlation between mechanical properties and retained austenite characteristics in a low-carbon medium manganese alloyed steel plate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Jun, E-mail: cjer19841011@163.com; Lv, Mengyang; Tang, Shuai

2015-08-15

The effects of retained austenite characteristics on tensile properties and low-temperature impact toughness have been investigated by means of transmission electron microscopy and X-ray diffraction. It was found that only part of austenite phase formed during heat treating was left at room temperature. Moreover, the film-like retained austenite is displayed between bcc-martensite laths after heat treating at 600 °C, while the block-form retained austenite with thin hcp-martensite laths is observed after heat treating at 650 °C. It has been demonstrated that the film-like retained austenite possesses relatively high thermal and mechanical stability, and it can greatly improve low-temperature impact toughness,more » but its contribution to strain hardening capacity is limited. However, the block-form retained austenite can greatly enhance ultimate tensile strength and strain hardening capacity, but its contribution to low-temperature impact toughness is poor. - Highlights: • Correlation between retained austenite and impact toughness was elucidated. • The impact toughness is related to mechanical stability of retained austenite. • The effect of retained austenite on tensile and impact properties is inconsistent.« less

24 CFR 266.210 - HUD-retained review functions.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 24 Housing and Urban Development 2 2010-04-01 2010-04-01 false HUD-retained review functions. 266.210 Section 266.210 Housing and Urban Development Regulations Relating to Housing and Urban... Program Requirements § 266.210 HUD-retained review functions. Certain functions are retained by the...

17 CFR 256.215 - Appropriated retained earnings.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 17 Commodity and Securities Exchanges 3 2010-04-01 2010-04-01 false Appropriated retained earnings... UTILITY HOLDING COMPANY ACT OF 1935 Liabilities and Other Credit Accounts § 256.215 Appropriated retained earnings. This account shall include the amount of retained earnings which has been appropriated or set...

Stainless hooks to bond lower lingual retainer.

PubMed

Durgekar, Sujala G; Nagaraj, K

2011-01-01

We introduced a simple and economical technique for precise placement of lower lingual retainers. Two stainless steel hooks made of 0.6mm wire are placed interdentally in the embrasure area between canine and lateral incisor bilaterally to lock the retainer wire in the correct position. Etch, rinse and dry the enamel surfaces with the retainer passively in place, then bond the retainer with light-cured adhesive. Hooks are simple to fabricate and eliminate the need for a transfer tray.

Failure Rates of Orthodontic Fixed Lingual Retainers bonded with Two Flowable Light-cured Adhesives: A Comparative Prospective Clinical Trial.

PubMed

Talic, Nabeel F

2016-08-01

This comparative prospective randomized clinical trial examined the in vivo failure rates of fixed mandibular and maxillary lingual retainers bonded with two light-cured flowable composites over 6 months. Consecutive patients were divided into two groups on a 1:1 basis. Two hundred fixed lingual retainers were included, and their failures were followed for 6 months. One group (n = 50) received retainers bonded with a nano-hybrid composite based on nano-optimized technology (Tetric-N-Flow, Ivoclar Vivadent). Another group (n = 50) received retainers bonded with a low viscosity (LV) composite (Transbond Supreme LV, 3M Unitek). There was no significant difference between the overall failure rates of mandibular retainers bonded with Transbond (8%) and those bonded with Tetric-N-Flow (18%). However, the odds ratio for failure using Tetric-N-flow was 2.52-fold greater than that of Transbond. The failure rate of maxillary retainers bonded with Transbond was higher (14%), but not significantly different, than that of maxillary retainers bonded with Tetric-N-flow (10%). There was no significant difference in the estimated mean survival times of the maxillary and mandibular retainers bonded with the two composites. Both types of composites tested in the current study can be used to bond fixed maxillary and mandibular lingual retainers, with low failure rates.

Does Gene Tree Discordance Explain the Mismatch between Macroevolutionary Models and Empirical Patterns of Tree Shape and Branching Times?

PubMed Central

Stadler, Tanja; Degnan, James H.; Rosenberg, Noah A.

2016-01-01

Classic null models for speciation and extinction give rise to phylogenies that differ in distribution from empirical phylogenies. In particular, empirical phylogenies are less balanced and have branching times closer to the root compared to phylogenies predicted by common null models. This difference might be due to null models of the speciation and extinction process being too simplistic, or due to the empirical datasets not being representative of random phylogenies. A third possibility arises because phylogenetic reconstruction methods often infer gene trees rather than species trees, producing an incongruity between models that predict species tree patterns and empirical analyses that consider gene trees. We investigate the extent to which the difference between gene trees and species trees under a combined birth–death and multispecies coalescent model can explain the difference in empirical trees and birth–death species trees. We simulate gene trees embedded in simulated species trees and investigate their difference with respect to tree balance and branching times. We observe that the gene trees are less balanced and typically have branching times closer to the root than the species trees. Empirical trees from TreeBase are also less balanced than our simulated species trees, and model gene trees can explain an imbalance increase of up to 8% compared to species trees. However, we see a much larger imbalance increase in empirical trees, about 100%, meaning that additional features must also be causing imbalance in empirical trees. This simulation study highlights the necessity of revisiting the assumptions made in phylogenetic analyses, as these assumptions, such as equating the gene tree with the species tree, might lead to a biased conclusion. PMID:26968785

Tree Nut Allergies

MedlinePlus

... 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 ...

Placental location, postpartum hemorrhage and retained placenta in women with a previous cesarean section delivery: a prospective cohort study.

PubMed

Belachew, Johanna; Eurenius, Karin; Mulic-Lutvica, Ajlana; Axelsson, Ove

2017-08-01

Women previously giving birth with cesarean section have an increased risk of postpartum hemorrhage (PPH) and retained placenta. The objective of this study was to determine if anterior placental location increased the risk of PPH and retained placenta in such women. We performed a prospective cohort study on 400 women with cesarean section delivery in a previous pregnancy. Ultrasound examinations were performed at gestational week 28-30, and placental location, myometrial thickness, and three-dimensional vascularization index (VI) were recorded. Data on maternal age, parity, BMI, smoking, gestational week at delivery, induction, delivery mode, oxytocin, preeclampsia, PPH, retained placenta, and birth weight were obtained for all women. Outcome measures were PPH (≥1,000 mL) and retained placenta. The overall incidence of PPH was 11.0% and of retained placenta 3.5%. Twenty-three women (11.8%) with anterior placenta had PPH compared to 12 (6.9%) with posterior or fundal locations. The odds ratio was 1.94, but it did not reach statistical significance. There was no significant risk increase for retained placenta in women with anterior placentae. Seven of eight women with placenta previa had PPH, and four had retained placenta. The overall risk of PPH and retained placenta was high for women with previous cesarean section. Anterior location of the placenta in such women tended to impose an increased risk for PPH but no risk increase of retained placenta. Placenta previa in women with previous cesarean section is associated with a high risk for PPH and retained placenta.

7 CFR 1416.4 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... agricultural products. Owner means one who had legal ownership of the trees, bushes, vines, or livestock for... hurricanes. Tree means a tree (including a Christmas tree, ornamental tree, nursery tree, and potted tree...

30 CFR 57.20010 - Retaining dams.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Retaining dams. 57.20010 Section 57.20010 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR METAL AND NONMETAL MINE....20010 Retaining dams. If failure of a water or silt retaining dam will create a hazard, it shall be of...

30 CFR 56.20010 - Retaining dams.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 30 Mineral Resources 1 2011-07-01 2011-07-01 false Retaining dams. 56.20010 Section 56.20010 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR METAL AND NONMETAL MINE... Retaining dams. If failure of a water or silt retaining dam will create a hazard, it shall be of substantial...

30 CFR 57.20010 - Retaining dams.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Retaining dams. 57.20010 Section 57.20010 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR METAL AND NONMETAL MINE....20010 Retaining dams. If failure of a water or silt retaining dam will create a hazard, it shall be of...

30 CFR 56.20010 - Retaining dams.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Retaining dams. 56.20010 Section 56.20010 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR METAL AND NONMETAL MINE... Retaining dams. If failure of a water or silt retaining dam will create a hazard, it shall be of substantial...

18 CFR 367.4390 - Account 439, Adjustments to retained earnings.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Account 439, Adjustments to retained earnings. 367.4390 Section 367.4390 Conservation of Power and Water Resources FEDERAL... NATURAL GAS ACT Retained Earnings Accounts § 367.4390 Account 439, Adjustments to retained earnings. (a...

12 CFR 704.19 - Wholesale corporate credit unions.

Code of Federal Regulations, 2010 CFR

2010-01-01

...) Earnings retention requirement. A wholesale corporate credit union must increase retained earnings if the prior month-end retained earnings ratio is less than 1 percent. (1) Its retained earnings must increase... month-end retained earnings ratio is less than 1 percent and the core capital ratio is less than 3...

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

PubMed

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.

MASTtreedist: visualization of tree space based on maximum agreement subtree.

PubMed

Huang, Hong; Li, Yongji

2013-01-01

Phylogenetic tree construction process might produce many candidate trees as the "best estimates." As the number of constructed phylogenetic trees grows, the need to efficiently compare their topological or physical structures arises. One of the tree comparison's software tools, the Mesquite's Tree Set Viz module, allows the rapid and efficient visualization of the tree comparison distances using multidimensional scaling (MDS). Tree-distance measures, such as Robinson-Foulds (RF), for the topological distance among different trees have been implemented in Tree Set Viz. New and sophisticated measures such as Maximum Agreement Subtree (MAST) can be continuously built upon Tree Set Viz. MAST can detect the common substructures among trees and provide more precise information on the similarity of the trees, but it is NP-hard and difficult to implement. In this article, we present a practical tree-distance metric: MASTtreedist, a MAST-based comparison metric in Mesquite's Tree Set Viz module. In this metric, the efficient optimizations for the maximum weight clique problem are applied. The results suggest that the proposed method can efficiently compute the MAST distances among trees, and such tree topological differences can be translated as a scatter of points in two-dimensional (2D) space. We also provide statistical evaluation of provided measures with respect to RF-using experimental data sets. This new comparison module provides a new tree-tree pairwise comparison metric based on the differences of the number of MAST leaves among constructed phylogenetic trees. Such a new phylogenetic tree comparison metric improves the visualization of taxa differences by discriminating small divergences of subtree structures for phylogenetic tree reconstruction.

Characterizing the phylogenetic tree-search problem.

PubMed

Money, Daniel; Whelan, Simon

2012-03-01

Phylogenetic trees are important in many areas of biological research, ranging from systematic studies to the methods used for genome annotation. Finding the best scoring tree under any optimality criterion is an NP-hard problem, which necessitates the use of heuristics for tree-search. Although tree-search plays a major role in obtaining a tree estimate, there remains a limited understanding of its characteristics and how the elements of the statistical inferential procedure interact with the algorithms used. This study begins to answer some of these questions through a detailed examination of maximum likelihood tree-search on a wide range of real genome-scale data sets. We examine all 10,395 trees for each of the 106 genes of an eight-taxa yeast phylogenomic data set, then apply different tree-search algorithms to investigate their performance. We extend our findings by examining two larger genome-scale data sets and a large disparate data set that has been previously used to benchmark the performance of tree-search programs. We identify several broad trends occurring during tree-search that provide an insight into the performance of heuristics and may, in the future, aid their development. These trends include a tendency for the true maximum likelihood (best) tree to also be the shortest tree in terms of branch lengths, a weak tendency for tree-search to recover the best tree, and a tendency for tree-search to encounter fewer local optima in genes that have a high information content. When examining current heuristics for tree-search, we find that nearest-neighbor-interchange performs poorly, and frequently finds trees that are significantly different from the best tree. In contrast, subtree-pruning-and-regrafting tends to perform well, nearly always finding trees that are not significantly different to the best tree. Finally, we demonstrate that the precise implementation of a tree-search strategy, including when and where parameters are optimized, can change the character of tree-search, and that good strategies for tree-search may combine existing tree-search programs.

An efficient and extensible approach for compressing phylogenetic trees

PubMed Central

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. PMID:22165819

An efficient and extensible approach for compressing phylogenetic trees.

PubMed

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.

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

PubMed Central

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 well as phylogenetic error may contribute to gene tree discord. In experiments, the MulRF method estimated species trees accurately and quickly, demonstrating MulRF as an efficient alternative approach for phylogenetic inference from large-scale genomic data sets. PMID:24180377

Thresholds of Disturbance: Land Management Effects on Vegetation and Nitrogen Dynamics

DTIC Science & Technology

2005-03-31

Legume 3 18 0.0435 Rhus aromatica Shrub 2 35 0.0002 Aesculus pavia Tree 0 10 0.0198 Celtis sp. Tree 1 30 0.0002 Crataegus sp. Tree 13 62 0.0001...Shrub 37 63 0.0001 Aesculus pavia Tree 0 12 0.0043 Cercis canadensis Tree 0 13 0.0021 Crataegus sp. Tree 22 49 0.0222 Fraxinus americana Tree 0 11... Aesculus pavia Tree 0 15 0.0126 Ilex opaca Tree 0 27 0.0003 Liquidambar styraciflua Tree 18 75 0.0001 Quercus falcata Tree 9 79 0.0001 Quercus

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

PubMed

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

Encoding phylogenetic trees in terms of weighted quartets.

PubMed

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.

TreeCmp: Comparison of Trees in Polynomial Time

PubMed Central

Bogdanowicz, Damian; Giaro, Krzysztof; Wróbel, Borys

2012-01-01

When a phylogenetic reconstruction does not result in one tree but in several, tree metrics permit finding out how far the reconstructed trees are from one another. They also permit to assess the accuracy of a reconstruction if a true tree is known. TreeCmp implements eight metrics that can be calculated in polynomial time for arbitrary (not only bifurcating) trees: four for unrooted (Matching Split metric, which we have recently proposed, Robinson-Foulds, Path Difference, Quartet) and four for rooted trees (Matching Cluster, Robinson-Foulds cluster, Nodal Splitted and Triple). TreeCmp is the first implementation of Matching Split/Cluster metrics and the first efficient and convenient implementation of Nodal Splitted. It allows to compare relatively large trees. We provide an example of the application of TreeCmp to compare the accuracy of ten approaches to phylogenetic reconstruction with trees up to 5000 external nodes, using a measure of accuracy based on normalized similarity between trees.

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

NASA Technical Reports Server (NTRS)

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.

There's Life in Hazard Trees

Treesearch

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...

Audubon Tree Study Program.

ERIC Educational Resources Information Center

National Audubon Society, New York, NY.

Included are an illustrated student reader, "The Story of Trees," a leaders' guide, and a large tree chart with 37 colored pictures. The student reader reviews several aspects of trees: a definition of a tree; where and how trees grow; flowers, pollination and seed production; how trees make their food; how to recognize trees; seasonal changes;…

Heterogeneous Compression of Large Collections of Evolutionary Trees.

PubMed

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.

Retaining African Americans in Higher Education: Challenging Paradigms for Retaining Students, Faculty and Administrators.

ERIC Educational Resources Information Center

Jones, Lee, Ed.

This collection discusses some of the issues surrounding the retention of African Americans in higher education, and it challenges traditional paradigms for retaining African American students, administrators, and faculty at predominantly White colleges. The chapters of part 1, "Retaining African-American Students," are: (1) "Creating an Affirming…

Strain characteristics of Marburg double crown-retained implant overdentures compared with bar and ball-retained implant overdentures, with and without a rigid major connector.

PubMed

Kazokoğlu, F Şehnaz; Akaltan, Funda

2014-12-01

It is hard to identify the most favorable retainer type and the denture design when considering strain levels around implants and in edentulous ridges for implant overdentures (IOVD). The purpose of this study was to evaluate the strain transmitted to the implants and edentulous ridges by Marburg double crown (MDC)-retained IOVD as opposed to bar and ball-retained IOVD and the efficiency of a rigid major connector in the maxilla. An in vitro maxillary model was prepared with 4 implants, with strain gauges placed distally to each implant and also in the anterior and posterior edentulous ridges. Five overdentures were fabricated for each MDC and each ball and bar attachment retainers. Vertical loads of 280 N were applied bilaterally on the first molar region. Then the palatal bars of each IOVD were disconnected, and loading procedures were repeated for the prostheses. No significant difference was observed among the MDC and the bar and ball-retained IOVD, with and without a rigid bar according to the data taken from both the implants and edentulous ridges. However, when the strain values attained from each strain gauge separately were considered, a slight difference was observed around the implants of ball-retained overdentures and in the edentulous ridges of MDC-retained overdentures. Within the limitations of this in vitro study, MDC-retained maxillary overdentures with 4 parallel and symmetrically placed implants can be used safely without a rigid major connector as with bar and ball-retained IOVD with regard to the strains generated in the edentulous ridge and around implants. Copyright © 2014 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

Placental location, postpartum hemorrhage and retained placenta in women with a previous cesarean section delivery: a prospective cohort study

PubMed Central

Belachew, Johanna; Eurenius, Karin; Mulic-Lutvica, Ajlana; Axelsson, Ove

2017-01-01

Objective Women previously giving birth with cesarean section have an increased risk of postpartum hemorrhage (PPH) and retained placenta. The objective of this study was to determine if anterior placental location increased the risk of PPH and retained placenta in such women. Materials and methods We performed a prospective cohort study on 400 women with cesarean section delivery in a previous pregnancy. Ultrasound examinations were performed at gestational week 28–30, and placental location, myometrial thickness, and three-dimensional vascularization index (VI) were recorded. Data on maternal age, parity, BMI, smoking, gestational week at delivery, induction, delivery mode, oxytocin, preeclampsia, PPH, retained placenta, and birth weight were obtained for all women. Outcome measures were PPH (≥1,000 mL) and retained placenta. Results The overall incidence of PPH was 11.0% and of retained placenta 3.5%. Twenty-three women (11.8%) with anterior placenta had PPH compared to 12 (6.9%) with posterior or fundal locations. The odds ratio was 1.94, but it did not reach statistical significance. There was no significant risk increase for retained placenta in women with anterior placentae. Seven of eight women with placenta previa had PPH, and four had retained placenta. Conclusions The overall risk of PPH and retained placenta was high for women with previous cesarean section. Anterior location of the placenta in such women tended to impose an increased risk for PPH but no risk increase of retained placenta. Placenta previa in women with previous cesarean section is associated with a high risk for PPH and retained placenta. PMID:28826360

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

Code of Federal Regulations, 2011 CFR

2011-07-01

... 36 Parks, Forests, and Public Property 2 2011-07-01 2011-07-01 false Exchange of trees or portions of trees. 223.4 Section 223.4 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF... PRODUCTS General Provisions § 223.4 Exchange of trees or portions of trees. Trees or portions of trees may...

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

Code of Federal Regulations, 2012 CFR

2012-07-01

... 36 Parks, Forests, and Public Property 2 2012-07-01 2012-07-01 false Exchange of trees or portions of trees. 223.4 Section 223.4 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF... PRODUCTS General Provisions § 223.4 Exchange of trees or portions of trees. Trees or portions of trees may...

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

Code of Federal Regulations, 2014 CFR

2014-07-01

... 36 Parks, Forests, and Public Property 2 2014-07-01 2014-07-01 false Exchange of trees or portions of trees. 223.4 Section 223.4 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF... PRODUCTS General Provisions § 223.4 Exchange of trees or portions of trees. Trees or portions of trees may...

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

Code of Federal Regulations, 2013 CFR

2013-07-01

... 36 Parks, Forests, and Public Property 2 2013-07-01 2013-07-01 false Exchange of trees or portions of trees. 223.4 Section 223.4 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF... PRODUCTS General Provisions § 223.4 Exchange of trees or portions of trees. Trees or portions of trees may...

[The relationship between job retainment and job satisfaction of hospital nurses].

PubMed

Lee, H W

1994-01-01

The purpose of this study was to describe the job retainment factors and the level of job satisfaction, and to identify the relationship between job retainment and the level of job satisfaction among the registered nurses working in hospitals. Four hundred eight registered nurses currently employed at 8 hospitals in Seoul were surveyed for the study. The 39 item, 5 point likert scale questionnaire was developed by the researcher. The internal consistency of job satisfaction was. 86 and that of job retainment was. 90 in Cronbach's alpha test. The data sas collected from July 15 to July 30, 1993. The SPSS/PC+statistical program was used for data analysis. The descriptive analysis of the characteristics of the subjects, the level of job satisfaction and the job retainment factors was done. The relationship between the job satisfaction level and the job retainment factors was tested with the Pearson Correlation Coefficient analysis, and the differences of job retainment scores among the sample was tested with t-test and ANOVA. The results of the study were summarized. 1. The mean age of the subjects was 29.7 years, 41.7% of them were married. 71.1% of them were 3 years course graduates, 71.8% of them were staff nurses, and the mean duration of experience was 6 years. 2. The factors related to professionalism (3.43), society (3.31), and interpersonal relationship (3.29) were significant in job retainment. The maximum score was 5.0 Two other factors, personal (3.05) and organization (2.83) factors, also showed relatively high scores. 3. The factors to the job satisfaction showed similar pattern as job retainment: professionalism (3.47), society (3.33), finance (3.31), interpersonal relationship (3.02), and organization (2.72). 4. Society related factors (r = .7420, p < .001) and professionalism (r = .7249, p < .001) had high correlation with job retainment. Personal (r = .6372, p < .001) and organizational (r = .3597, p < .001) factors had moderate relationship to job retainment. Finance (r = .3597, p < .001) had significant but weak relationship to job retainment. 5. Age, marital status, job position, departmental involvement, experience, and continuity of employment of the sample showed significant differences in job retainment. However, the period of job retainment, number of children, educational level, type of hospital, previous employment experience were not significant. 6. Individuals older than 40 years of age, who were married, who held the position of charge or head nurse position, who worked in central supply or nursing administration showed significantly high job retainment score.4+ among nurses.

7 CFR 1416.701 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 2005 Hurricane Tree Assistance Program § 1416.701 Definitions. Application means the “2005 Hurricane Tree Assistance Program” Application form. Fruit tree means a woody perennial plant having a single... acreage of the same crop of trees (including Christmas trees, ornamental trees, nursery trees, and potted...

A throughfall collection method using mixed bed ion exchange resin columns.

PubMed

Fenn, Mark E; Poth, Mark A; Arbaugh, Michael J

2002-01-15

Measurement of ionic deposition in throughfall is a widely used method for measuring deposition inputs to the forest floor. Many studies have been published, providing a large database of throughfall deposition inputs to forests. However, throughfall collection and analysis is labor intensive and expensive because of the large number of replicate collectors needed and because sample collection and chemical analyses are required on a stochastic precipitation event-based schedule. Therefore we developed and tested a throughfall collector system using a mixed bed ion exchange resin column. We anticipate that this method will typically require only one to three samplings per year. With this method, bulk deposition and bulk throughfall are collected by a funnel or snow tube and ions are retained as the solution percolates through the resin column. Ions retained by the resin are then extracted in the same column with 2 N KCl and analyzed for nitrate and ammonium. Deposition values in throughfall from conventional throughfall solution collectors and colocated ion exchange samplers were not significantly different during consecutive 3- and 4-month exposure periods at a high (Camp Paivika; >35 kg N ha(-1) year(-1)) and a low deposition (Barton Flats; 5-9 kg N ha(-1) year(-1)) site in the San Bernardino Mountains in southern California. N deposition in throughfall under mature pine trees at Camp Paivika after 7 months of exposure was extremely high (87 and 92 kg ha-1 based on the two collector types) compared to Barton Flats (11 and 13 kg ha(-1)). A large proportion of the N deposited in throughfall at Camp Paivika occurred as fog drip, demonstrating the importance of fog deposition as an input source of N at this site. By comparison, bulk deposition rates in open areas were 5.1 and 5.4 kg ha(-1) at Camp Paivika based on the two collector types, and 1.9 and 3.0 kg ha(-1) at Barton Flats.

The Histone Modification H3K27me3 Is Retained after Gene Duplication and Correlates with Conserved Noncoding Sequences in Arabidopsis

PubMed Central

Berke, Lidija; Snel, Berend

2014-01-01

The histone modification H3K27me3 is involved in repression of transcription and plays a crucial role in developmental transitions in both animals and plants. It is deposited by PRC2 (Polycomb repressive complex 2), a conserved protein complex. In Arabidopsis thaliana, H3K27me3 is found at 15% of all genes. These tend to encode transcription factors and other regulators important for development. However, it is not known how PRC2 is recruited to target loci nor how this set of target genes arose during Arabidopsis evolution. To resolve the latter, we integrated A. thaliana gene families with five independent genome-wide H3K27me3 data sets. Gene families were either significantly enriched or depleted of H3K27me3, showing a strong impact of shared ancestry to H3K27me3 distribution. To quantify this, we performed ancestral state reconstruction of H3K27me3 on phylogenetic trees of gene families. The set of H3K27me3-marked genes changed less than expected by chance, suggesting that H3K27me3 was retained after gene duplication. This retention suggests that the PRC2-recruiting signal could be encoded in the DNA and also conserved among certain duplicated genes. Indeed, H3K27me3-marked genes were overrepresented among paralogs sharing conserved noncoding sequences (CNSs) that are enriched with transcription factor binding sites. The association of upstream CNSs with H3K27me3-marked genes represents the first genome-wide connection between H3K27me3 and potential regulatory elements in plants. Thus, we propose that CNSs likely function as part of the PRC2 recruitment in plants. PMID:24567304

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

PubMed

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.

Liana competition with tropical trees varies seasonally but not with tree species identity.

PubMed

Leonor, Alvarez-Cansino; Schnitzer, Stefan A; Reid, Joseph P; Powers, Jennifer S

2015-01-01

Lianas in tropical forests compete intensely with trees for above- and belowground resources and limit tree growth and regeneration. Liana competition with adult canopy trees may be particularly strong, and, if lianas compete more intensely with some tree species than others, they may influence tree species composition. We performed the first systematic, large-scale liana removal experiment to assess the competitive effects of lianas on multiple tropical tree species by measuring sap velocity and growth in a lowland tropical forest in Panama. Tree sap velocity increased 60% soon after liana removal compared to control trees, and tree diameter growth increased 25% after one year. Although tree species varied in their response to lianas, this variation was not significant, suggesting that lianas competed similarly with all tree species examined. The effect of lianas on tree sap velocity was particularly strong during the dry season, when soil moisture was low, suggesting that lianas compete intensely with trees for water. Under the predicted global change scenario of increased temperature and drought intensity, competition from lianas may become more prevalent in seasonal tropical forests, which, according to our data, should have a negative effect on most tropical tree species.

ColorTree: a batch customization tool for phylogenic trees

PubMed Central

Chen, Wei-Hua; Lercher, Martin J

2009-01-01

Background 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. Findings 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. Conclusion ColorTree allows efficient and flexible visual customization of large tree sets through the application of a user-supplied configuration file to multiple tree files. PMID:19646243

ColorTree: a batch customization tool for phylogenic trees.

PubMed

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.

26 CFR 20.2036-1 - Transfers with retained life estate.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 26 Internal Revenue 14 2010-04-01 2010-04-01 false Transfers with retained life estate. 20.2036-1... Transfers with retained life estate. (a) In general. A decedent's gross estate includes under section 2036... money or money's worth (see § 20.2043-1), if the decedent retained or reserved— (1) For his life; (2...

26 CFR 20.2036-1 - Transfers with retained life estate.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 26 Internal Revenue 14 2011-04-01 2010-04-01 true Transfers with retained life estate. 20.2036-1... Transfers with retained life estate. (a) In general. A decedent's gross estate includes under section 2036... money or money's worth (see § 20.2043-1), if the decedent retained or reserved— (1) For his life; (2...

25 CFR 1000.400 - Can a Tribe/Consortium retain savings from programs?

Code of Federal Regulations, 2013 CFR

2013-04-01

... 25 Indians 2 2013-04-01 2013-04-01 false Can a Tribe/Consortium retain savings from programs? 1000...-DETERMINATION AND EDUCATION ACT Miscellaneous Provisions § 1000.400 Can a Tribe/Consortium retain savings from programs? Yes, for BIA programs, the Tribe/Consortium may retain savings for each fiscal year during which...

5 CFR 536.309 - Converting retained rates on May 1, 2005.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Converting retained rates on May 1, 2005... REGULATIONS GRADE AND PAY RETENTION Pay Retention § 536.309 Converting retained rates on May 1, 2005. (a) Consistent with section 301(d)(2) of Public Law 108-411, an agency must convert an employee's retained rate...

5 CFR 536.305 - Adjusting an employee's retained rate when a pay schedule is adjusted.

Code of Federal Regulations, 2010 CFR

2010-01-01

... conversion under § 536.303(b) or any other simultaneous pay action. The retained rate adjustment under... new retained rate must be determined under the geographic conversion rule in § 536.303(b). (4... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false Adjusting an employee's retained rate...

17 CFR 240.17g-2 - Records to be made and retained by nationally recognized statistical rating organizations.

Code of Federal Regulations, 2010 CFR

2010-04-01

... retained by nationally recognized statistical rating organizations. 240.17g-2 Section 240.17g-2 Commodity... Recognized Statistical Rating Organizations § 240.17g-2 Records to be made and retained by nationally recognized statistical rating organizations. (a) Records required to be made and retained. A nationally...

Spin bearing retainer design optimization

NASA Technical Reports Server (NTRS)

Boesiger, Edward A.; Warner, Mark H.

1991-01-01

The dynamics behavior of spin bearings for momentum wheels (control-moment gyroscope, reaction wheel assembly) is critical to satellite stability and life. Repeated bearing retainer instabilities hasten lubricant deterioration and can lead to premature bearing failure and/or unacceptable vibration. These instabilities are typically distinguished by increases in torque, temperature, audible noise, and vibration induced by increases into the bearing cartridge. Ball retainer design can be optimized to minimize these occurrences. A retainer was designed using a previously successful smaller retainer as an example. Analytical methods were then employed to predict its behavior and optimize its configuration.

7 CFR 1416.4 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... perished or suffered losses due to an eligible hurricane. Tier means the geographic bands of damage... hurricanes. Tree means a tree (including a Christmas tree, ornamental tree, nursery tree, and potted tree...

7 CFR 1416.4 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... perished or suffered losses due to an eligible hurricane. Tier means the geographic bands of damage... hurricanes. Tree means a tree (including a Christmas tree, ornamental tree, nursery tree, and potted tree...

7 CFR 1416.4 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... perished or suffered losses due to an eligible hurricane. Tier means the geographic bands of damage... hurricanes. Tree means a tree (including a Christmas tree, ornamental tree, nursery tree, and potted tree...

7 CFR 1416.4 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... perished or suffered losses due to an eligible hurricane. Tier means the geographic bands of damage... hurricanes. Tree means a tree (including a Christmas tree, ornamental tree, nursery tree, and potted tree...

Technical Tree Climbing.

ERIC Educational Resources Information Center

Jenkins, Peter

Tree climbing offers a safe, inexpensive adventure sport that can be performed almost anywhere. Using standard procedures practiced in tree surgery or rock climbing, almost any tree can be climbed. Tree climbing provides challenge and adventure as well as a vigorous upper-body workout. Tree Climbers International classifies trees using a system…

47 CFR 32.4550 - Retained earnings.

Code of Federal Regulations, 2010 CFR

2010-10-01

... FOR TELECOMMUNICATIONS COMPANIES Instructions for Balance Sheet Accounts § 32.4550 Retained earnings. (a) This account shall include the undistributed balance of retained earnings derived from the...

The potential of the tree water potential.

PubMed

Steppe, Kathy

2018-06-12

Non-invasive quantification of tree water potential is one of the grand challenges for assessing the fate of trees and forests in the coming decades. Tree water potential is a robust and direct indicator of tree water status and is preferably used to track how trees, forests and vegetation in general respond to changes in climate and drought. In this issue of Tree Physiology, Dietrich et al. (2018) predict the daily canopy water potential of mature temperate trees from tree water deficit derived from stem diameter variation measurements.

[Difference of water relationships of poplar trees in Zhangbei County, Hebei, China based on stable isotope and thermal dissipation method].

PubMed

Miao, Bo; Meng, Ping; Zhang, Jin Song; He, Fang Jie; Sun, Shou Jia

2017-07-18

The water sources and transpiration of poplar trees in Zhangbei County were measured using stable hydrogen isotope and thermal dissipation method. The differences in water relationships between dieback and non-dieback poplar trees were analyzed. The results showed that the dieback trees mainly used shallow water from 0-30 cm soil layer during growing season while the non-dieback trees mainly used water from 30-80 cm soil layer. There was a significant difference in water source between them. The non-dieback trees used more water from middle and deep soil layers than that of the dieback trees during the dry season. The percentage of poplar trees using water from 0-30 cm soil layer increased in wet season, and the increase of dieback trees was higher than that of non-dieback trees. The contributions of water from 30-180 cm soil layer of dieback and non-dieback trees both decreased in wet season. The sap flow rate of non-dieback trees was higher than that of dieback trees. There was a similar variation tend of sap flow rate between dieback and non-dieback trees in different weather conditions, but the start time of sap flow of non-dieback trees was earlier than that of dieback trees. Correlation analysis showed that the sap flow rate of either dieback or non-dieback poplar trees strongly related to soil temperature, wind speed, photosynthetically active radiation, relative humidity and air temperature. The sap flow rate of die-back poplar trees strongly negatively related to soil temperature and relative humidity, and strongly positively related to the other factors. The sap flow rate of non-dieback poplar trees only strongly negatively related to relative humidity but positively related to the other factors. The results revealed transpiration of both poplar trees was easily affected by environmental factors. The water consumption of dieback trees was less than non-dieback trees because the cumulative sap flow amount of dieback trees was lower. Reduced transpiration of dieback trees couldn't help to prevent poplar forest declining due to shallow water source.

Tree Rings: Timekeepers of the Past.

ERIC Educational Resources Information Center

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…

Terpenoid Variations within and among Half-Sibling Avocado Trees, Persea americana Mill. (Lauraceae)

PubMed Central

Niogret, Jerome; Epsky, Nancy D.; Schnell, Raymond J.; Boza, Edward J.; Kendra, Paul E.; Heath, Robert R.

2013-01-01

Chemical analyses were conducted to determine the qualitative and quantitative differences in monoterpenes and sesquiterpenes in plant material from avocado trees, Persea americana Mill. (Lauraceae). The initial study analyzed plant material sampled from the trunk to the leaves through different branch diameters to quantify proximo-distal spatial differences within a tree. All trees were seedlings initiated from a single maternal tree. Two-way analysis of variance was conducted on 34 chemicals that comprised at least 3% of the total chemical content of at least one tree and/or location within a tree. There were significant interactions between genotype and location sampled for most chemicals. Parentage analysis using microsatellite molecular markers (SSR's) determined that the four trees had three fathers and that they represented two full-siblings and two half-sibling trees. Descriptive discriminant analysis found that both genotype and location within a tree could be separated based on chemical content, and that the chemical content from full-siblings tended to be more similar than chemical content from half-siblings. To further explore the relationship between genetic background and chemical content, samples were analyzed from leaf material from 20 trees that included two sets of full-sibling seedling trees, the maternal tree and the surviving paternal tree. Descriptive discriminant analysis found good separation between the two full-sibling groups, and that the separation was associated with chemistry of the parental trees. Six groups of chemicals were identified that explained the variation among the trees. We discuss the results in relation to the discrimination process used by wood-boring insects for site-selection on host trees, for tree selection among potential host trees, and the potential use of terpenoid chemical content in chemotaxonomy of avocado trees. PMID:24039994

Terpenoid variations within and among half-sibling avocado trees, Persea americana Mill. (Lauraceae).

PubMed

Niogret, Jerome; Epsky, Nancy D; Schnell, Raymond J; Boza, Edward J; Kendra, Paul E; Heath, Robert R

2013-01-01

Chemical analyses were conducted to determine the qualitative and quantitative differences in monoterpenes and sesquiterpenes in plant material from avocado trees, Persea americana Mill. (Lauraceae). The initial study analyzed plant material sampled from the trunk to the leaves through different branch diameters to quantify proximo-distal spatial differences within a tree. All trees were seedlings initiated from a single maternal tree. Two-way analysis of variance was conducted on 34 chemicals that comprised at least 3% of the total chemical content of at least one tree and/or location within a tree. There were significant interactions between genotype and location sampled for most chemicals. Parentage analysis using microsatellite molecular markers (SSR's) determined that the four trees had three fathers and that they represented two full-siblings and two half-sibling trees. Descriptive discriminant analysis found that both genotype and location within a tree could be separated based on chemical content, and that the chemical content from full-siblings tended to be more similar than chemical content from half-siblings. To further explore the relationship between genetic background and chemical content, samples were analyzed from leaf material from 20 trees that included two sets of full-sibling seedling trees, the maternal tree and the surviving paternal tree. Descriptive discriminant analysis found good separation between the two full-sibling groups, and that the separation was associated with chemistry of the parental trees. Six groups of chemicals were identified that explained the variation among the trees. We discuss the results in relation to the discrimination process used by wood-boring insects for site-selection on host trees, for tree selection among potential host trees, and the potential use of terpenoid chemical content in chemotaxonomy of avocado trees.

Current and Potential Tree Locations in Tree Line Ecotone of Changbai Mountains, Northeast China: The Controlling Effects of Topography

PubMed Central

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. PMID:25170918

The relationship between tree growth patterns and likelihood of mortality: A study of two tree species in the Sierra Nevada

USGS Publications Warehouse

Das, A.J.; Battles, J.J.; Stephenson, N.L.; van Mantgem, P.J.

2007-01-01

We examined mortality of Abies concolor (Gord. & Glend.) Lindl. (white fir) and Pinus lambertiana Dougl. (sugar pine) by developing logistic models using three growth indices obtained from tree rings: average growth, growth trend, and count of abrupt growth declines. For P. lambertiana, models with average growth, growth trend, and count of abrupt declines improved overall prediction (78.6% dead trees correctly classified, 83.7% live trees correctly classified) compared with a model with average recent growth alone (69.6% dead trees correctly classified, 67.3% live trees correctly classified). For A. concolor, counts of abrupt declines and longer time intervals improved overall classification (trees with DBH ???20 cm: 78.9% dead trees correctly classified and 76.7% live trees correctly classified vs. 64.9% dead trees correctly classified and 77.9% live trees correctly classified; trees with DBH <20 cm: 71.6% dead trees correctly classified and 71.0% live trees correctly classified vs. 67.2% dead trees correctly classified and 66.7% live trees correctly classified). In general, count of abrupt declines improved live-tree classification. External validation of A. concolor models showed that they functioned well at stands not used in model development, and the development of size-specific models demonstrated important differences in mortality risk between understory and canopy trees. Population-level mortality-risk models were developed for A. concolor and generated realistic mortality rates at two sites. Our results support the contention that a more comprehensive use of the growth record yields a more robust assessment of mortality risk. ?? 2007 NRC.

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

PubMed

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.

Usefulness of DIGE for the detection of protein profile in retained and released bovine placental tissues.

PubMed

Kankofer, M; Wawrzykowski, J; Miller, I; Hoedemaker, M

2015-02-01

Regardless intensive research, the etiology and mechanisms of retention of fetal membranes in cows, still require elucidation. In our research approach, difference in gel electrophoresis (DIGE) and matrix-assisted laser desorption/ionization (MALDI) identification were used to obtain first results on protein profile of bovine placental membranes which were properly released or retained for more than 12 h after parturition. Placentomes from 6 cows that released placenta and from 6 cows that retained fetal membranes were homogenized, fluorescence labeled and subjected to DIGE. Selected spots that significantly differed between retained and released placenta as well as spots with constant appearance were identified by MALDI. This allowed identification of the following proteins with high statistical reliability: Transforming growth factor beta 2 - high expression in maternal and fetal part of retained fetal membranes, Short transient receptor potential channel 5 -high expression in maternal part of retained and not retained fetal membranes, Rab GDP dissociation inhibitor beta - high expression in fetal part of retained and not retained fetal membranes, Proline dehydrogenase 2 - similar expression in all examined samples, Ras-related protein Rab-7b -high expression only in maternal part of not retained fetal membranes. Up to now, these proteins have not been considered as possibly important molecules for the separation/retention of fetal membranes, but their biological roles may suggest it. Further studies are necessary to establish a full profile of bovine placental proteins and define target molecules that may be involved in separation/retention of fetal membranes. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

PubMed

Feragen, Aasa; Owen, Megan; Petersen, Jens; Wille, Mathilde M W; Thomsen, Laura H; Dirksen, Asger; de Bruijne, Marleen

2013-01-01

Statistical analysis of anatomical trees is hard to perform due to differences in the topological structure of the trees. In this paper we define statistical properties of leaf-labeled anatomical trees with geometric edge attributes by considering the anatomical trees as points in the geometric space of leaf-labeled trees. This tree-space is a geodesic metric space where any two trees are connected by a unique shortest path, which corresponds to a tree deformation. However, tree-space is not a manifold, and the usual strategy of performing statistical analysis in a tangent space and projecting onto tree-space is not available. Using tree-space and its shortest paths, a variety of statistical properties, such as mean, principal component, hypothesis testing and linear discriminant analysis can be defined. For some of these properties it is still an open problem how to compute them; others (like the mean) can be computed, but efficient alternatives are helpful in speeding up algorithms that use means iteratively, like hypothesis testing. In this paper, we take advantage of a very large dataset (N = 8016) to obtain computable approximations, under the assumption that the data trees 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 healthy ones. Software is available from http://image.diku.dk/aasa/software.php.

The effect of prior sandblasting of the wire on the shear bond strength of two different types of lingual retainers.

PubMed

Kilinç, Delal Dara; Sayar, Gülşilay

2018-04-07

The aim of this study was to evaluate the effect of total surface sandblasting on the shear bond strength of two different retainer wires. The null hypothesis was that there is no difference in the bond strength of the two types of lingual retainer wires when they are sandblasted. One hundred and sixty human premolar teeth were equally divided into four groups (n=40). A pair of teeth was embedded in self-curing acrylic resin and polished. Retainer wires were applied on the etched and rinsed surfaces of the teeth. Four retainers were used: group 1: braided retainer (0.010×0.028″, Ortho Technology); group 2: sandblasted braided retainer (0.010×0.028″, Ortho Technology); group 3: coaxial retainer (0.0215″ Coaxial, 3M) and group 4: sandblasted coaxial retainer (0.0215″ Coaxial, 3M). The specimens were tested using a universal test machine in shear mode with a crosshead speed of one mm/min. One-way analysis of variance (Anova) was used to determine the significant differences among the groups. There was no significant difference (P=0.117) among the groups according to this test. The null hypothesis was accepted. There was no statistically significant difference among the shear bond strength values of the four groups. Copyright © 2018 CEO. Published by Elsevier Masson SAS. All rights reserved.

The Practice and Effects of a School District's Retention Policies

ERIC Educational Resources Information Center

Hamlin, Christine

2013-01-01

During conferences to decide whether or not to retain a child, usually two questions are asked. The first is, "Will retention bring success in school?" The other is, "If we retain him, will he perform better in school than if we don't retain him?" The goal of this research was to see if retained students would make enough…

Trees are good, but…

Treesearch

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...

Efficient tree tensor network states (TTNS) for quantum chemistry: Generalizations of the density matrix renormalization group algorithm

NASA Astrophysics Data System (ADS)

Nakatani, Naoki; Chan, Garnet Kin-Lic

2013-04-01

We investigate tree tensor network states for quantum chemistry. Tree tensor network states represent one of the simplest generalizations of matrix product states and the density matrix renormalization group. While matrix product states encode a one-dimensional entanglement structure, tree tensor network states encode a tree entanglement structure, allowing for a more flexible description of general molecules. We describe an optimal tree tensor network state algorithm for quantum chemistry. We introduce the concept of half-renormalization which greatly improves the efficiency of the calculations. Using our efficient formulation we demonstrate the strengths and weaknesses of tree tensor network states versus matrix product states. We carry out benchmark calculations both on tree systems (hydrogen trees and π-conjugated dendrimers) as well as non-tree molecules (hydrogen chains, nitrogen dimer, and chromium dimer). In general, tree tensor network states require much fewer renormalized states to achieve the same accuracy as matrix product states. In non-tree molecules, whether this translates into a computational savings is system dependent, due to the higher prefactor and computational scaling associated with tree algorithms. In tree like molecules, tree network states are easily superior to matrix product states. As an illustration, our largest dendrimer calculation with tree tensor network states correlates 110 electrons in 110 active orbitals.

Coalescent histories for caterpillar-like families.

PubMed

Rosenberg, Noah A

2013-01-01

A coalescent history is an assignment of branches of a gene tree to branches of a species tree on which coalescences in the gene tree occur. The number of coalescent histories for a pair consisting of a labeled gene tree topology and a labeled species tree topology is important in gene tree probability computations, and more generally, in studying evolutionary possibilities for gene trees on species trees. Defining the Tr-caterpillar-like family as a sequence of n-taxon trees constructed by replacing the r-taxon subtree of n-taxon caterpillars by a specific r-taxon labeled topology Tr, we examine the number of coalescent histories for caterpillar-like families with matching gene tree and species tree labeled topologies. For each Tr with size r≤8, we compute the number of coalescent histories for n-taxon trees in the Tr-caterpillar-like family. Next, as n→∞, we find that the limiting ratio of the numbers of coalescent histories for the Tr family and caterpillars themselves is correlated with the number of labeled histories for Tr. The results support a view that large numbers of coalescent histories occur when a tree has both a relatively balanced subtree and a high tree depth, contributing to deeper understanding of the combinatorics of gene trees and species trees.

Retrospective Analysis of the Incidence of Retained Placenta in 3 Large Colonies of NHP

PubMed Central

Bauer, Cassondra; Harrison, Tara

2016-01-01

During 1999 through 2014, retained placenta was the most common cause of clinical admission for reproductive complications in breeding colonies of baboons (approximate colony size, 2000 animals), cynomolgus macaques (approximately 1000), and rhesus macaques (approximately 500) at the Southwest National Primate Research Center. Retained placentas occurred in 2.7% of baboons, 3.3% of cynomolgus macaques, and 1.0% of rhesus macaques. Apparent risk factors for retained placenta included stillbirth or abortion and at least one prior cesarean section. There was a significant association between stillbirth and retained placenta in all species. Cesarean sections were performed routinely for baboons to meet research objectives but occurred only as needed for cynomolgus and rhesus macaques. Having had at least one prior cesarean section was an incidence factor for retained placenta in 37.0% of baboons and 4.7% of cynomolgus macaques; none of the rhesus macaques with retained placentas had undergone cesarean section previously. More than 90% of dams with retained placenta returned to a successful reproductive life or assignment to a nonbreeding research protocol. Advances in reproductive management will benefit from prospective studies that capture additional data from all members of a breeding group prior to reproductive complications. PMID:27053569

Retrospective Analysis of the Incidence of Retained Placenta in 3 Large Colonies of NHP.

PubMed

Bauer, Cassondra; Harrison, Tara

2016-04-01

During 1999 through 2014, retained placenta was the most common cause of clinical admission for reproductive complications in breeding colonies of baboons (approximate colony size, 2000 animals), cynomolgus macaques (approximately 1000), and rhesus macaques (approximately 500) at the Southwest National Primate Research Center. Retained placentas occurred in 2.7% of baboons, 3.3% of cynomolgus macaques, and 1.0% of rhesus macaques. Apparent risk factors for retained placenta included stillbirth or abortion and at least one prior cesarean section. There was a significant association between stillbirth and retained placenta in all species. Cesarean sections were performed routinely for baboons to meet research objectives but occurred only as needed for cynomolgus and rhesus macaques. Having had at least one prior cesarean section was an incidence factor for retained placenta in 37.0% of baboons and 4.7% of cynomolgus macaques; none of the rhesus macaques with retained placentas had undergone cesarean section previously. More than 90% of dams with retained placenta returned to a successful reproductive life or assignment to a nonbreeding research protocol. Advances in reproductive management will benefit from prospective studies that capture additional data from all members of a breeding group prior to reproductive complications.

[Sectional structure of a tree. Model analysis of the vertical biomass distribution].

PubMed

Galitskiĭ, V V

2010-01-01

A model has been proposed for the architecture of a tree in which virtual trees appear rhythmically on the treetop. Each consecutive virtual tree is a part of the previous tree. The difference between two adjacent virtual trees is a section--an element of the real tree structure. In case of a spruce, the section represents a verticil of a stem with the corresponding internode. Dynamics of a photosynthesizing part of the physiologically active biomass of each section differ from the corresponding dynamics of the virtual trees and the whole real tree. If the tree biomass dynamics has a sigma-shaped form, then the section dynamics have to be bell-shaped. It means that the lower stem should accordingly become bare, which is typically observed in nature. Model analysis reveals the limiting, in the age, form of trees to be an "umbrella". It can be observed in nature and is an outcome of physical limitation of the tree height combined with the sigma-shaped form of the tree biomass dynamics. Variation of model parameters provides for various forms of the tree biomass distribution along the height, which can be associated with certain biological species of trees.

Notch-modifying xylosyltransferase-substrate complexes support an SNi-like retaining mechanism

PubMed Central

Yu, Hongjun; Takeuchi, Megumi; LeBarron, Jamie; Kantharia, Joshua; London, Erwin; Bakker, Hans; Haltiwanger, Robert S.; Li, Huilin; Takeuchi, Hideyuki

2015-01-01

A major remaining question in glycobiology is how a glycosyltransferase (GT) that retains the anomeric linkage of a sugar catalyzes the reaction. Xylosideα1–3 Xylosyltransferase (XXYLT1) is a retaining GT that regulates Notch receptor activation by adding xylose to the Notch extracellular domain. Here, using natural acceptor and donor substrates and active Mus musculus XXYLT1, we report a series of crystallographic snapshots along the reaction, including an unprecedented natural and competent Michaelis reaction complex for retaining enzymes. These structures strongly support the SNi-like reaction as the retaining mechanism for XXYLT1. Unexpectedly the Epidermal Growth Factor-like repeat acceptor substrate undergoes a large conformational change upon binding to the active site, providing a structural basis for substrate specificity. Our improved understanding of this retaining enzyme will accelerate the design of retaining GT inhibitors that can modulate Notch activity in pathological situations where dysregulation of Notch is known to cause cancer or developmental disorders. PMID:26414444

Notch-modifying xylosyltransferase structures support an S Ni-like retaining mechanism

DOE PAGES

Yu, Hongjun; Li, Huilin; Takeuchi, Megumi; ...

2015-09-28

A major question remaining in glycobiology is how a glycosyltransferase (GT) that retains the anomeric linkage of a sugar catalyzes the reaction. Xyloside α-1,3-xylosyltransferase (XXYLT1) is a retaining GT that regulates Notch receptor activation by adding xylose to the Notch extracellular domain. Here, using natural acceptor and donor substrates and active Mus musculus XXYLT1, we report a series of crystallographic snapshots along the reaction, including an unprecedented natural and competent Michaelis reaction complex for retaining enzymes. These structures strongly support the SNi-like reaction as the retaining mechanism for XXYLT1. Unexpectedly, the epidermal growth factor–like repeat acceptor substrate undergoes a largemore » conformational change upon binding to the active site, providing a structural basis for substrate specificity. As a result, our improved understanding of this retaining enzyme will accelerate the design of retaining GT inhibitors that can modulate Notch activity in pathological situations in which Notch dysregulation is known to cause cancer or developmental disorders.« less

Notch-modifying xylosyltransferase structures support an S Ni-like retaining mechanism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Hongjun; Li, Huilin; Takeuchi, Megumi

A major question remaining in glycobiology is how a glycosyltransferase (GT) that retains the anomeric linkage of a sugar catalyzes the reaction. Xyloside α-1,3-xylosyltransferase (XXYLT1) is a retaining GT that regulates Notch receptor activation by adding xylose to the Notch extracellular domain. Here, using natural acceptor and donor substrates and active Mus musculus XXYLT1, we report a series of crystallographic snapshots along the reaction, including an unprecedented natural and competent Michaelis reaction complex for retaining enzymes. These structures strongly support the SNi-like reaction as the retaining mechanism for XXYLT1. Unexpectedly, the epidermal growth factor–like repeat acceptor substrate undergoes a largemore » conformational change upon binding to the active site, providing a structural basis for substrate specificity. As a result, our improved understanding of this retaining enzyme will accelerate the design of retaining GT inhibitors that can modulate Notch activity in pathological situations in which Notch dysregulation is known to cause cancer or developmental disorders.« less

Growth of a Pine Tree

ERIC Educational Resources Information Center

Rollinson, Susan Wells

2012-01-01

The growth of a pine tree is examined by preparing "tree cookies" (cross-sectional disks) between whorls of branches. The use of Christmas trees allows the tree cookies to be obtained with inexpensive, commonly available tools. Students use the tree cookies to investigate the annual growth of the tree and how it corresponds to the number of whorls…

A Metric on Phylogenetic Tree Shapes.

PubMed

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.

Three-dimensional study of grain boundary engineering effects on intergranular stress corrosion cracking of 316 stainless steel in high temperature water

NASA Astrophysics Data System (ADS)

Liu, Tingguang; Xia, Shuang; Bai, Qin; Zhou, Bangxin; Zhang, Lefu; Lu, Yonghao; Shoji, Tetsuo

2018-01-01

The intergranular cracks and grain boundary (GB) network of a GB-engineered 316 stainless steel after stress corrosion cracking (SCC) test in high temperature high pressure water of reactor environment were investigated by two-dimensional and three-dimensional (3D) characterization in order to expose the mechanism that GB-engineering mitigates intergranular SCC. The 3D microstructure shown that the essential characteristic of the GB-engineered microstructure is formation of many large twin-boundaries as a result of multiple-twinning, which results in the formation of large grain-clusters. The large grain-clusters played a key role to the improvement of intergranular SCC resistance by GB-engineering. The main intergranular cracks propagated in a zigzag along the outer boundaries of these large grain-clusters because all inner boundaries of the grain-clusters were twin-boundaries (∑3) or twin-related boundaries (∑3n) which had much lower susceptibility to SCC than random boundaries. These large grain-clusters had tree-ring-shaped topology structure and very complex morphology. They got tangled so that difficult to be separated during SCC, resulting in some large crack-bridges retained in the crack surface.

Wood specific gravity variation among five important hardwood species of Kashmir Himalaya.

PubMed

Wani, Bilal Ahmad; Bodha, R H; Khan, Amina

2014-02-01

Wood Specific Gravity (SG) is a measure of the amount of structural material a tree species allocates to support and strength. In the present study, specific gravity varied among the five different woods at three different sites from 0.40 in Populus nigra at site III (Shopian) to 0.80 in Parrotiopsis jacquemontiana at site II (Surasyar). Among the three different sites, specific gravity varied from 0.73 to 0.80 in Parroptiosis jacquemontiana; in Robinia pseudoacacia it varied from 0.71 to 0.79; in Salix alba, it varied from 0.42 to 0.48; In Populus nigra it varied from 0.40 to 0.48 and in Juglans regia it varied from 0.59 to 0.66. On the basis of the specific gravity variation patterns these woods were categorized as light (Salix alba, Populus nigra) moderately heavy (Juglans regia) and moderately heavy to heavy (Robinia pseudoacacia, Parrotiopsis jacquemontiana) which predicts their properties like strength, dimensional stability with moisture content change, ability to retain paint, fiber yield per unit volume, suitability for making particleboard and related wood composite materials and suitability as a raw material for making paper.

Genome Re-Sequencing of Semi-Wild Soybean Reveals a Complex Soja Population Structure and Deep Introgression

PubMed Central

Wu, Sanling; Wang, Ying-Ying; Ye, Chu-Yu; Bai, Xuefei; Li, Zefeng; Yan, Chenghai; Wang, Weidi; Wang, Ziqiang; Shu, Qingyao; Xie, Jiahua; Lee, Suk-Ha; Fan, Longjiang

2014-01-01

Semi-wild soybean is a unique type of soybean that retains both wild and domesticated characteristics, which provides an important intermediate type for understanding the evolution of the subgenus Soja population in the Glycine genus. In this study, a semi-wild soybean line (Maliaodou) and a wild line (Lanxi 1) collected from the lower Yangtze regions were deeply sequenced while nine other semi-wild lines were sequenced to a 3-fold genome coverage. Sequence analysis revealed that (1) no independent phylogenetic branch covering all 10 semi-wild lines was observed in the Soja phylogenetic tree; (2) besides two distinct subpopulations of wild and cultivated soybean in the Soja population structure, all semi-wild lines were mixed with some wild lines into a subpopulation rather than an independent one or an intermediate transition type of soybean domestication; (3) high heterozygous rates (0.19–0.49) were observed in several semi-wild lines; and (4) over 100 putative selective regions were identified by selective sweep analysis, including those related to the development of seed size. Our results suggested a hybridization origin for the semi-wild soybean, which makes a complex Soja population structure. PMID:25265539

Forest regeneration composition and development in upland, mixed-oak forests.

PubMed

Fei, Songlin; Gould, Peter J; Steiner, Kim C; Finley, James C; McDill, Marc E

2005-12-01

Advance regeneration in 52 mature mixed-oak stands was analyzed and described. Red maple (Acer rubrum L.) was the most abundant species in the study area. Among oak (Quercus) species, northern red oak (Q. rubra L.) was the most abundant within the Allegheny Plateau physiographic province, whereas chestnut oak (Q. montana L.) was the most abundant within the Ridge and Valley physiographic province. Sixteen stands, for which data are available through the fourth growing season following harvest, were used to describe stand development. Cumulative height, a composite measure of size and density, was used to describe early stand development. Black gum (Nyssa sylvatica Marsh.) and black birch (Betula lenta L.) had dramatic increases in stand density and cumulative height after overstory removal. Cumulative height of northern red oak and chestnut oak showed a faster positive response to overstory removal than red maple. Oak retained its dominance in cumulative height for at least 4 years after harvest. Red maple nevertheless remained the most abundant tree species after overstory removal. Our results suggest that the principal advantage of red maple regeneration is its ability to accumulate in large numbers prior to harvest.

The Irreversible Loss of a Decomposition Pathway Marks the Single Origin of an Ectomycorrhizal Symbiosis

PubMed Central

Wolfe, Benjamin E.; Tulloss, Rodham E.; Pringle, Anne

2012-01-01

Microbial symbioses have evolved repeatedly across the tree of life, but the genetic changes underlying transitions to symbiosis are largely unknown, especially for eukaryotic microbial symbionts. We used the genus Amanita, an iconic group of mushroom-forming fungi engaged in ectomycorrhizal symbioses with plants, to identify both the origins and potential genetic changes maintaining the stability of this mutualism. A multi-gene phylogeny reveals one origin of the symbiosis within Amanita, with a single transition from saprotrophic decomposition of dead organic matter to biotrophic dependence on host plants for carbon. Associated with this transition are the losses of two cellulase genes, each of which plays a critical role in extracellular decomposition of organic matter. However a third gene, which acts at later stages in cellulose decomposition, is retained by many, but not all, ectomycorrhizal species. Experiments confirm that symbiotic Amanita species have lost the ability to grow on complex organic matter and have therefore lost the capacity to live in forest soils without carbon supplied by a host plant. Irreversible losses of decomposition pathways are likely to play key roles in the evolutionary stability of these ubiquitous mutualisms. PMID:22815710

Facilitation between woody and herbaceous plants that associate with arbuscular mycorrhizal fungi in temperate European forests.

PubMed

Veresoglou, Stavros D; Wulf, Monika; Rillig, Matthias C

2017-02-01

In late-successional environments, low in available nutrient such as the forest understory, herbaceous plant individuals depend strongly on their mycorrhizal associates for survival. We tested whether in temperate European forests arbuscular mycorrhizal (AM) woody plants might facilitate the establishment of AM herbaceous plants in agreement with the mycorrhizal mediation hypothesis. We used a dataset spanning over 400 vegetation plots in the Weser-Elbe region (northwest Germany). Mycorrhizal status information was obtained from published resources, and Ellenberg indicator values were used to infer environmental data. We carried out tests for both relative richness and relative abundance of herbaceous plants. We found that the subset of herbaceous individuals that associated with AM profited when there was a high cover of AM woody plants. These relationships were retained when we accounted for environmental filtering effects using path analysis. Our findings build on the existing literature highlighting the prominent role of mycorrhiza as a coexistence mechanism in plant communities. From a nature conservation point of view, it may be possible to promote functional diversity in the forest understory through introducing AM woody trees in stands when absent.

Deciphering the evolutionary history of open and closed mitosis

PubMed Central

Sazer, Shelley; Lynch, Michael; Needleman, Daniel

2014-01-01

Summary The origin of the nucleus at the prokaryote to eukaryote transition represents one of the most important events in the evolution of cellular organization. The nuclear envelope encircles the chromosomes in interphase and is a selectively permeable barrier between the nucleoplasm and cytoplasm and an organizational scaffold for the nucleus. It remains intact in the "closed" mitosis of some yeast but loses its integrity in the "open" mitosis of mammals. Instances of both types of mitosis within two evolutionary clades indicate multiple evolutionary transitions between open and closed mitosis, although the underlying genetic changes that influenced these transitions remain unknown. A survey of the diversity of mitotic nuclei that fall between these extremes is the starting point from which to determine the physiologically relevant characteristics distinguishing open from closed mitosis and to understand how they evolved and why they are retained in present-day organisms. The field is now poised to begin addressing these issues by defining and document patterns of mitotic nuclear variation within and among species and map them onto a phylogenic tree. Deciphering the evolutionary history of open and closed mitosis will complement cell biological and genetic approaches aimed at deciphering the fundamental organizational principles of the nucleus. PMID:25458223

Multiple maternal origins of Indonesian crowing chickens revealed by mitochondrial DNA analysis.

PubMed

Ulfah, Maria; Perwitasari, Dyah; Jakaria, Jakaria; Muladno, Muhammad; Farajallah, Achmad

2017-03-01

The utilization of Indonesian crowing chickens is increasing; as such, assessing their genetic structures is important to support the conservation of their genetic resources. This study analyzes the matrilineal evolution of Indonesian crowing chickens based on the mtDNA displacement loop D-loop region to clarify their phylogenetic relationships, possible maternal origin, and possible routes of chicken dispersal. The neighbor-joining tree reveals that the majority of Indonesian crowing chickens belong to haplogroups B, D, and E, but haplogroup D harbored most of them. The Bayesian analysis also reveals that Indonesian crowing chickens derive from Bekisar chicken, a hybrid of the green junglefowl, suggesting the possible contribution of green junglefowl to chicken domestication. There appear at least three maternal lineages of Indonesian chicken origins indicated by the median network profile of mtDNA D-loop haplotypes, namely (1) Chinese; (2) Chinese, Indian, and other Southeast Asian chickens; and (3) Indian, Chinese, Southeast Asian, Japanese, and European chickens. Chicken domestication might be centered in China, India, Indonesia, and other Southeast Asian countries, supporting multiple maternal origins of Indonesian crowing chickens. A systematic breeding program of indigenous chickens will be very important to retain the genetic diversity for future use and conservation.

[Acumen function in leaves and its vertical distribution in a tropical rain forest of Costa Rica].

PubMed

Farji-Brener, Alejandro G; Valverde, Oscar; Paolini, Leonardo; de los Angeles La Torre, María; Quintero, Estela; Bonaccorso, Elisa; Arnedo, Luisa; Villalobos, Richard

2002-06-01

Water retention on the leaf surface can be maladaptive to the plant because it increases the colonization of epiphylls and interferes with the physiologic processes of the leaf, diminishing the photosynthetic capacity. To test if leaf driptips facilitate leaf drying after rainfall in a tropical rain forest of Costa Rica, we (1) experimentally measured the capacity to retain water on leaf surfaces of 30 plant species before and after driptip removal, and (2) analyzed the development of driptips along forest strata. We expected leaf driptips to be less developed in the upper strata due to the environmental conditions of the canopy (i.e., high solar radiation, strong winds and low relative humidity), which favor the natural drying of leaves. The presence of driptips increased 100% the water run off capacity of leaves in all the analyzed species. Also, the development of leaf driptips was smaller in canopy species than in understory species. Additionally, they became less developed in canopy species as trees increased in height. These results support the hypothesis that the adaptive role of driptips is to facilitate the drying of leaf surfaces.

Exopolysaccharide microchannels direct bacterial motility and organize multicellular behavior

DOE PAGES

Berleman, James E.; Zemla, Marcin; Remis, Jonathan P.; ...

2016-05-06

The myxobacteria are a family of soil bacteria that form biofilms of complex architecture, aligned multilayered swarms or fruiting body structures that are simple or branched aggregates containing myxospores. Here, we examined the structural role of matrix exopolysaccharide (EPS) in the organization of these surface-dwelling bacterial cells. Using time-lapse light and fluorescence microscopy, as well as transmission electron microscopy and focused ion beam/scanning electron microscopy (FIB/SEM) electron microscopy, we found that Myxococcus xanthus cell organization in biofilms is dependent on the formation of EPS microchannels. Cells are highly organized within the three-dimensional structure of EPS microchannels that are required formore » cell alignment and advancement on surfaces. Mutants lacking EPS showed a lack of cell orientation and poor colony migration. Purified, cell-free EPS retains a channel-like structure, and can complement EPS - mutant motility defects. In addition, EPS provides the cooperative structure for fruiting body formation in both the simple mounds of M. xanthus and the complex, tree-like structures of Chondromyces crocatus. We furthermore investigated the possibility that EPS impacts community structure as a shared resource facilitating cooperative migration among closely related isolates of M. xanthus.« less

Dynamic publication model for neurophysiology databases.

PubMed

Gardner, D; Abato, M; Knuth, K H; DeBellis, R; Erde, S M

2001-08-29

We have implemented a pair of database projects, one serving cortical electrophysiology and the other invertebrate neurones and recordings. The design for each combines aspects of two proven schemes for information interchange. The journal article metaphor determined the type, scope, organization and quantity of data to comprise each submission. Sequence databases encouraged intuitive tools for data viewing, capture, and direct submission by authors. Neurophysiology required transcending these models with new datatypes. Time-series, histogram and bivariate datatypes, including illustration-like wrappers, were selected by their utility to the community of investigators. As interpretation of neurophysiological recordings depends on context supplied by metadata attributes, searches are via visual interfaces to sets of controlled-vocabulary metadata trees. Neurones, for example, can be specified by metadata describing functional and anatomical characteristics. Permanence is advanced by data model and data formats largely independent of contemporary technology or implementation, including Java and the XML standard. All user tools, including dynamic data viewers that serve as a virtual oscilloscope, are Java-based, free, multiplatform, and distributed by our application servers to any contemporary networked computer. Copyright is retained by submitters; viewer displays are dynamic and do not violate copyright of related journal figures. Panels of neurophysiologists view and test schemas and tools, enhancing community support.

Use of an implant o-ring attachment for the tooth supported mandibular overdenture: a clinical report.

PubMed

Guttal, Satyabodh S; Tavargeri, Anand K; Nadiger, Ramesh K; Thakur, Srinath L

2011-07-01

Retention of a mandibular denture can be achieved by an implant-retained or natural tooth-retained bar and stud attachment in the anterior segment of the mandible. The same design principles holds true for both implant-retained and tooth-retained methods of anchoring the bar and stud attachment. A simple and cost effective treatment for more complex implant overdenture is the concept of conventional tooth-retained overdentures. When few firm teeth still remain in a compromised dentition, preservation of these teeth for overdentures can improve retention and stability. The authors present a clinical report of a patient treated with a mandibular tooth-borne overdenture with bar and O-ring attachment. A splinted bar supported the prosthesis and an O-ring retained the denture.

Use of an Implant O-Ring Attachment for the Tooth Supported Mandibular Overdenture: A Clinical Report

PubMed Central

Guttal, Satyabodh S.; Tavargeri, Anand K.; Nadiger, Ramesh K.; Thakur, Srinath L.

2011-01-01

Retention of a mandibular denture can be achieved by an implant-retained or natural tooth-retained bar and stud attachment in the anterior segment of the mandible. The same design principles holds true for both implant-retained and tooth-retained methods of anchoring the bar and stud attachment. A simple and cost effective treatment for more complex implant overdenture is the concept of conventional tooth-retained overdentures. When few firm teeth still remain in a compromised dentition, preservation of these teeth for overdentures can improve retention and stability. The authors present a clinical report of a patient treated with a mandibular tooth-borne overdenture with bar and O-ring attachment. A splinted bar supported the prosthesis and an O-ring retained the denture. PMID:21769276

A Metric on Phylogenetic Tree Shapes

PubMed Central

Plazzotta, G.

2018-01-01

Abstract 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. PMID:28472435

Spatial Distribution Patterns in the Very Rare and Species-Rich Picea chihuahuana Tree Community (Mexico).

PubMed

Wehenkel, Christian; Brazão-Protázio, João Marcelo; Carrillo-Parra, Artemio; Martínez-Guerrero, José Hugo; Crecente-Campo, Felipe

2015-01-01

The very rare Mexican Picea chihuahuana tree community covers an area of no more than 300 ha in the Sierra Madre Occidental. This special tree community has been the subject of several studies aimed at learning more about the genetic structure and ecology of the species and the potential effects of climate change. The spatial distribution of trees is a result of many ecological processes and can affect the degree of competition between neighbouring trees, tree density, variability in size and distribution, regeneration, survival, growth, mortality, crown formation and the biological diversity within forest communities. Numerous scale-dependent measures have been established in order to describe spatial forest structure. The overall aim of most of these studies has been to obtain data to help design preservation and conservation strategies. In this study, we examined the spatial distribution pattern of trees in the P. chihuahuana tree community in 12 localities, in relation to i) tree stand density, ii) diameter distribution (vertical structure), iii) tree species diversity, iv) geographical latitude and v) tree dominance at a fine scale (in 0.25 ha plots), with the aim of obtaining a better understanding of the complex ecosystem processes and biological diversity. Because of the strongly mixed nature of this tree community, which often produces low population densities of each tree species and random tree fall gaps caused by tree death, we expect aggregated patterns in individual Picea chihuahuana trees and in the P. chihuahuana tree community, repulsive Picea patterns to other tree species and repulsive patterns of young to adult trees. Each location was represented by one plot of 50 x 50 m (0.25 ha) established in the centre of the tree community. The findings demonstrate that the hypothesis of aggregated tree pattern is not applicable to the mean pattern measured by Clark-Evans index, Uniform Angle index and Mean Directional index of the uneven-aged P. chihuahuana trees and P. chihuahuana tree community and but to specific spatial scales measured by the univariate L-function. The spatial distribution pattern of P. chihuahuana trees was found to be independent of patches of other tree species measured by the bivariate L-function. The spatial distribution was not significantly related to tree density, diameter distribution or tree species diversity. The index of Clark and Evans decreased significantly from the southern to northern plots containing all tree species. Self-thinning due to intra and inter-specific competition-induced mortality is probably the main cause of the decrease in aggregation intensity during the course of population development in this tree community. We recommend the use of larger sampling plots (> 0.25 ha) in uneven-aged and species-rich forest ecosystems to detect less obvious, but important, relationships between spatial tree pattern and functioning and diversity in these forests.

Spatial Distribution Patterns in the Very Rare and Species-Rich Picea chihuahuana Tree Community (Mexico)

PubMed Central

Wehenkel, Christian; Brazão-Protázio, João Marcelo; Carrillo-Parra, Artemio; Martínez-Guerrero, José Hugo; Crecente-Campo, Felipe

2015-01-01

The very rare Mexican Picea chihuahuana tree community covers an area of no more than 300 ha in the Sierra Madre Occidental. This special tree community has been the subject of several studies aimed at learning more about the genetic structure and ecology of the species and the potential effects of climate change. The spatial distribution of trees is a result of many ecological processes and can affect the degree of competition between neighbouring trees, tree density, variability in size and distribution, regeneration, survival, growth, mortality, crown formation and the biological diversity within forest communities. Numerous scale-dependent measures have been established in order to describe spatial forest structure. The overall aim of most of these studies has been to obtain data to help design preservation and conservation strategies. In this study, we examined the spatial distribution pattern of trees in the P. chihuahuana tree community in 12 localities, in relation to i) tree stand density, ii) diameter distribution (vertical structure), iii) tree species diversity, iv) geographical latitude and v) tree dominance at a fine scale (in 0.25 ha plots), with the aim of obtaining a better understanding of the complex ecosystem processes and biological diversity. Because of the strongly mixed nature of this tree community, which often produces low population densities of each tree species and random tree fall gaps caused by tree death, we expect aggregated patterns in individual Picea chihuahuana trees and in the P. chihuahuana tree community, repulsive Picea patterns to other tree species and repulsive patterns of young to adult trees. Each location was represented by one plot of 50 x 50 m (0.25 ha) established in the centre of the tree community. The findings demonstrate that the hypothesis of aggregated tree pattern is not applicable to the mean pattern measured by Clark-Evans index, Uniform Angle index and Mean Directional index of the uneven-aged P. chihuahuana trees and P. chihuahuana tree community and but to specific spatial scales measured by the univariate L-function. The spatial distribution pattern of P. chihuahuana trees was found to be independent of patches of other tree species measured by the bivariate L-function. The spatial distribution was not significantly related to tree density, diameter distribution or tree species diversity. The index of Clark and Evans decreased significantly from the southern to northern plots containing all tree species. Self-thinning due to intra and inter-specific competition-induced mortality is probably the main cause of the decrease in aggregation intensity during the course of population development in this tree community. We recommend the use of larger sampling plots (> 0.25 ha) in uneven-aged and species-rich forest ecosystems to detect less obvious, but important, relationships between spatial tree pattern and functioning and diversity in these forests. PMID:26496189

Forest Management Intensity Affects Aquatic Communities in Artificial Tree Holes.

PubMed

Petermann, Jana S; Rohland, Anja; Sichardt, Nora; Lade, Peggy; Guidetti, Brenda; Weisser, Wolfgang W; Gossner, Martin M

2016-01-01

Forest management could potentially affect organisms in all forest habitats. However, aquatic communities in water-filled tree-holes may be especially sensitive because of small population sizes, the risk of drought and potential dispersal limitation. We set up artificial tree holes in forest stands subject to different management intensities in two regions in Germany and assessed the influence of local environmental properties (tree-hole opening type, tree diameter, water volume and water temperature) as well as regional drivers (forest management intensity, tree-hole density) on tree-hole insect communities (not considering other organisms such as nematodes or rotifers), detritus content, oxygen and nutrient concentrations. In addition, we compared data from artificial tree holes with data from natural tree holes in the same area to evaluate the methodological approach of using tree-hole analogues. We found that forest management had strong effects on communities in artificial tree holes in both regions and across the season. Abundance and species richness declined, community composition shifted and detritus content declined with increasing forest management intensity. Environmental variables, such as tree-hole density and tree diameter partly explained these changes. However, dispersal limitation, indicated by effects of tree-hole density, generally showed rather weak impacts on communities. Artificial tree holes had higher water temperatures (on average 2°C higher) and oxygen concentrations (on average 25% higher) than natural tree holes. The abundance of organisms was higher but species richness was lower in artificial tree holes. Community composition differed between artificial and natural tree holes. Negative management effects were detectable in both tree-hole systems, despite their abiotic and biotic differences. Our results indicate that forest management has substantial and pervasive effects on tree-hole communities and may alter their structure and functioning. We furthermore conclude that artificial tree-hole analogues represent a useful experimental alternative to test effects of changes in forest management on natural communities.

Forest Management Intensity Affects Aquatic Communities in Artificial Tree Holes

PubMed Central

Petermann, Jana S.; Rohland, Anja; Sichardt, Nora; Lade, Peggy; Guidetti, Brenda; Weisser, Wolfgang W.; Gossner, Martin M.

2016-01-01

Forest management could potentially affect organisms in all forest habitats. However, aquatic communities in water-filled tree-holes may be especially sensitive because of small population sizes, the risk of drought and potential dispersal limitation. We set up artificial tree holes in forest stands subject to different management intensities in two regions in Germany and assessed the influence of local environmental properties (tree-hole opening type, tree diameter, water volume and water temperature) as well as regional drivers (forest management intensity, tree-hole density) on tree-hole insect communities (not considering other organisms such as nematodes or rotifers), detritus content, oxygen and nutrient concentrations. In addition, we compared data from artificial tree holes with data from natural tree holes in the same area to evaluate the methodological approach of using tree-hole analogues. We found that forest management had strong effects on communities in artificial tree holes in both regions and across the season. Abundance and species richness declined, community composition shifted and detritus content declined with increasing forest management intensity. Environmental variables, such as tree-hole density and tree diameter partly explained these changes. However, dispersal limitation, indicated by effects of tree-hole density, generally showed rather weak impacts on communities. Artificial tree holes had higher water temperatures (on average 2°C higher) and oxygen concentrations (on average 25% higher) than natural tree holes. The abundance of organisms was higher but species richness was lower in artificial tree holes. Community composition differed between artificial and natural tree holes. Negative management effects were detectable in both tree-hole systems, despite their abiotic and biotic differences. Our results indicate that forest management has substantial and pervasive effects on tree-hole communities and may alter their structure and functioning. We furthermore conclude that artificial tree-hole analogues represent a useful experimental alternative to test effects of changes in forest management on natural communities. PMID:27187741

Comparison of Stability of the Results of Orthodontic Treatment and Gingival Health between Hawley and Vacuum-formed Retainers.

PubMed

Moslemzadeh, Seyed H; Sohrabi, Aydin; Rafighi, Ali; Farshidnia, Somaieh

2018-04-01

Aim: Retention is one of the stages of orthodontic treatment, which is an attempt to retain teeth in their corrected positions after active treatment with the use of fixed orthodontic appliances. The aim of the present study was to compare the stability of the results of orthodontic treatment and the gingival health between Hawley retainer (HR) and vacuum-formed retainer (VFR) with two different thicknesses. Materials and methods: In this randomized clinical trial, 66 patients undergoing comprehensive orthodontic treatment in a private office were evaluated after completion of treatment. The subjects were randomly assigned to three groups. At the end of orthodontic treatment, the subjects in all the groups received a fixed bonded retainer in the mandible; in the maxilla, group I received an HR, group II received a VFR with a thickness of 1.5 mm, and group III received a VFR with a thickness of 1 mm. The American Board of Orthodontics objective grading system (ABO-OGS) index was used at the end of treatment (before the delivery of the retainers) and 6 months after the use of retainers to evaluate the stability of the results of orthodontic treatment. Gingival index (GI) was used at the two above-mentioned intervals to evaluate gingival health. The ABO-OGS measurements were carried out on dental casts by a clinician who was blinded to the types of retainers the patients wore. Data were analyzed with Statistical Package for the Social Sciences (SPSS) version 20, using proper statistical analyses. Results: Six months after the delivery of retainers, ABO-OGS and GI scores with the 1.5 mm VFR were higher than those in the two other groups, with no significant differences between the three groups. There were no significant differences between the ABO-OGS scores before the delivery of retainers and 6 months after the use of retainers in any of the study groups. In the HR and 1.5 mm VFR groups, there were significant differences in GI scores between the period before the delivery of the retainers and 6 months after their delivery; however, in the 1 mm VFR group, no significant differences were observed in GI scores between the two time intervals. Conclusion: Hawley retainer and 1 mm thick and 1.5 mm thick VFRs were equally effective in preserving and stabilizing the results of orthodontic treatment during the 6-month interval after the completion of orthodontic treatment. In addition, there were no significant differences between the three retainers in relation to gingival health. Clinical significance: The VFR might be a good alternative for HR due to its better esthetic appearance and greater popularity with orthodontic patients. Keywords: American Board of Orthodontics model grading system, American Board of Orthodontics objective frading system, Gingival index, Hawley retainers, Vacuum-formed retainers.

Trees in the Landscape.

ERIC Educational Resources Information Center

Webb, Richard; Forbatha, Ann

1982-01-01

Strategies for using trees in classroom instruction are provided. Includes: (1) activities (such as tree identification, mapping, measuring tree height/width); (2) list of asthetic, architectural, engineering, climate, and wildlife functions of trees; (3) tree discussion questions; and (4) references. (JN)

Evaluation of the effects of treating dairy cows with meloxicam at calving on retained fetal membranes risk

PubMed Central

Newby, Nathalie C.; Renaud, David; Tremblay, Robert; Duffield, Todd F.

2014-01-01

Some non-steroidal anti-inflammatory drugs increase the risk of retained fetal membranes. This is the first study to investigate the effects of meloxicam on the risk of retained fetal membranes. Administration of meloxicam to dairy cattle immediately following calving revealed no differences in the incidence of retained fetal membranes between meloxicam-treated and untreated animals. There was no difference between the 2 groups in the incidence of periparturient diseases following calving. Meloxicam can be used on the day of calving in lactating cows without increasing the risk of retained fetal membranes. PMID:25477550

Memotain: A CAD/CAM nickel-titanium lingual retainer.

PubMed

Kravitz, Neal D; Grauer, Dan; Schumacher, Pascal; Jo, Yong-Min

2017-04-01

Approximately 1/2 of maxillary and 1/5 of mandibular multi-stranded lingual retainers fail during retention in some form, either bond failure or wire breakage. Memotain is a new CAD/CAM fabricated lingual retainer wire made of custom-cut nickel-titanium, as an alternative to multi-stranded lingual retainers. It offers numerous perceived advantages to the traditional multi-stranded stainless steel wire, including precision fit, avoidance of interferences, corrosion resistance and even the potential for minor tooth movement as an active lingual retainer. Copyright © 2017 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

Tree-mediated methane emissions from tropical and temperate peatlands.

NASA Astrophysics Data System (ADS)

Pangala, S. R.; Gauci, V.; Hornibrook, E. R. C.; Gowing, D. J.

2012-04-01

Methane production and transport processes in peatlands are fairly well understood, but growing evidence for emission of methane through trees has highlighted the need to revisit methane transport processes. In wetland trees, morphological adaptations such as development of hypertrophied lenticels, aerenchyma and adventitious roots in response to soil anoxia mediates gas transport, transporting both oxygen from the atmosphere to oxygen-deprived roots and soil-produced methane from the root-zone to the atmosphere. Although, tree-mediated methane emissions from temperate tree species have been confirmed, methane emissions from tropical tree species and processes that control tree-mediated methane emissions remain unclear. This study explains the role of trees in transporting soil-produced methane to the atmosphere and uncovers the principal mechanisms of tree-mediated methane emissions. Methane emissions from eight tropical tree species and two temperate tree species were studied in situ. The mechanisms and controls on tree-mediated methane emissions were investigated using three year old common alder (Alnus glutinosa; 50 trees) grown under two artificially controlled water-table positions. Methane fluxes from whole mesocosms, the soil surface and tree stems were measured using static closed chambers. Both temperate and tropical tree species released significant quantities of methane, with tropical trees dominating ecosystem level methane fluxes. In temperate peatlands, both the methane gas transport mechanism and quantity of methane emitted from stems is tree-species dependent. In Alnus glutinosa, no correlations were observed between stomatal behaviour and tree-mediated methane emissions, however, stem methane emissions were positively correlated with both stem lenticel density and dissolved soil methane concentration. In Alnus glutinosa, no emissions were observed from leaf surfaces. The results demonstrate that exclusion of tree-mediated methane emissions from flux measurement campaigns in forested peatlands will lead to an underestimation of ecosystem-wide methane emissions.

The Inference of Gene Trees with Species Trees

PubMed Central

Szöllősi, Gergely J.; Tannier, Eric; Daubin, Vincent; Boussau, Bastien

2015-01-01

This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can coexist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree–species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a more reliable basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree–species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution. PMID:25070970

Effects of open-top chambers on 'Valencia' orange trees

DOE Office of Scientific and Technical Information (OSTI.GOV)

Olszyk, D.M.; Takemoto, B.K.; Kats, G.

1992-01-01

Young 'Valencia' orange trees (Citrus sinensis(L) Osbeck) were grown for four years in large open-top chambers with ambient (nonfiltered) air or in outside air to determine any effects of the chambers on the air pollutant susceptibility of the trees. Long-term ozone average concentrations (12 hours, growing season) were 8% lower, and cumulative ozone dose (hourly values >0.1 microL/L) was 29% lower in ambient chambers compared to outside air. Fruit yields were much higher (>39%) for ambient chamber trees than for outside trees over three harvests, due at least partly to less fruit drop during the growing season for ambient chambermore » trees. Ambient chamber trees were much larger than outside trees and produced over twice as much leaf material over four years of study. Leaves on ambient chamber trees were larger and less dense than on outside trees. Leaves on ambient chamber trees were under more stress than leaves on outside trees during summer months; with lower stomatal conductances (14% average) and transpiration rates (12%), and more negative leaf water pressure potentials (28%). In contrast, leaves on ambient chamber trees had higher net photosynthetic rates (13%) and higher leaf starch concentrations prior to tree flowering (31%), than leaves on outside trees. While these results indicated large long-term impacts on tree growth which must be considered when using open-top chambers, they did not indicate any net effect of chambers on the air pollutant susceptibility of trees which would limit the usefulness of chamber tree data for air quality impact assessment purposes.« less

Size Matters a Lot: Drought-Affected Italian Oaks Are Smaller and Show Lower Growth Prior to Tree Death.

PubMed

Colangelo, Michele; Camarero, Jesús J; Borghetti, Marco; Gazol, Antonio; Gentilesca, Tiziana; Ripullone, Francesco

2017-01-01

Hydraulic theory suggests that tall trees are at greater risk of drought-triggered death caused by hydraulic failure than small trees. In addition the drop in growth, observed in several tree species prior to death, is often interpreted as an early-warning signal of impending death. We test these hypotheses by comparing size, growth, and wood-anatomy patterns of living and now-dead trees in two Italian oak forests showing recent mortality episodes. The mortality probability of trees is modeled as a function of recent growth and tree size. Drift-diffusion-jump (DDJ) metrics are used to detect early-warning signals. We found that the tallest trees of the anisohydric Italian oak better survived drought contrary to what was predicted by the theory. Dead trees were characterized by a lower height and radial-growth trend than living trees in both study sites. The growth reduction of now-dead trees started about 10 years prior to their death and after two severe spring droughts during the early 2000s. This critical transition in growth was detected by DDJ metrics in the most affected site. Dead trees were also more sensitive to drought stress in this site indicating different susceptibility to water shortage between trees. Dead trees did not form earlywood vessels with smaller lumen diameter than surviving trees but tended to form wider latewood vessels with a higher percentage of vessel area. Since living and dead trees showed similar competition we did not expect that moderate thinning and a reduction in tree density would increase the short-term survival probability of trees.

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

Treesearch

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...

Cavity tree selection by red-cockaded woodpeckers in relation to tree age

Treesearch

D. Craig Rudolph; Richard N. Conner

1991-01-01

We aged over 1350 Red-cockaded Woodpecker (Picoides borealis) cavity trees and a comparable number of randomly selected trees. Resulting data strongly support the hypothesis that Red-cockaded Woodpeckers preferentially select older trees. Ages of recently initiated cavity trees in the Texas study areas generally were similar to those of cavity trees...

Foraging Behaviour in Magellanic Woodpeckers Is Consistent with a Multi-Scale Assessment of Tree Quality

PubMed Central

Vergara, Pablo M.; Soto, Gerardo E.; Rodewald, Amanda D.; Meneses, Luis O.; Pérez-Hernández, Christian G.

2016-01-01

Theoretical models predict that animals should make foraging decisions after assessing the quality of available habitat, but most models fail to consider the spatio-temporal scales at which animals perceive habitat availability. We tested three foraging strategies that explain how Magellanic woodpeckers (Campephilus magellanicus) assess the relative quality of trees: 1) Woodpeckers with local knowledge select trees based on the available trees in the immediate vicinity. 2) Woodpeckers lacking local knowledge select trees based on their availability at previously visited locations. 3) Woodpeckers using information from long-term memory select trees based on knowledge about trees available within the entire landscape. We observed foraging woodpeckers and used a Brownian Bridge Movement Model to identify trees available to woodpeckers along foraging routes. Woodpeckers selected trees with a later decay stage than available trees. Selection models indicated that preferences of Magellanic woodpeckers were based on clusters of trees near the most recently visited trees, thus suggesting that woodpeckers use visual cues from neighboring trees. In a second analysis, Cox’s proportional hazards models showed that woodpeckers used information consolidated across broader spatial scales to adjust tree residence times. Specifically, woodpeckers spent more time at trees with larger diameters and in a more advanced stage of decay than trees available along their routes. These results suggest that Magellanic woodpeckers make foraging decisions based on the relative quality of trees that they perceive and memorize information at different spatio-temporal scales. PMID:27416115

Foraging Behaviour in Magellanic Woodpeckers Is Consistent with a Multi-Scale Assessment of Tree Quality.

PubMed

Vergara, Pablo M; Soto, Gerardo E; Moreira-Arce, Darío; Rodewald, Amanda D; Meneses, Luis O; Pérez-Hernández, Christian G

2016-01-01

Theoretical models predict that animals should make foraging decisions after assessing the quality of available habitat, but most models fail to consider the spatio-temporal scales at which animals perceive habitat availability. We tested three foraging strategies that explain how Magellanic woodpeckers (Campephilus magellanicus) assess the relative quality of trees: 1) Woodpeckers with local knowledge select trees based on the available trees in the immediate vicinity. 2) Woodpeckers lacking local knowledge select trees based on their availability at previously visited locations. 3) Woodpeckers using information from long-term memory select trees based on knowledge about trees available within the entire landscape. We observed foraging woodpeckers and used a Brownian Bridge Movement Model to identify trees available to woodpeckers along foraging routes. Woodpeckers selected trees with a later decay stage than available trees. Selection models indicated that preferences of Magellanic woodpeckers were based on clusters of trees near the most recently visited trees, thus suggesting that woodpeckers use visual cues from neighboring trees. In a second analysis, Cox's proportional hazards models showed that woodpeckers used information consolidated across broader spatial scales to adjust tree residence times. Specifically, woodpeckers spent more time at trees with larger diameters and in a more advanced stage of decay than trees available along their routes. These results suggest that Magellanic woodpeckers make foraging decisions based on the relative quality of trees that they perceive and memorize information at different spatio-temporal scales.

[The Application of the Fault Tree Analysis Method in Medical Equipment Maintenance].

PubMed

Liu, Hongbin

2015-11-01

In this paper, the traditional fault tree analysis method is presented, detailed instructions for its application characteristics in medical instrument maintenance is made. It is made significant changes when the traditional fault tree analysis method is introduced into the medical instrument maintenance: gave up the logic symbolic, logic analysis and calculation, gave up its complicated programs, and only keep its image and practical fault tree diagram, and the fault tree diagram there are also differences: the fault tree is no longer a logical tree but the thinking tree in troubleshooting, the definition of the fault tree's nodes is different, the composition of the fault tree's branches is also different.

Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest.

PubMed

Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

2016-11-18

Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest.

Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest

PubMed Central

Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

2016-01-01

Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest. PMID:27857198

TreeNetViz: revealing patterns of networks over tree structures.

PubMed

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

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

PubMed

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.

Is epidural analgesia during labor related to retained placenta?

PubMed

Sarit, Avraham; Sokolov, Amit; Many, Ariel

2016-05-01

To explore the influence of epidural analgesia on the course of the third stage of labor and on the incidence of the complete retained placenta as well as retained parts of the placenta. This is a population-based cohort study in a tertiary medical center. We collected data from all 4227 spontaneous singleton vaginal deliveries during 6 months and compared the incidence of retained placenta in deliveries with epidural analgesia with those without analgesia. Multivariable logistic regression was used to control for possible confounders. More than two-thirds of the women (69.25%) used epidural analgesia during their delivery. A need for intervention due to placental disorder during the third stage of labor was noted in 4.2% of all deliveries. Epidural analgesia appeared to be significantly (P=0.028) related to placental disorders compared with no analgesia: 4.8% vs. 3%, respectively. Deliveries with manual interventions during the third stage, for either complete retained placenta or suspected retained parts of the placenta, were associated with the use of epidural analgesia (P=0.008), oxytocin (P=0.002) and older age at delivery (P=0.000), but when including all factors in a multivariable analysis, using a stepwise logistic regression, the factors that were independently associated with interventions for placental disruption during the third stage of delivery were previous cesarean section, oxytocin use and, marginally, older age. Complete retained placenta and retained parts of the placenta share the same risk factors. Epidural analgesia does not directly influence the incidence of complete retained placenta or retained parts, though clinically linked through increased oxytocin use. The factors that were independently associated with interventions for placental disruption during the third stage of delivery were previous cesarean section, oxytocin use and older age.

[The impact of personality traits on adolescents' adaptation and compliance to clear retainers].

PubMed

Xu, Fan; Tang, Guo-Hua

2017-02-01

The aim of this study was to evaluate the adolescents' adaptation and compliance to clear retainers, and to investigate their associations with personality traits. Fifty adolescents at the end of fixed orthodontic treatment were consecutively recruited. After debonding the fixed orthodontic appliances, clear retainers were used. Participants were asked to fill questionnaires 2 months after wearing the clear retainers. A questionnaire was designed to evaluate their adaptation and compliance for clear retianers. Eysenck personality questionnaire was used to assess the personality traits. Spearman rank correlation was used to analyze the associations between personality traits with the adaptation and compliance to clear retainers using SAS8.0 software package. Forty-two of 50 adolescents accomplished the questionnaires. 76% felt no mucous irritation, 95% felt no influence on socializing. However, 75% showed oral constraint, 71% felt impaired speech. Moreover, 40% adolescents wore the retainers less than 18 hours per day. 31% patients had their aligner lost. 83% patients did not brush their teeth after each meal. Neuroticism was positively associated with the effect of impaired chewing (r=0.32). Psychoticism was positively associated with the oral constraint (r=0.31) and facial muscular soreness (r=0.35), but negatively associated with the influence on emotion (r=-0.34). Extraversion was positively associated with the retainers' damage (r=0.31). Adolescents showed good adaptation for clear retainers, but unsatisfactory compliance. There are associations between adolescents' adaptation and compliance for clear retainers and personality traits. These results suggest that clinicians should pay more attention to the compliance of adolescents when using clear retainer. Personality traits could be a useful prediction to assess the compliance for clear aligners.

Two-year survival analysis of twisted wire fixed retainer versus spiral wire and fiber-reinforced composite retainers: a preliminary explorative single-blind randomized clinical trial.

PubMed

Sobouti, Farhad; Rakhshan, Vahid; Saravi, Mahdi Gholamrezaei; Zamanian, Ali; Shariati, Mahsa

2016-03-01

Traditional retainers (both metal and fiber-reinforced composite [FRC]) have limitations, and a retainer made from more flexible ligature wires might be advantageous. We aimed to compare an experimental design with two traditional retainers. In this prospective preliminary clinical trial, 150 post-treatment patients were enrolled and randomly divided into three groups of 50 patients each to receive mandibular canine-to-canine retainers made of FRC, flexible spiral wire (FSW), and twisted wire (TW). The patients were monitored monthly. The time at which the first signs of breakage/debonding were detected was recorded. The success rates of the retainers were compared using chi-squared, Kaplan-Meier, and Cox proportional-hazard regression analyses (α = 0.05). In total, 42 patients in the FRC group, 41 in the FSW group, and 45 in the TW group completed the study. The 2-year failure rates were 35.7% in the FRC group, 26.8% in the FSW group, and 17.8% in the TW group. These rates differed insignificantly (chi-squared p = 0.167). According to the Kaplan-Meier analysis, failure occurred at 19.95 months in the FRC group, 21.37 months in the FSW group, and 22.36 months in the TW group. The differences between the survival rates in the three groups were not significant (Cox regression p = 0.146). Although the failure rate of the experimental retainer was two times lower than that of the FRC retainer, the difference was not statistically significant. The experimental TW retainer was successful, and larger studies are warranted to verify these results.

Two-year survival analysis of twisted wire fixed retainer versus spiral wire and fiber-reinforced composite retainers: a preliminary explorative single-blind randomized clinical trial

PubMed Central

Sobouti, Farhad; Rakhshan, Vahid; Saravi, Mahdi Gholamrezaei; Zamanian, Ali

2016-01-01

Objective Traditional retainers (both metal and fiber-reinforced composite [FRC]) have limitations, and a retainer made from more flexible ligature wires might be advantageous. We aimed to compare an experimental design with two traditional retainers. Methods In this prospective preliminary clinical trial, 150 post-treatment patients were enrolled and randomly divided into three groups of 50 patients each to receive mandibular canine-to-canine retainers made of FRC, flexible spiral wire (FSW), and twisted wire (TW). The patients were monitored monthly. The time at which the first signs of breakage/debonding were detected was recorded. The success rates of the retainers were compared using chi-squared, Kaplan-Meier, and Cox proportional-hazard regression analyses (α = 0.05). Results In total, 42 patients in the FRC group, 41 in the FSW group, and 45 in the TW group completed the study. The 2-year failure rates were 35.7% in the FRC group, 26.8% in the FSW group, and 17.8% in the TW group. These rates differed insignificantly (chi-squared p = 0.167). According to the Kaplan-Meier analysis, failure occurred at 19.95 months in the FRC group, 21.37 months in the FSW group, and 22.36 months in the TW group. The differences between the survival rates in the three groups were not significant (Cox regression p = 0.146). Conclusions Although the failure rate of the experimental retainer was two times lower than that of the FRC retainer, the difference was not statistically significant. The experimental TW retainer was successful, and larger studies are warranted to verify these results. PMID:27019825

Long-term outcome of cemented versus screw-retained implant-supported partial restorations.

PubMed

Nissan, Joseph; Narobai, Demitri; Gross, Ora; Ghelfan, Oded; Chaushu, Gavriel

2011-01-01

The present study was designed to compare the long-term outcome and complications of cemented versus screw-retained implant restorations in partially edentulous patients. Consecutive patients with bilateral partial posterior edentulism comprised the study group. Implants were placed, and cemented or screw-retained restorations were randomly assigned to the patients in a split-mouth design. Follow-up (up to 15 years) examinations were performed every 6 months in the first year and every 12 months in subsequent years. The following parameters were evaluated and recorded at each recall appointment: ceramic fracture, abutment screw loosening, metal frame fracture, Gingival Index, and marginal bone loss. Thirty-eight patients were treated with 221 implants to support partial prostheses. No implants during the follow-up period (mean follow-up, 66 ± 47 months for screw-retained restorations [range, 18 to 180 months] and 61 ± 40 months for cemented restorations [range, 18 to 159 months]). Ceramic fracture occurred significantly more frequently (P < .001) in screw-retained (38% ± 0.3%) than in cemented (4% ± 0.1%) restorations. Abutment screw loosening occurred statistically significantly more often (P = .001) in screw-retained (32% ± 0.3%) than in cement-retained (9% ± 0.2%) restorations. There were no metal frame fractures in either type of restoration. The mean Gingival Index scores were statistically significantly higher (P < .001) for screw-retained (0.48 ± 0.5) than for cemented (0.09 ± 0.3) restorations. The mean marginal bone loss was statistically significantly higher (P < .001) for screw-retained (1.4 ± 0.6 mm) than for cemented (0.69 ± 0.5 mm) restorations. The long-term outcome of cemented implant-supported restorations was superior to that of screw-retained restorations, both clinically and biologically.

A comparison of preload values in gold and titanium dental implant retaining screws.

PubMed

Doolabh, R; Dullabh, H D; Sykes, L M

2014-08-01

This in vitro investigation compared the effect of using either gold or titanium retaining screws on preload in the dental implant- abutment complex. Inadequate preload can result in screw loosening, whilst fracture may occur if preload is excessive. These are the most commonly reported complications in implant-retained prostheses, and result in unscheduled, costly and time-consuming visits for the patient and the clinician. This study investigated changes in preload generation after repeated torque applications to gold and titanium screws. The test set-up consisted of an implant body, a cylindrical transmucosa abutment, and the test samples of gold and of titanium retaining screws. The implant bodies were anchored using a load cell, and the transmucosal abutments were attached using either gold or titanium retaining screws. A torque gauge was used to apply torque of 20Ncm, 32Ncm, and 40Ncm to the retaining screws. The preloads generated in each screw type were compared at each torque setting, and after repeated tightening episodes. In addition, the effect of applying torque beyond the manufacturers' recommendations was also examined. Gold retaining screws were found to achieve consistently higher preload values than titanium retaining screws. Preload values were not significantly different from the first to the tenth torque cycle. Titanium screws showed more consistent preload values, albeit lower than those of the gold screws. However due to possible galling of the internal thread of the implant body by titanium screws, gold screws remain the retaining screw of choice. Based on the findings of this study, gold retaining screws generate better preload than titanium. Torque beyond the manufacturers' recommendations resulted in a more stable implant complex. However, further investigations, with torque applications repeated until screw breakage, are needed to advise on ideal maintenance protocols.

PhyloExplorer: a web server to validate, explore and query phylogenetic trees

PubMed Central

Ranwez, Vincent; Clairon, Nicolas; Delsuc, Frédéric; Pourali, Saeed; Auberval, Nicolas; Diser, Sorel; Berry, Vincent

2009-01-01

Background Many important problems in evolutionary biology require molecular phylogenies to be reconstructed. Phylogenetic trees must then be manipulated for subsequent inclusion in publications or analyses such as supertree inference and tree comparisons. However, no tool is currently available to facilitate the management of tree collections providing, for instance: standardisation of taxon names among trees with respect to a reference taxonomy; selection of relevant subsets of trees or sub-trees according to a taxonomic query; or simply computation of descriptive statistics on the collection. Moreover, although several databases of phylogenetic trees exist, there is currently no easy way to find trees that are both relevant and complementary to a given collection of trees. Results We propose a tool to facilitate assessment and management of phylogenetic tree collections. Given an input collection of rooted trees, PhyloExplorer provides facilities for obtaining statistics describing the collection, correcting invalid taxon names, extracting taxonomically relevant parts of the collection using a dedicated query language, and identifying related trees in the TreeBASE database. Conclusion PhyloExplorer is a simple and interactive website implemented through underlying Python libraries and MySQL databases. It is available at: and the source code can be downloaded from: . PMID:19450253

Recursive algorithms for phylogenetic tree counting.

PubMed

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.

Fuel cell cassette with compliant seal

DOEpatents

Karl, Haltiner, Jr. J.; Anthony, Derose J.; Klotzbach, Darasack C.; Schneider, Jonathan R.

2017-11-07

A fuel cell cassette for forming a fuel cell stack along a fuel cell axis includes a cell retainer, a plate positioned axially to the cell retainer and defining a space axially with the cell retainer, and a fuel cell having an anode layer and a cathode layer separated by an electrolyte layer. The outer perimeter of the fuel cell is positioned in the space between the plate and the cell retainer, thereby retaining the fuel cell and defining a cavity between the cell retainer, the fuel cell, and the plate. The fuel cell cassette also includes a seal disposed within the cavity for sealing the edge of the fuel cell. The seal is compliant at operational temperatures of the fuel cell, thereby allowing lateral expansion and contraction of the fuel cell within the cavity while maintaining sealing at the edge of the fuel cell.

Macroscopic and histological characteristics of retained placenta: A prospectively collected case-control study.

PubMed

Endler, Margit; Saltvedt, Sissel; Papadogiannakis, Nikos

2016-05-01

Retained placenta is a potentially fatal obstetric disorder due to postpartum hemorrhage, its pathophysiology is however unknown. We aimed to assess if retained placenta was associated with increased macroscopic and histological signs of placental maternal underperfusion, a pattern otherwise seen in preeclampsia and other disorders of defective placentation. This was a case-control study of retained (n = 49) and non-retained (n = 47) placentas, collected from full-term singleton and otherwise healthy pregnancies, carried out at a tertiary level obstetric department. Macroscopic and histological analysis was performed. Signs of maternal placental underperfusion and signs of placental inflammation, fetal vascular thrombo-occlusive disease and increased placental attachment were recorded in a primary and secondary analysis respectively. Variables were compared groupwise using unconditional logistic regression or comparison of median or mean values. Compared to non-retained placentas retained placentas had a significantly smaller surface area (p = 0.05), were more oblong in shape (OR 5.24 95% CI:1.34-20.21) and showed overall more signs of maternal underperfusion (OR 2.52 95% CI: 1.07-5.87). There was no significant difference in signs of placental inflammation, fetal vascular thrombo-occlusive disease or placenta accreta but basal plate myometrial fibers were more common among retained placentas. In regard to shape, surface area and histological signs of maternal placental underperfusion, retained placentas showed a histological pattern similar to that seen in preeclamptic placentas. Copyright © 2016 Elsevier Ltd. All rights reserved.

Directional phytoscreening: contaminant gradients in trees for plume delineation.

PubMed

Limmer, Matt A; Shetty, Mikhil K; Markus, Samantha; Kroeker, Ryan; Parker, Beth L; Martinez, Camilo; Burken, Joel G

2013-08-20

Tree sampling methods have been used in phytoscreening applications to delineate contaminated soil and groundwater, augmenting traditional investigative methods that are time-consuming, resource-intensive, invasive, and costly. In the past decade, contaminant concentrations in tree tissues have been shown to reflect the extent and intensity of subsurface contamination. This paper investigates a new phytoscreening tool: directional tree coring, a concept originating from field data that indicated azimuthal concentrations in tree trunks reflected the concentration gradients in the groundwater around the tree. To experimentally test this hypothesis, large diameter trees were subjected to subsurface contaminant concentration gradients in a greenhouse study. These trees were then analyzed for azimuthal concentration gradients in aboveground tree tissues, revealing contaminant centroids located on the side of the tree nearest the most contaminated groundwater. Tree coring at three field sites revealed sufficiently steep contaminant gradients in trees reflected nearby groundwater contaminant gradients. In practice, trees possessing steep contaminant gradients are indicators of steep subsurface contaminant gradients, providing compass-like information about the contaminant gradient, pointing investigators toward higher concentration regions of the plume.

Measuring (bio)physical tree properties using accelerometers

NASA Astrophysics Data System (ADS)

van Emmerik, Tim; Steele-Dunne, Susan; Hut, Rolf; Gentine, Pierre; Selker, John; van de Giesen, Nick

2017-04-01

Trees play a crucial role in the water, carbon and nitrogen cycle on local, regional and global scales. Understanding the exchange of heat, water, and CO2 between trees and the atmosphere is important to assess the impact of drought, deforestation and climate change. Unfortunately, ground measurements of tree dynamics are often expensive, or difficult due to challenging environments. We demonstrate the potential of measuring (bio)physical properties of trees using robust and affordable acceleration sensors. Tree sway is dependent on e.g. mass and wind energy absorption of the tree. By measuring tree acceleration we can relate the tree motion to external loads (e.g. precipitation), and tree (bio)physical properties (e.g. mass). Using five months of acceleration data of 19 trees in the Brazilian Amazon, we show that the frequency spectrum of tree sway is related to mass, precipitation, and canopy drag. This presentation aims to show the concept of using accelerometers to measure tree dynamics, and we acknowledge that the presented example applications is not an exhaustive list. Further analyses are the scope of current research, and we hope to inspire others to explore additional applications.

Size Matters a Lot: Drought-Affected Italian Oaks Are Smaller and Show Lower Growth Prior to Tree Death

PubMed Central

Colangelo, Michele; Camarero, Jesús J.; Borghetti, Marco; Gazol, Antonio; Gentilesca, Tiziana; Ripullone, Francesco

2017-01-01

Hydraulic theory suggests that tall trees are at greater risk of drought-triggered death caused by hydraulic failure than small trees. In addition the drop in growth, observed in several tree species prior to death, is often interpreted as an early-warning signal of impending death. We test these hypotheses by comparing size, growth, and wood-anatomy patterns of living and now-dead trees in two Italian oak forests showing recent mortality episodes. The mortality probability of trees is modeled as a function of recent growth and tree size. Drift-diffusion-jump (DDJ) metrics are used to detect early-warning signals. We found that the tallest trees of the anisohydric Italian oak better survived drought contrary to what was predicted by the theory. Dead trees were characterized by a lower height and radial-growth trend than living trees in both study sites. The growth reduction of now-dead trees started about 10 years prior to their death and after two severe spring droughts during the early 2000s. This critical transition in growth was detected by DDJ metrics in the most affected site. Dead trees were also more sensitive to drought stress in this site indicating different susceptibility to water shortage between trees. Dead trees did not form earlywood vessels with smaller lumen diameter than surviving trees but tended to form wider latewood vessels with a higher percentage of vessel area. Since living and dead trees showed similar competition we did not expect that moderate thinning and a reduction in tree density would increase the short-term survival probability of trees. PMID:28270816

Paleoecological insights on fixed tree island development in the Florida Everglades: I. environmental controls: Chapter 4

USGS Publications Warehouse

Willard, Debra A.; Murray, James B.; Holmes, Charles W.; Korvela, Michael S.; Mason, Daniel; Orem, William H.; Towles, D. Timothy; Sklar, Fred H.; van der Valk, A.

2002-01-01

Palynological and geochemical analyses of sediment cores collected on two tree islands in the Florida Everglades indicate long-term hydrologic and chemical differences between tree islands and surrounding marshes and sloughs. Gumbo Limbo and Nuthouse tree islands are elongate, teardrop-shaped islands in Water Conservation Area 3B. Prior to tree island formation at both sites, pollen records indicate that sites on modern tree island heads were covered with sawgrass marshes with abundant weedy annuals. Such vegetation is characteristic of moderate water depths and hydroperiods with frequent droughts or disturbances. Contemporaneously deposited sediments on tree island tails indicate progressively deeper water conditions with increasing distance from the head; wetlands surrounding tree islands were covered by sloughs with deep water and long hydroperiods. Tree island formation occurred at about 1200 BC on Gumbo Limbo Island, with mature tree island vegetation established by about 800 AD. On Nuthouse Island, tree island formation occurred around 300 AD, shifting to mature tree island vegetation around 1400 AD. Thus, tree island formation began on these islands between 3.2 Ka and 1.7 Ka. Maturation of tree islands took between 1,000 and 2,000 years, and vegetation on these tree islands has been relatively stable for the last 600–1,200 years. Phosphorus levelson tree island heads have been extremely high (approximately six times greaterthan baseline levels in marshes) throughout the history of the sites, and phosphorus content in tree island tails began increasing when tree island formation occurred. Elevated phosphorus content may reflect the long-termpresence of wading birds at these sites and provide a proxy for reconstructing the historic distribution of wading bird populations.

Understory plant communities and the functional distinction between savanna trees, forest trees, and pines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Veldman, Joseph W.; Mattingly, W. Brett; Brudvig, Lars A.

Although savanna trees and forest trees are thought to represent distinct functional groups with different effects on ecosystem processes, few empirical studies have examined these effects. In particular, it remains unclear if savanna and forest trees differ in their ability to coexist with understory plants, which comprise the majority of plant diversity in most savannas. We used structural equation modeling (SEM) and data from 157 sites across three locations in the southeastern United States to understand the effects of broadleaf savanna trees, broadleaf forest trees, and pine trees on savanna understory plant communities. After accounting for underlying gradients in firemore » frequency and soil moisture, abundances (i.e., basal area and stem density) of forest trees and pines, but not savanna trees, were negatively correlated with the cover and density (i.e., local-scale species richness) of C4 graminoid species, a defining savanna understory functional group that is linked to ecosystem flammability. In analyses of the full understory community, abundances of trees from all functional groups were negatively correlated with species density and cover. For both the C4 and full communities, fire frequency promoted understory plants directly, and indirectly by limiting forest tree abundance. There was little indirect influence of fire on the understory mediated through savanna trees and pines, which are more fire tolerant than forest trees. We conclude that tree functional identity is an important factor that influences overstory tree relationships with savanna understory plant communities. In particular, distinct relationships between trees and C4 graminoids have implications for grass-tree coexistence and vegetation-fire feedbacks that maintain savanna environments and their associated understory plant diversity.« less

Tree-ring δ13C and δ18O, leaf δ13C and wood and leaf N status demonstrate tree growth strategies and predict susceptibility to disturbance

PubMed Central

Billings, S.A.; Boone, A.S.; Stephen, F.M.

2016-01-01

Understanding how tree growth strategies may influence tree susceptibility to disturbance is an important goal, especially given projected increases in diverse ecological disturbances this century. We use growth responses of tree rings to climate, relationships between tree-ring stable isotopic signatures of carbon (δ13C) and oxygen (δ18O), wood nitrogen concentration [N], and contemporary leaf [N] and δ13C values to assess potential historic drivers of tree photosynthesis in dying and apparently healthy co-occurring northern red oak (Quercus rubra L. (Fagaceae)) during a region-wide oak decline event in Arkansas, USA. Bole growth of both healthy and dying trees responded negatively to drought severity (Palmer Drought Severity Index) and temperature; healthy trees exhibited a positive, but small, response to growing season precipitation. Contrary to expectations, tree-ring δ13C did not increase with drought severity. A significantly positive relationship between tree-ring δ13C and δ18O was evident in dying trees (P < 0.05) but not in healthy trees. Healthy trees’ wood exhibited lower [N] than that of dying trees throughout most of their lives (P < 0.05), and we observed a significant, positive relationship (P < 0.05) in healthy trees between contemporary leaf δ13C and leaf N (by mass), but not in dying trees. Our work provides evidence that for plants in which strong relationships between δ13C and δ18O are not evident, δ13C may be governed by plant N status. The data further imply that historic photosynthesis in healthy trees was linked to N status and, perhaps, C sink strength to a greater extent than in dying trees, in which tree-ring stable isotopes suggest that historic photosynthesis was governed primarily by stomatal regulation. This, in turn, suggests that assessing the relative dominance of photosynthetic capacity vs stomatal regulation as drivers of trees’ C accrual may be a feasible means of predicting tree responses to some disturbance events. Our work demonstrates that a dual isotope, tree-ring approach can be integrated with tree N status to begin to unravel a fundamental question in forest ecology: why do some trees die during a disturbance, while other conspecifics with apparently similar access to resources remain healthy? PMID:26960389

Uncoupling between soil and xylem water isotopic composition: how to discriminate mobile and tightly-bound water?

NASA Astrophysics Data System (ADS)

Martín Gómez, Paula; Aguilera, Mònica; Pemán, Jesús; Gil Pelegrín, Eustaquio; Ferrio, Juan Pedro

2014-05-01

As a general rule, no isotopic fractionation occurs during water uptake and water transport, thus, xylem water reflects source water. However, this correspondence does not always happen. Isotopic enrichment of xylem water has been found in several cases and has been either associated to 'stem processes' like cuticular evaporation 1 and xylem-phloem communication under water stress 2,3 or to 'soil processes' such as species-specific use of contrasting water sources retained at different water potential forces in soil. In this regard, it has been demonstrated that mobile and tightly-bound water may show different isotopic signature 4,5. However, standard cryogenic distillation does not allow to separate different water pools within soil samples. Here, we carried out a study in a mixed adult forest (Pinus sylvestris, Quercus subpyrenaica and Buxus sempervirens) growing in a relatively deep loamy soil in the Pre-Pyrenees. During one year, we sampled xylem from twigs and soil at different depths (10, 30 and 50 cm). We also sampled xylem from trunk and bigger branches to assess whether xylem water was enriched in the distal parts of the tree. We found average deviations in the isotopic signature from xylem to soil of 4o 2o and 2.4o in δ18O and 18.3o 7.3o and 8.9o in δ2H, for P.sylvestris, Q.subpyrenaica and B.sempervirens respectively. Xylem water was always enriched compared to soil. In contrast, we did not find clear differences in isotopic composition between xylem samples along the tree. Declining the hypothesis that 'stem processes' would cause these uncoupling between soil and xylem isotopic values, we tested the possibility to separate mobile and tightly-bound water by centrifugation. Even though we could separate two water fractions in soils close to saturation, we could not recover a mobile fraction in drier soils. In this regard, we welcome suggestions on alternatives to separate different soil fractions in order to find the correspondence between soil and xylem water. References 1. Dawson, T. E. & Ehleringer, J. R. Isotopic enrichment of water in the 'woody' tissues of plants: Implications for plant water source, water uptake, and other studies which use the stable isotopic composition of cellulose. (1993). 2. Cernusak, L. a, Farquhar, G. D. & Pate, J. S. Environmental and physiological controls over oxygen and carbon isotope composition of Tasmanian blue gum, Eucalyptus globulus. Tree Physiol. 25, 129-46 (2005). 3. Bertrand, G. et al. Determination of spatiotemporal variability of tree water uptake using stable isotopes (δ 18 O, δ 2 H) in an alluvial system supplied by a high-altitude watershed, Pfyn forest, Switzerland. Ecohydrology (2012). doi:10.1002/eco.1347 4. Tang, K. & Feng, X. The effect of soil hydrology on the oxygen and hydrogen isotopic compositions of plants ' source water. 185, (2001). 5. Brooks, J. R., Barnard, H. R., Coulombe, R. & McDonnell, J. J. Ecohydrologic separation of water between trees and streams in a Mediterranean climate. Nat. Geosci. 3, 100-104 (2009). Acknowledgements This study was funded by RESILFOR project (AGL 2012-40039-C02-02) and FPU fellowship from the Spanish Ministry of Science and Innovation (FPU12/00648). We thank Instituto de Formación Agroambiental de Jaca and Unidad de Salud de los Bosques de Aragón for their support on field work and we feel very grateful to Miguel Ángel Lázaro for climbing the studied trees, José María Alcaire for one year of rain collection and Pilar Sopeña and Ma Josep Pau for laboratory analysis. Helpful comments by Jordi Voltas on statistical analysis have improved the quality of the work.

Bats in a Farming Landscape Benefit from Linear Remnants and Unimproved Pastures

PubMed Central

Lentini, Pia E.; Gibbons, Philip; Fischer, Joern; Law, Brad; Hanspach, Jan; Martin, Tara G.

2012-01-01

Schemes designed to make farming landscapes less hostile to wildlife have been questioned because target taxa do not always respond in the expected manner. Microbats are often overlooked in this process, yet persist in agricultural landscapes and exert top-down control of crop pests. We investigated the relationship between microbats and measures commonly incorporated into agri-environment schemes, to derive management recommendations for their ongoing conservation. We used acoustic detectors to quantify bat species richness, activity, and feeding in 32 linear remnants and adjacent fields across an agricultural region of New South Wales, Australia. Nocturnal arthropods were simultaneously trapped using black-light traps. We recorded 91,969 bat calls, 17,277 of which could be attributed to one of the 13 taxa recorded, and 491 calls contained feeding buzzes. The linear remnants supported higher bat activity than the fields, but species richness and feeding activity did not significantly differ. We trapped a mean 87.6 g (±17.6 g SE) of arthropods per night, but found no differences in biomass between land uses. Wider linear remnants with intact native vegetation supported more bat species, as did those adjacent to unsealed, as opposed to sealed roads. Fields of unimproved native pastures, with more retained scattered trees and associated hollows and logs, supported the greatest bat species richness and activity. We conclude that the juxtaposition of linear remnants of intact vegetation and scattered trees in fields, coupled with less-intensive land uses such as unimproved pastures will benefit bat communities in agricultural landscapes, and should be incorporated into agri-environment schemes. In contrast, sealed roads may act as a deterrent. The “wildlife friendly farming” vs “land sparing” debate has so far primarily focussed on birds, but here we have found evidence that the integration of both approaches could particularly benefit bats. PMID:23155378

N cycling and the composition of terpenes and tannins in boreal forest soils: Effects of logging residues

NASA Astrophysics Data System (ADS)

Smolander, Aino; Kitunen, Veikko; Kukkola, Mikko; Tamminen, Pekka

2014-05-01

There is increasing evidence available that certain terpenes and tannins may mediate substantial changes in nitrogen cycling processes in boreal forest soils. Terpenes and tannins are two important groups of plant secondary metabolites: Terpenes are hydrocarbons having different number of isoprene-derived units and tannins are complex polyphenolic compounds able to interact with proteins. Logging residues, consisting of fresh tree tops and branches with needles contain large amounts of terpenes and tannins. Currently there is increasing demand for forest biomass for bioenergy production. Therefore, harvesting of logging residues has become more common from both clear-cutting and thinning stands, instead of conventional stem-only harvest where logging residues are retained on the site. Our aim was to determine how logging residues affect soil N cycling processes in Scots pine and Norway spruce thinning stands in long-term, and how these processes are related to the composition of terpenes and tannins in the soil. Samples were taken from the humus layer of pine and spruce experiments which had been thinned 4-to-19 years before; in the thinning different amounts of logging residues had been distributed on the plots. Logging residues had only little effect on soil microbial biomass N or C. However, in several sites logging residues increased the rate of net N mineralization and the ratios net N mineralization/ C mineralization and net N mineralization/microbial biomass N, and these positive effects were very long-lasting. Logging residues also changed the composition of different terpenes and condensed tannins in soil. In general, with regard to the processes and ratios indicating N availability, stem-only harvest seems to be more favorable than whole-tree harvest. The results from long-term field experiments will be discussed in relation to the effects of different terpenes and tannins, observed in short-term laboratory experiments, on N cycling processes.

Explaining evolution via constrained persistent perfect phylogeny

PubMed Central

2014-01-01

Background The perfect phylogeny is an often used model in phylogenetics since it provides an efficient basic procedure for representing the evolution of genomic binary characters in several frameworks, such as for example in haplotype inference. The model, which is conceptually the simplest, is based on the infinite sites assumption, that is no character can mutate more than once in the whole tree. A main open problem regarding the model is finding generalizations that retain the computational tractability of the original model but are more flexible in modeling biological data when the infinite site assumption is violated because of e.g. back mutations. A special case of back mutations that has been considered in the study of the evolution of protein domains (where a domain is acquired and then lost) is persistency, that is the fact that a character is allowed to return back to the ancestral state. In this model characters can be gained and lost at most once. In this paper we consider the computational problem of explaining binary data by the Persistent Perfect Phylogeny model (referred as PPP) and for this purpose we investigate the problem of reconstructing an evolution where some constraints are imposed on the paths of the tree. Results We define a natural generalization of the PPP problem obtained by requiring that for some pairs (character, species), neither the species nor any of its ancestors can have the character. In other words, some characters cannot be persistent for some species. This new problem is called Constrained PPP (CPPP). Based on a graph formulation of the CPPP problem, we are able to provide a polynomial time solution for the CPPP problem for matrices whose conflict graph has no edges. Using this result, we develop a parameterized algorithm for solving the CPPP problem where the parameter is the number of characters. Conclusions A preliminary experimental analysis shows that the constrained persistent perfect phylogeny model allows to explain efficiently data that do not conform with the classical perfect phylogeny model. PMID:25572381

Using tree diversity to compare phylogenetic heuristics.

PubMed

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.

Tree-ring isotopes reveal drought sensitivity in trees killed by spruce beetle outbreaks in south-central Alaska.

PubMed

Csank, Adam Z; Miller, Amy E; Sherriff, Rosemary L; Berg, Edward E; Welker, Jeffrey M

2016-10-01

Increasing temperatures have resulted in reduced growth and increased tree mortality across large areas of western North American forests. We use tree-ring isotope chronologies (δ 13 C and δ 18 O) from live and dead trees from four locations in south-central Alaska, USA, to test whether white spruce trees killed by recent spruce beetle (Dendroctonus rufipennis Kirby) outbreaks showed evidence of drought stress prior to death. Trees that were killed were more sensitive to spring/summer temperature and/or precipitation than trees that survived. At two of our sites, we found greater correlations between the δ 13 C and δ 18 O chronologies and spring/summer temperatures in dead trees than in live trees, suggesting that trees that are more sensitive to temperature-induced drought stress are more likely to be killed. At one site, the difference between δ 13 C in live and dead trees was related to winter/spring precipitation, with dead trees showing stronger correlations between δ 13 C and precipitation, again suggesting increased water stress in dead trees. At all sites where δ 18 O was measured, δ 18 O chronologies showed the greatest difference in climate response between live and dead groups, with δ 18 O in live trees correlating more strongly with late winter precipitation than dead trees. Our results indicate that sites where trees are already sensitive to warm or dry early growing-season conditions experienced the most beetle-kill, which has important implications for forecasting future mortality events in Alaska. © 2016 by the Ecological Society of America.

Polynomial-Time Algorithms for Building a Consensus MUL-Tree

PubMed Central

Cui, Yun; Jansson, Jesper

2012-01-01

Abstract A multi-labeled phylogenetic tree, or MUL-tree, is a generalization of a phylogenetic tree that allows each leaf label to be used many times. MUL-trees have applications in biogeography, the study of host–parasite cospeciation, gene evolution studies, and computer science. Here, we consider the problem of inferring a consensus MUL-tree that summarizes a given set of conflicting MUL-trees, and present the first polynomial-time algorithms for solving it. In particular, we give a straightforward, fast algorithm for building a strict consensus MUL-tree for any input set of MUL-trees with identical leaf label multisets, as well as a polynomial-time algorithm for building a majority rule consensus MUL-tree for the special case where every leaf label occurs at most twice. We also show that, although it is NP-hard to find a majority rule consensus MUL-tree in general, the variant that we call the singular majority rule consensus MUL-tree can be constructed efficiently whenever it exists. PMID:22963134

Polynomial-time algorithms for building a consensus MUL-tree.

PubMed

Cui, Yun; Jansson, Jesper; Sung, Wing-Kin

2012-09-01

A multi-labeled phylogenetic tree, or MUL-tree, is a generalization of a phylogenetic tree that allows each leaf label to be used many times. MUL-trees have applications in biogeography, the study of host-parasite cospeciation, gene evolution studies, and computer science. Here, we consider the problem of inferring a consensus MUL-tree that summarizes a given set of conflicting MUL-trees, and present the first polynomial-time algorithms for solving it. In particular, we give a straightforward, fast algorithm for building a strict consensus MUL-tree for any input set of MUL-trees with identical leaf label multisets, as well as a polynomial-time algorithm for building a majority rule consensus MUL-tree for the special case where every leaf label occurs at most twice. We also show that, although it is NP-hard to find a majority rule consensus MUL-tree in general, the variant that we call the singular majority rule consensus MUL-tree can be constructed efficiently whenever it exists.

Estimating the probability of survival of individual shortleaf pine (Pinus echinata mill.) trees

Treesearch

Sudip Shrestha; Thomas B. Lynch; Difei Zhang; James M. Guldin

2012-01-01

A survival model is needed in a forest growth system which predicts the survival of trees on individual basis or on a stand basis (Gertner, 1989). An individual-tree modeling approach is one of the better methods available for predicting growth and yield as it provides essential information about particular tree species; tree size, tree quality and tree present status...

The Concept of Cosmic Tree in Armenian and Iranian Cosmologies

NASA Astrophysics Data System (ADS)

Farmanyan, S. V.; Mickaelian, A. M.

2016-09-01

Cosmic Tree or Tree of Life is a common motif in various world theologies, mythologies, and philosophies. In the present study we focus on Armenian and Iranian Cosmic Tree. In ancient Armenia, the Tree of Life (Կենաց Ծառ) is a religious symbol and is drawn on walls of fortresses and carved on the armour of warriors. According to ancient Armenians the center of the Universe is located at the crown of the tree or the column, which is the closest to the sky. We explore the idea of cosmic tree in the riddles, prayers, medieval rituals and miniatures. In the riddles, the tree mostly symbolizes the celestial phenomena (Sun, Stars, and Heavens), different units of time (years, months, weeks, days, and seasons), the people, Jerusalem, the apostles and Jesus Christ. The branches of the tree were equally divided on the right and left sides of the stem, with each branch having one leaf, and one leaf on the apex of the tree. Servants stood on each side of the tree with one of their hands up as if they are taking care of the tree. In pre-Islamic Persian mythology, the Gaokerena world tree is a large, sacred Haoma tree which bears all seeds. Ahriman created a frog to invade the tree and destroy it, aiming at preventing all trees from growing on the Earth. As a reaction, God (Ahura Mazda) created two kar fish staring at the frog to guard the tree. The concept of world tree in Persian Mythology is very closely related to the concept of the Tree of Life. Another related issue in ancient mythology of Iran is the myth of Mashya and Mashyane, two trees who were the ancestors of all living beings. This myth can be considered as a prototype for the creation myth where living beings are created by Gods (who have human forms). We come to the conclusion that in both cultures, no matter of the present different religions, the perception of Cosmic Tree is interconnected to the life on our planet and served as a metaphor for common descent in the evolutionary sense.

A new fast method for inferring multiple consensus trees using k-medoids.

PubMed

Tahiri, Nadia; Willems, Matthieu; Makarenkov, Vladimir

2018-04-05

Gene trees carry important information about specific evolutionary patterns which characterize the evolution of the corresponding gene families. However, a reliable species consensus tree cannot be inferred from a multiple sequence alignment of a single gene family or from the concatenation of alignments corresponding to gene families having different evolutionary histories. These evolutionary histories can be quite different due to horizontal transfer events or to ancient gene duplications which cause the emergence of paralogs within a genome. Many methods have been proposed to infer a single consensus tree from a collection of gene trees. Still, the application of these tree merging methods can lead to the loss of specific evolutionary patterns which characterize some gene families or some groups of gene families. Thus, the problem of inferring multiple consensus trees from a given set of gene trees becomes relevant. We describe a new fast method for inferring multiple consensus trees from a given set of phylogenetic trees (i.e. additive trees or X-trees) defined on the same set of species (i.e. objects or taxa). The traditional consensus approach yields a single consensus tree. We use the popular k-medoids partitioning algorithm to divide a given set of trees into several clusters of trees. We propose novel versions of the well-known Silhouette and Caliński-Harabasz cluster validity indices that are adapted for tree clustering with k-medoids. The efficiency of the new method was assessed using both synthetic and real data, such as a well-known phylogenetic dataset consisting of 47 gene trees inferred for 14 archaeal organisms. The method described here allows inference of multiple consensus trees from a given set of gene trees. It can be used to identify groups of gene trees having similar intragroup and different intergroup evolutionary histories. The main advantage of our method is that it is much faster than the existing tree clustering approaches, while providing similar or better clustering results in most cases. This makes it particularly well suited for the analysis of large genomic and phylogenetic datasets.

Arthropod but Not Bird Predation in Ethiopian Homegardens Is Higher in Tree-Poor than in Tree-Rich Landscapes

PubMed Central

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. PMID:25961306

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

PubMed

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.

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

PubMed Central

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

2018-01-01

Abstract 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. PMID:29106675

Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference.

PubMed

Chernomor, Olga; Minh, Bui Quang; von Haeseler, Arndt

2015-12-01

In phylogenomic analysis the collection of trees with identical score (maximum likelihood or parsimony score) may hamper tree search algorithms. Such collections are coined phylogenetic terraces. For sparse supermatrices with a lot of missing data, the number of terraces and the number of trees on the terraces can be very large. If terraces are not taken into account, a lot of computation time might be unnecessarily spent to evaluate many trees that in fact have identical score. To save computation time during the tree search, it is worthwhile to quickly identify such cases. The score of a species tree is the sum of scores for all the so-called induced partition trees. Therefore, if the topological rearrangement applied to a species tree does not change the induced partition trees, the score of these partition trees is unchanged. Here, we provide the conditions under which the three most widely used topological rearrangements (nearest neighbor interchange, subtree pruning and regrafting, and tree bisection and reconnection) change the topologies of induced partition trees. During the tree search, these conditions allow us to quickly identify whether we can save computation time on the evaluation of newly encountered trees. We also introduce the concept of partial terraces and demonstrate that they occur more frequently than the original "full" terrace. Hence, partial terrace is the more important factor of timesaving compared to full terrace. Therefore, taking into account the above conditions and the partial terrace concept will help to speed up the tree search in phylogenomic inference.

NE-TWIGS update: Incorporating tree quality

Treesearch

Daniel A. Yaussy

1993-01-01

A method to distribute tree quality was incorporated into the NE-TWIGS individual-tree growth and yield simulator. The program uses potential tree grade to allow changes in actual tree grade over time. Volume is reported by grade and value is calculated using tree grades. Example screens are shown.

40 CFR 98.87 - Records that must be retained.

Code of Federal Regulations, 2014 CFR

2014-07-01

... (CONTINUED) MANDATORY GREENHOUSE GAS REPORTING Cement Production § 98.87 Records that must be retained. (a... § 98.3(g), you must retain the records specified in this paragraph (b) for each portland cement...

40 CFR 98.87 - Records that must be retained.

Code of Federal Regulations, 2013 CFR

2013-07-01

... (CONTINUED) MANDATORY GREENHOUSE GAS REPORTING Cement Production § 98.87 Records that must be retained. (a... § 98.3(g), you must retain the records specified in this paragraph (b) for each portland cement...

40 CFR 98.87 - Records that must be retained.

Code of Federal Regulations, 2012 CFR

2012-07-01

... (CONTINUED) MANDATORY GREENHOUSE GAS REPORTING Cement Production § 98.87 Records that must be retained. (a... § 98.3(g), you must retain the records specified in this paragraph (b) for each portland cement...

Efficient Exploration of the Space of Reconciled Gene Trees

PubMed Central

Szöllősi, Gergely J.; Rosikiewicz, Wojciech; Boussau, Bastien; Tannier, Eric; Daubin, Vincent

2013-01-01

Gene trees record the combination of gene-level events, such as duplication, transfer and loss (DTL), and species-level events, such as speciation and extinction. Gene tree–species tree reconciliation methods model these processes by drawing gene trees into the species tree using a series of gene and species-level events. The reconstruction of gene trees based on sequence alone almost always involves choosing between statistically equivalent or weakly distinguishable relationships that could be much better resolved based on a putative species tree. To exploit this potential for accurate reconstruction of gene trees, the space of reconciled gene trees must be explored according to a joint model of sequence evolution and gene tree–species tree reconciliation. Here we present amalgamated likelihood estimation (ALE), a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (Szöllősi et al. 2013), which allows for the DTL of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees. We demonstrate using simulations that gene trees reconstructed using the joint likelihood are substantially more accurate than those reconstructed using sequence alone. Using realistic gene tree topologies, branch lengths, and alignment sizes, we demonstrate that ALE produces more accurate gene trees even if the model of sequence evolution is greatly simplified. Finally, examining 1099 gene families from 36 cyanobacterial genomes we find that joint likelihood-based inference results in a striking reduction in apparent phylogenetic discord, with respectively. 24%, 59%, and 46% reductions in the mean numbers of duplications, transfers, and losses per gene family. The open source implementation of ALE is available from https://github.com/ssolo/ALE.git. [amalgamation; gene tree reconciliation; gene tree reconstruction; lateral gene transfer; phylogeny.] PMID:23925510

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

PubMed

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-age forests.

Interspecific variation in growth responses to tree size, competition and climate of western Canadian boreal mixed forests.

PubMed

Jiang, Xinyu; Huang, Jian-Guo; Cheng, Jiong; Dawson, Andria; Stadt, Kenneth J; Comeau, Philip G; Chen, Han Y H

2018-08-01

Tree growth of boreal forest plays an important role on global carbon (C) cycle, while tree growth in the western Canadian boreal mixed forests has been predicted to be negatively affected by regional drought. Individual tree growth can be controlled by many factors, such as competition, climate, tree size and age. However, information about contributions of different factors to tree growth is still limited in this region. In order to address this uncertainty, tree rings of two dominant tree species, trembling aspen (Populus tremuloides Michx.) and white spruce (Picea glauca (Moench.) Voss), were sampled from boreal mixed forest stands distributed across Alberta, Canada. Tree growth rates over different time intervals (10years interval, 1998-2007; 20years interval, 1988-2007; 30years interval, 1978-2007) were calculated to study the effects of different factors (tree size, competition, climate, and age) on tree growth. Results indicated that tree growth of two species were both primarily affected by competition or tree size, while climatic indices showed less effects on tree growth. Growth of trembling aspen was significantly affected by inter- and intraspecific competition, while growth of white spruce was primarily influenced by tree size, followed by competition. Positive relationship was found between growth of white spruce and competition index of coniferous group, suggesting an intraspecific mutualism mechanism within coniferous group. Our results further suggested that competition driven succession was the primary process of forest composition shift in the western Canadian boreal mixed forest. Although drought stress increased tree mortality, decline of stem density under climate change released competition stress of surviving trees, which in turn sustained growth of surviving trees. Therefore, climatic indices showed fewer effects on growth of dominant tree species compared to other factors in our study. Copyright © 2018 Elsevier B.V. All rights reserved.

Towards lidar-based mapping of tree age at the Arctic forest tundra ecotone.

NASA Astrophysics Data System (ADS)

Jensen, J.; Maguire, A.; Oelkers, R.; Andreu-Hayles, L.; Boelman, N.; D'Arrigo, R.; Griffin, K. L.; Jennewein, J. S.; Hiers, E.; Meddens, A. J.; Russell, M.; Vierling, L. A.; Eitel, J.

2017-12-01

Climate change may cause spatial shifts in the forest-tundra ecotone (FTE). To improve our ability to study these spatial shifts, information on tree demography along the FTE is needed. The objective of this study was to assess the suitability of lidar derived tree heights as a surrogate for tree age. We calculated individual tree age from 48 tree cores collected at basal height from white spruce (Picea glauca) within the FTE in northern Alaska. Tree height was obtained from terrestrial lidar scans (<1cm spatial resolution). The relationship between age and height was examined using a linear regression model forced through the origin. We found a very strong predictive relationship between tree height and age (R2 = 0.90, RMSE = 19.34 years) for trees that ranged between 14 to 230 years. Separate regression models were also developed for small (height < 3 m) and large trees (height >= 3 m), yielding strong predictive relationships between height and age (R2 = 0.86, RMSE 12.21 years, and R2 = 0.93, RMSE = 25.16 years, respectively). The slope coefficient for small and large tree models (16.83 and 12.98 years/m, respectively) indicate that small trees grow 1.3 times faster than large trees at these FTE study sites. Although a strong, predictive relationship between age and height is uncommon in light-limited forest environments, our findings suggest that the sparseness of trees within the FTE may explain the strong tree height-age relationships found herein. Further analysis of 36 additional tree cores recently collected within the FTE near Inuvik, Canada will be performed. Our preliminary analysis suggests that lidar derived tree height could be a reliable proxy for tree age at the FTE, thereby establishing a new technique for scaling tree structure and demographics across larger portions of this sensitive ecotone.

i-Tree: Tools to assess and manage structure, function, and value of community forests

NASA Astrophysics Data System (ADS)

Hirabayashi, S.; Nowak, D.; Endreny, T. A.; Kroll, C.; Maco, S.

2011-12-01

Trees in urban communities can mitigate many adverse effects associated with anthropogenic activities and climate change (e.g. urban heat island, greenhouse gas, air pollution, and floods). To protect environmental and human health, managers need to make informed decisions regarding urban forest management practices. Here we present the i-Tree suite of software tools (www.itreetools.org) developed by the USDA Forest Service and their cooperators. This software suite can help urban forest managers assess and manage the structure, function, and value of urban tree populations regardless of community size or technical capacity. i-Tree is a state-of-the-art, peer-reviewed Windows GUI- or Web-based software that is freely available, supported, and continuously refined by the USDA Forest Service and their cooperators. Two major features of i-Tree are 1) to analyze current canopy structures and identify potential planting spots, and 2) to estimate the environmental benefits provided by the trees, such as carbon storage and sequestration, energy conservation, air pollution removal, and storm water reduction. To cover diverse forest topologies, various tools were developed within the i-Tree suite: i-Tree Design for points (individual trees), i-Tree Streets for lines (street trees), and i-Tree Eco, Vue, and Canopy (in the order of complexity) for areas (community trees). Once the forest structure is identified with these tools, ecosystem services provided by trees can be estimated with common models and protocols, and reports in the form of texts, charts, and figures are then created for users. Since i-Tree was developed with a client/server architecture, nationwide data in the US such as location-related parameters, weather, streamflow, and air pollution data are stored in the server and retrieved to a user's computer at run-time. Freely available remote-sensed images (e.g. NLCD and Google maps) are also employed to estimate tree canopy characteristics. As the demand for i-Tree grows internationally, environmental databases from more countries will be coupled with the software suite. Two more i-Tree applications, i-Tree Forecast and i-Tree Landscape are now under development. i-Tree Forecast simulates canopy structures for up to 100 years based on planting and mortality rates and adds capabilities for other i-Tree applications to estimate the benefits of future canopy scenarios. While most i-Tree applications employ a spatially lumped approach, i-Tree landscape employs a spatially distributed approach that allows users to map changes in canopy cover and ecosystem services through time and space. These new i-Tree tools provide an advanced platform for urban managers to assess the impact of current and future urban forests. i-Tree allows managers to promote effective urban forest management and sound arboricultural practices by providing information for advocacy and planning, baseline data for making informed decisions, and standardization for comparisons with other communities.

Urban park tree inventories

Treesearch

Joe R. McBride; David J. Nowak

1989-01-01

A survey of published reports on urban park tree inventories in the United States and the United Kingdom reveal two types of inventories: (1) Tree Location Inventories and (2) Generalized Information Inventories. Tree location inventories permit managers to relocate specific park trees, along with providing individual tree characteristics and condition data. In...

Simple street tree sampling

Treesearch

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...

The Tree Worker's Manual.

ERIC Educational Resources Information Center

Smithyman, S. J.

This manual is designed to prepare students for entry-level positions as tree care professionals. Addressed in the individual chapters of the guide are the following topics: the tree service industry; clothing, eqiupment, and tools; tree workers; basic tree anatomy; techniques of pruning; procedures for climbing and working in the tree; aerial…

What Makes a Tree a Tree?

ERIC Educational Resources Information Center

NatureScope, 1986

1986-01-01

Provides: (1) background information on trees, focusing on the parts of trees and how they differ from other plants; (2) eight activities; and (3) ready-to-copy pages dealing with tree identification and tree rings. Activities include objective(s), recommended age level(s), subject area(s), list of materials needed, and procedures. (JN)

INTRODUCTION TO PHYTOTECHNOLOGIES

EPA Science Inventory

A tree is a tree is a tree; or is it? To a child a tree is to climb, to a landscape architect a tree shapes the view, while to an environmental engineer a tree may be a self-assembling, solar- powered pump and treat system. Phytoremediation is the art and science of using plant...

Ring profiler: a new method for estimating tree-ring density for improved estimates of carbon storage

Treesearch

David W. Vahey; C. Tim Scott; J.Y. Zhu; Kenneth E. Skog

2012-01-01

Methods for estimating present and future carbon storage in trees and forests rely on measurements or estimates of tree volume or volume growth multiplied by specific gravity. Wood density can vary by tree ring and height in a tree. If data on density by tree ring could be obtained and linked to tree size and stand characteristics, it would be possible to more...

Management, morphological, and environmental factors influencing Douglas-fir bark furrows in the Oregon Coast Range

USGS Publications Warehouse

Sheridan, Christopher D.; Puettmann, Klaus J.; Huso, Manuela M.P.; Hagar, Joan C.; Falk, Kristen R.

2013-01-01

Many land managers in the Pacific Northwest have the goal of increasing late-successional forest structures. Despite the documented importance of Douglas-fir tree bark structure in forested ecosystems, little is known about factors influencing bark development and how foresters can manage development. This study investigated the relative importance of tree size, growth, environmental factors, and thinning on Douglas-fir bark furrow characteristics in the Oregon Coast Range. Bark furrow depth, area, and bark roughness were measured for Douglas-fir trees in young heavily thinned and unthinned sites and compared to older reference sites. We tested models for relationships between bark furrow response and thinning, tree diameter, diameter growth, and environmental factors. Separately, we compared bark responses measured on trees used by bark-foraging birds with trees with no observed usage. Tree diameter and diameter growth were the most important variables in predicting bark characteristics in young trees. Measured environmental variables were not strongly related to bark characteristics. Bark furrow characteristics in old trees were influenced by tree diameter and surrounding tree densities. Young trees used by bark foragers did not have different bark characteristics than unused trees. Efforts to enhance Douglas-fir bark characteristics should emphasize retention of larger diameter trees' growth enhancement.

Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees.

PubMed

Kordi, Misagh; Bansal, Mukul S

2017-06-01

Duplication-Transfer-Loss (DTL) reconciliation is a powerful method for studying gene family evolution in the presence of horizontal gene transfer. DTL reconciliation seeks to reconcile gene trees with species trees by postulating speciation, duplication, transfer, and loss events. Efficient algorithms exist for finding optimal DTL reconciliations when the gene tree is binary. In practice, however, gene trees are often non-binary due to uncertainty in the gene tree topologies, and DTL reconciliation with non-binary gene trees is known to be NP-hard. In this paper, we present the first exact algorithms for DTL reconciliation with non-binary gene trees. Specifically, we (i) show that the DTL reconciliation problem for non-binary gene trees is fixed-parameter tractable in the maximum degree of the gene tree, (ii) present an exponential-time, but in-practice efficient, algorithm to track and enumerate all optimal binary resolutions of a non-binary input gene tree, and (iii) apply our algorithms to a large empirical data set of over 4700 gene trees from 100 species to study the impact of gene tree uncertainty on DTL-reconciliation and to demonstrate the applicability and utility of our algorithms. The new techniques and algorithms introduced in this paper will help biologists avoid incorrect evolutionary inferences caused by gene tree uncertainty.

Simulation of Tsunami Resistance of a Pinus Thunbergii tree in Coastal Forest in Japan

NASA Astrophysics Data System (ADS)

Nanko, K.; Suzuki, S.; Noguchi, H.; Hagino, H.

2015-12-01

Forests reduce fluid force of tsunami, whereas extreme tsunami sometimes breaks down the forest trees. It is difficult to estimate the interactive relationship between the fluid and the trees because fluid deform tree architecture and deformed tree changes flow field. Dynamic tree deformation and fluid behavior should be clarified by fluid-structure interaction analysis. For the initial step, we have developed dynamic simulation of tree sway and breakage caused by tsunami based on a vibrating system with multiple degrees of freedom. The target specie of the simulation was Japanese black pine (pinus thunbergii), which is major specie in the coastal forest to secure livelihood area from the damage by blown sand and salt in Japanese coastal area. For the simulation, a tree was segmented into 0.2 m long circular truncated cones. Turning moment induced by tsunami and self-weight was calculated at each segment bottom. Tree deformation was computed on multi-degree-of-freedom vibration equation. Tree sway was simulated by iterative calculation of the tree deformation with time step 0.05 second with temporally varied flow velocity of tsunami. From the calculation of bending stress and turning moment at tree base, we estimated resistance of a Pinus thunbergii tree from tsunami against tree breakage.

Hide and vanish: data sets where the most parsimonious tree is known but hard to find, and their implications for tree search methods.

PubMed

Goloboff, Pablo A

2014-10-01

Three different types of data sets, for which the uniquely most parsimonious tree can be known exactly but is hard to find with heuristic tree search methods, are studied. Tree searches are complicated more by the shape of the tree landscape (i.e. the distribution of homoplasy on different trees) than by the sheer abundance of homoplasy or character conflict. Data sets of Type 1 are those constructed by Radel et al. (2013). Data sets of Type 2 present a very rugged landscape, with narrow peaks and valleys, but relatively low amounts of homoplasy. For such a tree landscape, subjecting the trees to TBR and saving suboptimal trees produces much better results when the sequence of clipping for the tree branches is randomized instead of fixed. An unexpected finding for data sets of Types 1 and 2 is that starting a search from a random tree instead of a random addition sequence Wagner tree may increase the probability that the search finds the most parsimonious tree; a small artificial example where these probabilities can be calculated exactly is presented. Data sets of Type 3, the most difficult data sets studied here, comprise only congruent characters, and a single island with only one most parsimonious tree. Even if there is a single island, missing entries create a very flat landscape which is difficult to traverse with tree search algorithms because the number of equally parsimonious trees that need to be saved and swapped to effectively move around the plateaus is too large. Minor modifications of the parameters of tree drifting, ratchet, and sectorial searches allow travelling around these plateaus much more efficiently than saving and swapping large numbers of equally parsimonious trees with TBR. For these data sets, two new related criteria for selecting taxon addition sequences in Wagner trees (the "selected" and "informative" addition sequences) produce much better results than the standard random or closest addition sequences. These new methods for Wagner trees and for moving around plateaus can be useful when analyzing phylogenomic data sets formed by concatenation of genes with uneven taxon representation ("sparse" supermatrices), which are likely to present a tree landscape with extensive plateaus. Copyright © 2014 Elsevier Inc. All rights reserved.

Ascorbic Acid Alleviates Water Stress in Young Peach Trees and Improves Their Performance after Rewatering.

PubMed

Penella, Consuelo; Calatayud, Ángeles; Melgar, Juan C

2017-01-01

Exogenous application of biochemicals has been found to improve water stress tolerance in herbaceous crops but there are limited studies on deciduous fruit trees. The goal of this research was to study if ascorbic acid applications could improve physiological mechanisms associated with water stress tolerance in young fruit trees. Ascorbic acid was foliarly applied at a concentration of 250 ppm to water-stressed and well-watered peach trees (control) of two cultivars ('Scarletprince' and 'CaroTiger'). Trees received either one or two applications, and 1 week after the second application all trees were rewatered to field capacity. Upon rewatering, CO 2 assimilation and stomatal conductance of water-stressed 'Scarletprince' trees sprayed with ascorbic acid (one or two applications) were similar to those of well-irrigated trees, but water-stressed trees that had not received ascorbic acid did not recover photosynthetical functions. Also, water status in sprayed water-stressed 'Scarletprince' trees was improved to values similar to control trees. On the other hand, water-stressed 'CaroTiger' trees needed two applications of ascorbic acid to reach values of CO 2 assimilation similar to control trees but these applications did not improve their water status. In general terms, different response mechanisms to cope with water stress in presence of ascorbic acid were found in each cultivar, with 'Scarletprince' trees preferentially using proline as compatible solute and 'CaroTiger' trees relying on stomatal regulation. The application of ascorbic acid reduced cell membrane damage and increased catalase activity in water-stressed trees of both cultivars. These results suggest that foliar applications of ascorbic acid could be used as a management practice for improving water stress tolerance of young trees under suboptimal water regimes.

Ascorbic Acid Alleviates Water Stress in Young Peach Trees and Improves Their Performance after Rewatering

PubMed Central

Penella, Consuelo; Calatayud, Ángeles; Melgar, Juan C.

2017-01-01

Exogenous application of biochemicals has been found to improve water stress tolerance in herbaceous crops but there are limited studies on deciduous fruit trees. The goal of this research was to study if ascorbic acid applications could improve physiological mechanisms associated with water stress tolerance in young fruit trees. Ascorbic acid was foliarly applied at a concentration of 250 ppm to water-stressed and well-watered peach trees (control) of two cultivars (‘Scarletprince’ and ‘CaroTiger’). Trees received either one or two applications, and 1 week after the second application all trees were rewatered to field capacity. Upon rewatering, CO2 assimilation and stomatal conductance of water-stressed ‘Scarletprince’ trees sprayed with ascorbic acid (one or two applications) were similar to those of well-irrigated trees, but water-stressed trees that had not received ascorbic acid did not recover photosynthetical functions. Also, water status in sprayed water-stressed ‘Scarletprince’ trees was improved to values similar to control trees. On the other hand, water-stressed ‘CaroTiger’ trees needed two applications of ascorbic acid to reach values of CO2 assimilation similar to control trees but these applications did not improve their water status. In general terms, different response mechanisms to cope with water stress in presence of ascorbic acid were found in each cultivar, with ‘Scarletprince’ trees preferentially using proline as compatible solute and ‘CaroTiger’ trees relying on stomatal regulation. The application of ascorbic acid reduced cell membrane damage and increased catalase activity in water-stressed trees of both cultivars. These results suggest that foliar applications of ascorbic acid could be used as a management practice for improving water stress tolerance of young trees under suboptimal water regimes. PMID:28979284

Foliar ozone injury on different-sized Prumus serotina Ehrh. trees

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fredericksen, T.S.; Skelly, J.M.; Steiner, K.C.

1995-06-01

Black cherry (Prunus serotina Ehrh.) is a common tree species in the eastern U.S. that is highly sensitive to ozone relative to other associated deciduous tree species. Because of difficulties in conducting exposure-response experiments on large trees, air pollution studies have often utilized seedlings and extrapolated the results to predict the potential response of larger forest trees. However, physiological differences between seedlings and mature forest trees may alter responses to air pollutants. A comparative study of seedling, sapling, and canopy black cherry trees was conducted to determine the response of different-sized trees to known ozone exposures and amounts of ozonemore » uptake. Apparent foliar sensitivity to ozone, observed as a dark adaxial leaf stipple, decreased with increasing tree size. An average of 46% of seedling leaf area was symptomatic by early September, compared to 15% - 20% for saplings and canopy trees. In addition to visible symptoms, seedlings also appeared to have greater rates of early leaf abscission than larger trees. Greater sensitivity (i.e., foliar symptoms) per unit exposure with decreasing tree size was closely correlated with rates of stomatal conductance. However, after accounting for differences in stomatal conductance, sensitivity appeared to increase with tree size.« less

Trees as templates for tropical litter arthropod diversity.

PubMed

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.

Intermediate tree cover can maximize groundwater recharge in the seasonally dry tropics

PubMed Central

Ilstedt, U.; Bargués Tobella, A.; Bazié, H. R.; Bayala, J.; Verbeeten, E.; Nyberg, G.; Sanou, J.; Benegas, L.; Murdiyarso, D.; Laudon, H.; Sheil, D.; Malmer, A.

2016-01-01

Water scarcity contributes to the poverty of around one-third of the world’s people. Despite many benefits, tree planting in dry regions is often discouraged by concerns that trees reduce water availability. Yet relevant studies from the tropics are scarce, and the impacts of intermediate tree cover remain unexplored. We developed and tested an optimum tree cover theory in which groundwater recharge is maximized at an intermediate tree density. Below this optimal tree density the benefits from any additional trees on water percolation exceed their extra water use, leading to increased groundwater recharge, while above the optimum the opposite occurs. Our results, based on groundwater budgets calibrated with measurements of drainage and transpiration in a cultivated woodland in West Africa, demonstrate that groundwater recharge was maximised at intermediate tree densities. In contrast to the prevailing view, we therefore find that moderate tree cover can increase groundwater recharge, and that tree planting and various tree management options can improve groundwater resources. We evaluate the necessary conditions for these results to hold and suggest that they are likely to be common in the seasonally dry tropics, offering potential for widespread tree establishment and increased benefits for hundreds of millions of people. PMID:26908158

Differences in xylogenesis between dominant and suppressed trees.

PubMed

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.

Intermediate tree cover can maximize groundwater recharge in the seasonally dry tropics

NASA Astrophysics Data System (ADS)

Ilstedt, U.; Bargués Tobella, A.; Bazié, H. R.; Bayala, J.; Verbeeten, E.; Nyberg, G.; Sanou, J.; Benegas, L.; Murdiyarso, D.; Laudon, H.; Sheil, D.; Malmer, A.

2016-02-01

Water scarcity contributes to the poverty of around one-third of the world’s people. Despite many benefits, tree planting in dry regions is often discouraged by concerns that trees reduce water availability. Yet relevant studies from the tropics are scarce, and the impacts of intermediate tree cover remain unexplored. We developed and tested an optimum tree cover theory in which groundwater recharge is maximized at an intermediate tree density. Below this optimal tree density the benefits from any additional trees on water percolation exceed their extra water use, leading to increased groundwater recharge, while above the optimum the opposite occurs. Our results, based on groundwater budgets calibrated with measurements of drainage and transpiration in a cultivated woodland in West Africa, demonstrate that groundwater recharge was maximised at intermediate tree densities. In contrast to the prevailing view, we therefore find that moderate tree cover can increase groundwater recharge, and that tree planting and various tree management options can improve groundwater resources. We evaluate the necessary conditions for these results to hold and suggest that they are likely to be common in the seasonally dry tropics, offering potential for widespread tree establishment and increased benefits for hundreds of millions of people.

Retained placenta aspect of clinical management in a tertiary health institution in Nigeria.

PubMed

Agwu, U M; Umeora, O U J; Ejikeme, B N; Egwuatu, V E

2008-01-01

Retained placenta is a significant cause of postpartum haemorrhage, maternal morbidity and occasionally mortality. This study assessed the clinical presentation, management and outcomes of retained placenta at the Ebonyi State University teaching Hospital. Analysis of records relating to retained placenta managed in the hospital over a three year period (August 2003 to July 2006. The incidence of retained placenta was 0.22% (1 in 456 vaginal deliveries). Eleven (32.4%) patients were admitted with retained placenta following home delivery. Two (5.6%) delivery in a peripheral hospital, 6 (17.7%) delivered in a. Health center and 2 (5.9%) delivered in a maternity home. Preterm deliveries accounted for 17.7% of the cases. Eighteen parturient were admitted in shock. One patient had hysterectomy for adherent placenta. Improved peripatum services, education on the dangers of unsupervised home deliveries, women empowernment and prompt referral for emergency obstetrics care will reduce the associated mortality and morbidity.

Translational and rotational knee joint stability in anterior and posterior cruciate-retaining knee arthroplasty.

PubMed

Lo, JiaHsuan; Müller, Otto; Dilger, Torsten; Wülker, Nikolaus; Wünschel, Markus

2011-12-01

This study investigated passive translational and rotational stability properties of the intact knee joint, after bicruciate-retaining bi-compartmental knee arthroplasty (BKA) and after posterior cruciate retaining total knee arthroplasty (TKA). Fourteen human cadaveric knee specimens were used in this study, and a robotic manipulator with six-axis force/torque sensor was used to test the joint laxity in anterior-posterior translation, valgus-varus, and internal-external rotation. The results show the knee joint stability after bicruciate-retaining BKA is similar to that of the native knee. On the other hand, the PCL-retaining TKA results in inferior joint stability in valgus, varus, external rotation, anterior and, surprisingly, posterior directions. Our findings suggest that, provided functional ligamentous structures, bicruciate-retaining BKA is a biomechanically attractive treatment for joint degenerative disease. Copyright © 2010 Elsevier B.V. All rights reserved.

Replacement bearing for Rocketdyne SSME HPOTPs using alternate self-lubricating retainer materials

NASA Technical Reports Server (NTRS)

Gleeson, J.; Dufrane, K.; Kannel, J.

1992-01-01

Research was conducted to develop replacement bearings for the Rocketdyne Space Shuttle main engine (SSME) high pressure oxidizer turbopumps (HPOTPs). The replacement bearings consisted of standard balls and races with a special Battelle Self-Lubricating Insert Configuration (BASIC) retainer. The BASIC retainer consists of a phosphor bronze housing with inserts consisting of a polytetrafluoretheylene (PTFE) and bronze compound. The PTFE contacts the balls and the land guiding surface on the outer race. A PTFE transfer film is formed on balls and races, which lubricates the critical interfaces. The BASIC retainer is a one-to-one replacement for the current Armalon retainer, but has superior lubricating properties and is stronger over the broad temperature range anticipated for the HPOTP bearings. As a part of the project 40 sets of balls and races (two sizes) and 52 BASIC retainers were shipped to NASA/MSFC.

Systems and methods for retaining and removing irradiation targets in a nuclear reactor

DOEpatents

Runkle, Gary A.; Matsumoto, Jack T.; Dayal, Yogeshwar; Heinold, Mark R.

2015-12-08

A retainer is placed on a conduit to control movement of objects within the conduit in access-restricted areas. Retainers can prevent or allow movement in the conduit in a discriminatory fashion. A fork with variable-spacing between prongs can be a retainer and be extended or collapsed with respect to the conduit to change the size of the conduit. Different objects of different sizes may thus react to the fork differently, some passing and some being blocked. Retainers can be installed in inaccessible areas and allow selective movement in remote portions of conduit where users cannot directly interface, including below nuclear reactors. Position detectors can monitor the movement of objects through the conduit remotely as well, permitting engagement of a desired level of restriction and object movement. Retainers are useable in a variety of nuclear power plants and with irradiation target delivery, harvesting, driving, and other remote handling or robotic systems.

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

NASA Astrophysics Data System (ADS)

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 microsite and at depths not normally reached by standard soil excavations. The non-invasive nature of ERT studies is especially important for protected areas as it was shown in the present study.