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Sample records for lacquer tree rhus

  1. Cytotoxicity of urushiols isolated from sap of Korean lacquer tree (Rhus vernicifera Stokes).

    PubMed

    Hong, D H; Han, S B; Lee, C W; Park, S H; Jeon, Y J; Kim, M J; Kwak, S S; Kim, H M

    1999-12-01

    Cytotoxicities of four urushiols, congeners isolated from the sap of Korean lacquer tree (Rhus vernicifera Stokes), to 29 human cancer cell lines originated from 9 organs were evaluated. Their values of 50% growth inhibition were below 4 microg/ml, and showed cell line specific cytotoxicity. The present result is the first report on the cytotoxicity of urushiols suggesting that they would have an anticancer activity to human cancer cells. PMID:10615873

  2. Heterogeneity of the Type 3 copper in Japanese-lacquer-tree (Rhus vernicifera) laccase.

    PubMed Central

    Morpurgo, L; Desideri, A; Rotilio, G

    1982-01-01

    The two steps of the titration of the Japanese-lacquer-tree (Rhus vernicifera) laccase with N3- [Morpurgo, Rotilio, Finazzi-Agr & Mondovi (1974) Biochim. Biophys. Acta 336, 324-328; LuBien, Winkler, Thamann, Scott, Co, Hodgson & Solomon (1981) J. Am. Chem. Soc. 103, 7014-7016] were shown to be two distinct reactions, each involving one different portion of the native enzyme molecules. The difference consists in the oxidation state of the Type 3 Cu, which is reduced in the portion with higher affinity for N3- and oxidized in the portion with lower affinity for N3-. The difference is eliminated by treatment with oxidizing (H2O2) or reducing agents, and a single N3- adduct is then formed. The e.p.r. spectra of the H2O2-treated enzyme and of its F- derivatives support this interpretation of the results. The similarity of the spectroscopic properties of the high-affinity N3- adduct to those of the N3- adducts of half-met-haemocyanins and half-met-tyrosinase is discussed. PMID:6299275

  3. Titrations with ferrocyanide of japanese-lacquer-tree (Rhus vernicifera) laccase and of the type 2 copper-depleted enzyme. Interrelation of the copper sites.

    PubMed Central

    Morpurgo, L; Graziani, M T; Desideri, A; Rotilio, G

    1980-01-01

    1. Redox titrations are reported of the metal centres in Japanese-lacquer-tree (Rhus vernicifera) laccase with ferrocyanide. 2. The redox potential of Type 1 Cu was found to increase with ferrocyanide concentration up to a limiting value similar to that for the Type 1 Cu in Type 2 Cu-depleted enzyme (which is independent of ferrocyanide concentration). 3. The redox potential of the two-electron acceptor (Type 3 Cu) is also independent of ferrocyanide concentration in Type 2 Cu-depleted enzyme and lower than values reported for the native enzyme. 4. The two-electron acceptor is present in the oxidized state in the Type 2 Cu-depleted enzyme, though the latter lacks the 330 nm absorption band. 5. The redox potential of Type 2 Cu also depends on ferrocyanide concentration, at least in the presence of azide. 6. The redox potentials are affected by freezing the solutions and/or addition of azide, the latter binding to Type 2 Cu with affinity dependent on the redox state of the two-electron acceptor. PMID:6446907

  4. Yeast copper-thionein can reconstitute the Japanese-lacquer-tree (Rhus vernicifera) laccase from the Type 2-copper-depleted enzyme via a direct copper(I)-transfer mechanism.

    PubMed Central

    Morpurgo, L; Hartmann, H J; Desideri, A; Weser, U; Rotilio, G

    1983-01-01

    The Type 2-Cu-depleted laccase from the Japanese lacquer tree (Rhus vernicifera) can be reconstituted with CuSO4 aerobically and much more rapidly and efficiently under anaerobic reducing conditions. This is to be related to a more favourable conformation of a laccase in the reduced state, rather than to reduction of the metal ion. In fact, reconstitution with Cu(I)-thionein from baker's yeast (Saccharomyces cerevisiae) only proceeds under anaerobic reducing conditions, via a direct transfer of Cu(I). PMID:6307284

  5. Yeast copper-thionein can reconstitute the Japanese-lacquer-tree (Rhus vernicifera) laccase from the Type 2-copper-depleted enzyme via a direct copper(I)-transfer mechanism.

    PubMed

    Morpurgo, L; Hartmann, H J; Desideri, A; Weser, U; Rotilio, G

    1983-05-01

    The Type 2-Cu-depleted laccase from the Japanese lacquer tree (Rhus vernicifera) can be reconstituted with CuSO4 aerobically and much more rapidly and efficiently under anaerobic reducing conditions. This is to be related to a more favourable conformation of a laccase in the reduced state, rather than to reduction of the metal ion. In fact, reconstitution with Cu(I)-thionein from baker's yeast (Saccharomyces cerevisiae) only proceeds under anaerobic reducing conditions, via a direct transfer of Cu(I). PMID:6307284

  6. Low-temperature resonance-Raman spectra of Japanese-lacquer-tree (Rhus vernicifera) laccase, type-2-copper-depleted laccase and H2O2-treated type-2-copper-depleted laccase.

    PubMed

    Musci, G; Desideri, A; Morpurgo, L; Garnier-Suillerot, A; Tosi, L

    1983-08-01

    Resonance-Raman spectra of Japanese-lacquer-tree (Rhus vernicifera) laccase, type-2-copper-depleted laccase and the latter form treated with H2O2 were measured in liquid and frozen solution, on excitation into the 600 nm absorption band. Significant changes in intensity and/or frequency of the bands lying in the 370-430 cm-1 region were observed on freezing, indicating local structural rearrangements taking place at the blue copper site. These findings corroborate previous suggestions based on e.p.r. measurements and redox data [Morpurgo, Calabrese, Desideri & Rotilio (1981) Biochem. J. 193, 639-642]. They show the strong dependence of the physical properties of blue copper centres on local symmetry. Some conclusions on the origin of the Raman bands are also drawn. PMID:6225424

  7. Low-temperature resonance-Raman spectra of Japanese-lacquer-tree (Rhus vernicifera) laccase, type-2-copper-depleted laccase and H2O2-treated type-2-copper-depleted laccase.

    PubMed Central

    Musci, G; Desideri, A; Morpurgo, L; Garnier-Suillerot, A; Tosi, L

    1983-01-01

    Resonance-Raman spectra of Japanese-lacquer-tree (Rhus vernicifera) laccase, type-2-copper-depleted laccase and the latter form treated with H2O2 were measured in liquid and frozen solution, on excitation into the 600 nm absorption band. Significant changes in intensity and/or frequency of the bands lying in the 370-430 cm-1 region were observed on freezing, indicating local structural rearrangements taking place at the blue copper site. These findings corroborate previous suggestions based on e.p.r. measurements and redox data [Morpurgo, Calabrese, Desideri & Rotilio (1981) Biochem. J. 193, 639-642]. They show the strong dependence of the physical properties of blue copper centres on local symmetry. Some conclusions on the origin of the Raman bands are also drawn. PMID:6225424

  8. Optical properties of japanese-lacquer-tree (Rhus vernicifera) laccase depleted of type 2 copper(II). Involvement of type-2 copper(II) in the 330nm chromophore.

    PubMed Central

    Morpurgo, L; Graziani, M T; Finazzi-Agr, A; Rotilio, G; Mondov, B

    1980-01-01

    1. Spectroscopic and functional properties of Japanese-lacquer-tree (Rhus vernicifera) laccase were re-investigated, with special emphasis on the relationships between the different types of copper centres (Types 1, 2, and 3). 2. On removal of the Type 2 Cu(II), a decrease of absorbance occurred in the wavelength region above 650 nm (delta epsilon 750 = 300 M-1 . cm-1) and around 330 nm (delta episom 330 up to 2200 M-1 . cm-1). 3. Reductive titrations with ascorbic acid or ferrocyanide showed that the electron-accepting capacity of the partial apoprotein is one electron-equivalent lower than that of the native protein, i.e. the protein two-electron acceptor is present in the oxidized state in spite of absorbance loss at 330 nm. 4. The 330 nm chromophore apparently depends on the presence of both the Type 2 and the Type 3 copper in the oxidized state. 5. This finding may have implications in the relative location of Type 2 and 3 copper centres and on the redox behaviour of laccase. PMID:6446906

  9. Clinical features of 31 patients with systemic contact dermatitis due to the ingestion of Rhus (lacquer).

    PubMed

    Park, S D; Lee, S W; Chun, J H; Cha, S H

    2000-05-01

    In Korea, Rhus has been used as a folk medicine to cure gastrointestinal diseases and as a health food. We review the clinicopathological and laboratory findings in patients with systemic contact dermatitis caused by intake of Rhus. We reviewed medical records and histopathological sections from 31 patients during a 10-year period. The male/female ratio was 1.4: 1 and the average age was 43.8 years (range 22-70). Ten patients (32%) had a known history of allergy to lacquer. Rhus was ingested to treat gastrointestinal problems including indigestion and gastritis (45%), and as a health food (39%), in cooked meat, in herbal medicine, or taken by inhalation. The patients developed skin lesions such as a maculopapular eruption (65%), erythema multiforme (EM, 32%), erythroderma (19%), pustules, purpura, weals and blisters. Erythroderma was very frequent in patients with a known history of allergy to lacquer, but maculopapular and EM-type eruptions were more frequently observed in those without a history of allergy. All patients experienced generalized or localized pruritus. Other symptoms included gastrointestinal problems (32%), fever (26%), chills and headache; many developed leucocytosis (70%) with neutrophilia (88%), while some showed toxic effects on liver and kidney. Fifty-nine per cent of patients observed cutaneous or general symptoms within a day after ingestion of Rhus. There was no difference in the time lag for symptoms to develop between patients allergic and not allergic to Rhus. All patients responded well to treatment with systemic steroids and antihistamines. Common histopathological findings were vascular dilatation, perivascular lymphohistiocytic infiltration, and extravasation of red blood cells in the upper dermis. Rhus lacquer should not be ingested in view of its highly allergic and toxic effects. PMID:10809851

  10. Assay for Laccase activity by microcalorimetry: laccase was extracted from china lacquer of Rhus vernicifera.

    PubMed

    Wang, T; Li, W; Wan, H W; Zhou, P J; Qu, S S

    2000-08-10

    The reactions between Laccase (extracted from China lacquer of Rhus vernicifera) and various substrates (3,4-Dihydroxybenzaldehyde, Guaiacol, Pyrogallol, Gallic acid) have been studied using LKB-2107 batch microcalorimetry system. Based on calorimetry, a new method has been proposed. Laccase activity and the Michaelis constant K(m) have been determined simultaneously by this method. The method is simple, sample-saving, and valid for a wider range of substrate concentrations. Furthermore, it can be extended for assaying other enzymes catalyzing reactions using this method. PMID:10899390

  11. Effects of lacquer polysaccharides, glycoproteins and isoenzymes on the activity of free and immobilised laccase from Rhus vernicifera.

    PubMed

    Wan, Yun-Yang; Lu, Rong; Akiyama, Kazuhiro; Okamoto, Katsuhisa; Honda, Takayuki; Du, Yu-Min; Yoshida, Takashi; Miyakoshi, Tetsuo; Knill, Charles J; Kennedy, John F

    2010-07-01

    The purified polysaccharides, glycoproteins, and isoenzymes of Rhus laccase, and crude enzymes, from Chinese lacquer (Rhus vernicifera sap) were used to determine their influence on the enzymic activity of Rhus laccase on several substrates (4-phenylenediamine, isoeugenol and coniferyl alcohol). No product identity changes were observed when these components were added singularly or in combination to the enzymic reactions (only relative product yields varied significantly), however, the polysaccharides (GP1 and GP2) and glycoprotein (stellacyanin, St) exhibited negative effects, and the two isoenzymes (L1 and L2) exhibited positive synergistic effects, on the activity of Rhus laccase. With respect to the activity of the crude enzymes, the negative effects of GP1, GP2 and St were greater than the positive effects of L1 and L2, compared with free Rhus laccase on its own (using 4-phenylenediamine as substrate), the estimated inhibitory effect (of GP1, GP2 and St) being by at least a factor of 50 (even with the positive effect of L1 and L2). This contributes to understanding of lacquer storage stability and drying rates. Immobilisation of crude enzymes using a variety of techniques (using natural and modified polysaccharides, and an inorganic support) where evaluated using isoeugenol as substrate. Agar embedding and zirconium chloride chelation methods resulted in the highest substrate conversion levels. The yields and products of isoeugenol catalysis using Vietnamese crude enzymes/purified Rhus laccase and commercial Denilite laccase were also compared and contrasted with their Chinese lacquer sap equivalents. PMID:20363247

  12. Three cases of severe Rhus dermatitis in an English primary school.

    PubMed

    Gach, J E; Tucker, W; Hill, V A

    2006-02-01

    We report three paediatric cases of severe allergic contact dermatitis caused by a Japanese lacquer tree (Rhus verniciflua), which is a rare specimen plant in the UK. The diagnosis of allergic contact dermatitis produced by plants that are not indigenous to a particular country is more likely to be delayed, as well as mistaken for cellulitis. PMID:16441636

  13. Studies on Acetone Powder and Purified Rhus Laccase Immobilized on Zirconium Chloride for Oxidation of Phenols

    PubMed Central

    Lu, Rong; Miyakoshi, Tetsuo

    2012-01-01

    Rhus laccase was isolated and purified from acetone powder obtained from the exudates of Chinese lacquer trees (Rhus vernicifera) from the Jianshi region, Hubei province of China. There are two blue bands appearing on CM-sephadex C-50 chromatography column, and each band corresponding to Rhus laccase 1 and 2, the former being the major constituent, and each had an average molecular weight of approximately 110?kDa. The purified and crude Rhus laccases were immobilized on zirconium chloride in ammonium chloride solution, and the kinetic properties of free and immobilized Rhus laccase, such as activity, molecular weight, optimum pH, and thermostability, were examined. In addition, the behaviors on catalytic oxidation of phenols also were conducted. PMID:22545205

  14. Lacquer poisoning

    MedlinePLUS

    Poisoning from lacquers is due to hydrocarbons, which are substances that contain only hydrogen and carbon. ... Lee DC. Hydrocarbons. In: Marx JA, Hockberger RS, Walls, RM, eds. Rosen’s Emergency Medicine: Concepts and Clinical Practice. 8th ed. Philadelphia, ...

  15. Eosinophilic Gastroenteritis Due to Rhus Ingestion Presenting with Gastrointestinal Hemorrhage

    PubMed Central

    Choi, Wonsuk; Choi, Chan; Cho, Kyuman; Park, Chang-Hwan; Kim, Hyun-Soo; Choi, Sung-Kyu; Rew, Jong-Sun

    2015-01-01

    Rhus-related illnesses in Korea are mostly caused by ingestion of parts of the Rhus tree. Contact dermatitis occurrence after ingestion of Rhus-related food is very common in Korea. However, Rhus-related gastrointestinal disease is very rare. Herein, we present a case of eosinophilic gastroenteritis caused by Rhus ingestion. A 75-year-old woman was admitted with hematemesis and hematochezia after Rhus extract ingestion. Routine laboratory tests revealed leukocytosis without eosinophilia. Endoscopy showed friable and granular mucosal changes with touch bleeding in the second portion of the duodenum. Abdominal computed tomography revealed edematous wall thickening of the duodenum and proximal jejunal loops. Patch testing with Rhus extracts showed a strong positive reaction, suggesting Rhus as the allergen. Her symptoms improved after avoidance of the allergen. PMID:25844348

  16. Drug-induced, photosensitive, erythema multiforme-like eruption: possible role for cell adhesion molecules in a flare induced by Rhus dermatitis.

    PubMed

    Shiohara, T; Chiba, M; Tanaka, Y; Nagashima, M

    1990-04-01

    Drug-induced, photosensitive erythema multiforme has not been reported, although drugs and sunlight are listed among precipitating factors in erythema multiforme. We describe a case of a drug-induced erythema multiforme-like eruption in a photodistribution that was reproduced by clinical challenge with the drug and sunlight. On contact with Rhus verniciflua, the Japanese lacquer tree, the patient had a flare of the eruption, which was limited to the areas previously exposed to sun. Immunohistochemical studies suggested that the keratinocytes in the skin that retain teh photoactivated substances may facilitate epidermal invasion of lymphocytes by persistent expression of intercellular adhesion molecule-1. PMID:1969427

  17. Seasonal conductivity and embolism in the roots and stems of two clonal ring-porous trees, Sassafras albidum (Lauraceae) and Rhus typhina (Anacardiaceae).

    PubMed

    Jaquish, L L; Ewers, F W

    2001-02-01

    Seasonal xylem (wood) conductivity and embolism (air blockage) patterns were monitored in roots vs. stems of two clonal ring-porous tree species, Sassafras albidum and Rhus typhina, throughout 1996 and 1997. Stems of both species were 100% embolized in the early spring and became conductive by late June following leaf expansion and maturation of new earlywood vessels. Dyes indicated the stem conduction was restricted almost exclusively to the current year's growth ring. Stems became totally embolized again by early October, before the first freezing temperatures. In contrast, woody roots of both species maintained low embolism values, many conductive growth rings, and high conductivity values regardless of the season. No positive root pressures were detected in either species. The mean frost depth (204 11 mm) was deeper than all sampled roots of Rhus and 47% of sampled roots of Sassafras. The roots that had been in frozen soil either avoided embolism altogether or they were able to reverse embolism by a mechanism other than positive root pressures. PMID:11222243

  18. Phylogenetic and biogeographic diversification of Rhus (Anacardiaceae) in the Northern Hemisphere.

    PubMed

    Yi, Tingshuang; Miller, Allison J; Wen, Jun

    2004-12-01

    Sequences of internal transcribed spacers (ITS) of nuclear ribosomal DNA, the chloroplast ndhF gene, and chloroplast trnL-F regions (trnL intron, and trnL [UAA] 3' exon-trnF [GAA] intergenic spacer) were used for phylogenetic analyses of Rhus, a genus disjunctly distributed in Asia, Europe, Hawaii, North America, and Northern Central America. Both ITS and cpDNA data sets support the monophyly of Rhus. The monophyly of subgenus Rhus was suggested by the combined cpDNA and ITS data, and largely supported in the cpDNA data except that Rhus microphylla of subgenus Lobadium was nested within it. The monophyly of subgenus Lobadium was strongly supported in the ITS data, whereas the cpDNA data revealed two main clades within the subgenus, which formed a trichotomy with the clade of subgenus Rhus plus R. microphylla. The ITS and cpDNA trees differ in the positions of Rhus michauxii, R. microphylla, and Rhus rubifolia, and hybridization may have caused this discordance. Fossil evidence indicates that Rhus dates back to the early Eocene. The penalized likelihood method was used to estimate divergence times, with fossils of Rhus subgenus Lobadium, Pistacia and Toxicodendron used for age constraints. Rhus diverged from its closest relative at 49.1+/-2.1 million years ago (Ma), the split of subgenus Lobadium and subgenus Rhus was at 38.1+/-3.0 Ma. Rhus most likely migrated from North America into Asia via the Bering Land Bridge during the Late Eocene (33.8+/-3.1 Ma). Rhus coriaria from southern Europe and western Asia diverged from its relatives in eastern Asia at 24.4+/-3.2 Ma. The Hawaiian Rhus sandwicensis diverged from the Asian Rhus chinensis at 13.5+/-3.0 Ma. Subgenus Lobadium was inferred to be of North American origin. Taxa of subgenus Lobadium then migrated southward to Central America. Furthermore, we herein make the following three nomenclatural combinations: (1) Searsia leptodictya (Diels) T. S. Yi, A. J. Miller and J. Wen, comb. nov., (2) Searsia pyroides (A. Rich.) T. S. Yi, A. J. Miller and J. Wen, comb. nov., and (3) Searsia undulata (Jacq.) T. S. Yi, A. J. Miller and J. Wen, because our analyses support the segregation of Searsia from Rhus. PMID:15522809

  19. Clinical and immunologic features of systemic contact dermatitis from ingestion of Rhus (Toxicodendron).

    PubMed

    Oh, Seok-Hun; Haw, Choong-Rim; Lee, Mu-Hyoung

    2003-05-01

    Oral or parenteral exposure to certain contact allergens may elicit an eczematous skin reaction in sensitized individuals. This phenomenon has been called systemic contact dermatitis (SCD) and is relatively rare when compared with classical contact dermatitis. We reviewed and analysed the clinical and immunologic features of 42 patients with SCD caused by ingestion of Rhus (Toxicodendron), 24 males and 18 females, average age 44 years (range 24-72). Several of such patients (33%) had a known history of allergy to lacquer. The patients developed skin lesions such as generalized maculopapular eruptions (50%), erythroderma (29%), vesiculobullous lesions (14%) and erythema multiform (EM)-like lesions (7%). Many patients (57%) developed leucocytosis with neutrophilia (74%). In some patients (5%), abnormalities of liver function developed. We also analysed lymphocyte subsets in the peripheral blood of 12 patients. The lymphocyte subsets studied were T cells (CD3), B cells (CD19), natural killer (NK) cells (CD3-CD16+/CD56+), helper/inducer cells (CD4), cytotoxic/suppressor cells (CD8) and helper/suppressor ratio (CD4/CD8). The lymphocyte subsets of all 12 patients studied were within the normal range. Moreover, there were no differences between patients with a history of allergy to lacquer and those without a history of allergy to lacquer. Therefore, rather than an immunologic response, the skin eruption seems to be caused by a toxic reaction because of Rhus. PMID:12868965

  20. Clinical Features of Systemic Contact Dermatitis Due to the Ingestion of Lacquer in the Province of Chungcheongnam-do

    PubMed Central

    Kim, Jung Eun; Lee, Jong Suk; Park, Young Lip; Whang, Kyu Uang

    2012-01-01

    Background Lacquer contains an allergen, which can cause severe contact dermatitis. Systemic dermatitis resulting from the ingestion of lacquer is quite common in Korea, until now. Objective The purpose of this study is to elucidate the clinical features and laboratory findings of systemic contact dermatitis (SCD), due to the ingestion of lacquer in Chungcheongnam-do. Methods We retrospectively reviewed the medical records of 33 patients with SCD, after ingestion of lacquer from Soonchunhyang University Hospital in Cheonan, over a 6-month period. Results In this study, 33.3% of patients ate lacquer, as a health food, and some (15.2%) by encouragement of friends or spouse. The most common way of ingestion was the lacquer-boiled chicken (48.5%), but many also ate lacquer tree sprouts (42.4%). The skin lesions developed as erythematous maculopapular eruptions, erythema multiforme, erythroderma, purpura, wheals and vesicles. On laboratory findings, 13 patients (52%) exhibited leukocytosis and 11 patients had elevated eosinophil counts. Conclusion The general public is becoming more aware of the toxic effects of lacquer ingestion, but still does not fully understand the dangers of lacquer tree sprouts, and this ignorance is frequently causing SCD in Chungcheongnam-do. PMID:22879716

  1. Antimicrobial constituents of Rhus glabra.

    PubMed

    Saxena, G; McCutcheon, A R; Farmer, S; Towers, G H; Hancock, R E

    1994-04-01

    The antimicrobial activity of the methanol extract and isolated constituents of Rhus glabra (Anacardiaceae), a species used in folk medicine by North American native people, was evaluated against 11 microorganisms, including gram-positive and gram-negative bacteria. The extract was subsequently fractionated and monitored by bioassays leading to the isolation of three antibacterial compounds, the methyl ester of 3,4,5-trihydroxybenzoic acid (methyl gallate) (minimal inhibition concentration (MIC) 12.5 micrograms/ml), 4-methoxy-3,5-dihydroxybenzoic acid (MIC 25 micrograms/ml) and gallic acid (MIC > 1000 micrograms/ml). The first two compounds are reported here for the first time from Rhus glabra. Their structures were established using spectroscopic and chemical methods. PMID:8072309

  2. Polymerized Urushiol of the Commercially Available Rhus Product in Korea

    PubMed Central

    Cheong, Seung Hyun; Choi, You Won; Min, Byung Sun

    2010-01-01

    Background Systemic contact dermatitis commonly occurs with the intake of rhus (boiled chicken with rhus) as a health food and a folk medicine to cure gastrointestinal diseases in Korea. Rhus companies insist they have the technology for rhus detoxification. However, the numbers of systemic allergic contact dermatitis patients, caused by rhus, have not decreased. The principle of present techniques for rhus detoxification is the induction of the polymerization of urushiol, but polymerized urushiol may still have antigenicity, although to a diminished degree. The Korean Food and Drug Administration (KFDA) has a regulation to control urushiol use as a food. However, the laboratory method that KFDA uses for detection of rhus can only detect the urushiol monomer. Objective We conducted experiments to detect polymerized urushiol in rhus products, which were considered not to include urushiol by the KFDA. Methods Rhus product approved by the KFDA was separated with chloroform. The chloroform fractionation was accomplished on a recycle HPLC system. Four peaks were achieved and evaporated to give an amorphous powder. Each powder was analyzed on a NMR system and mass spectrometer. Results The material considered to be urushiol dimer, with a 638 molecular weight (MW), was detected in one of the four powders as per the HPLC peaks. Conclusion We concluded that commercially available rhus product is comprised of material considered to be urushiol dimer. Therefore, even if the antigenicity of the rhus products is low, this product may cause adverse effects and is not completely detoxified. PMID:20548875

  3. An outbreak of contact dermatitis from Rhus verniciflua (Toxicodendron vernicifluum).

    PubMed

    Powell, S M; Barrett, D K

    1986-05-01

    Case reports are described of individuals who developed acute contact dermatitis after contact with the resin from the Rhus verniciflua (Toxidendron vernicifluum). Potential problems from possible extensive urban planting of this species are discussed. PMID:3743037

  4. Use of clobetasol in lacquer for plaque psoriasis treatment*

    PubMed Central

    da Silva, Suze Aparecida; Magalhães, Renata Ferreira; Torres, Rafael Augusto Tamasauskas; de Oliveira, Raquel Diana; Velho, Paulo Eduardo Neves Ferreira

    2016-01-01

    Clobetasol benefits to control psoriasis lesions are well defined, but there were not studies about its action when used in lacquer vehicle to control skin lesions. A double-blind study was conducted with 40 patients that utilized clobetasol 0.05% in one hemibody and just the vehicle in the other hemibody. Twenty of them used petrolatum as vehicle and the others used lacquer. An assessment was conducted using the clinical index PASI and a quality of life questionnaire (Dermatological Life Quality Index). There was no statistical difference between groups. There was a trend of favorable response particularly in the hemibody treated with clobetasol.

  5. Amorolfine vs. ciclopirox lacquers for the treatment of onychomycosis

    PubMed Central

    Szewczyk, Anna E.; Bienias, Wojciech; Wojciechowska, Agnieszka; Pastuszka, Marta; Oszukowska, Magdalena; Kaszuba, Andrzej

    2015-01-01

    Amorolfine 5% and ciclopirox 8% nail lacquers are commonly used in topical treatment of onychomycosis. These formulations may be used alone or in combination with oral antifungal agents. Amorolfine and ciclopirox are valuable therapeutic options, however, their usage in monotherapy should be limited. Proper amorolfine and ciclopirox penetration through the nail plate is provided by transungual drug delivery systems. Although amorolfine and ciclopirox have a different mode of action, they both exhibit a broad antifungal activity. The use of antifungal nail lacquers in combination with oral agents, such as terbinafine and itraconazole, improves efficacy of antifungal therapy. PMID:25821426

  6. Transungual delivery of ketoconazole using novel lacquer formulation.

    PubMed

    Hafeez, Farhaan; Hui, Xiaoying; Chiang, Audris; Hornby, Sidney; Maibach, Howard

    2013-11-18

    Onychomycosis, a common fungal infection of the nail, can have a substantial impact on quality of life. The success of topical therapy for onychomycosis depends on effective penetration, which can be enhanced using an appropriate delivery method. This study evaluated the effectiveness of a novel topical lacquer on enhancing [(14)C]-ketoconazole penetration by comparing nail absorption, nail distribution, and nail penetration of [(14)C]-ketoconazole dissolved in the novel lacquer versus a commercial ketoconazole cream. Using the in vitro finite dose model, the formulations were applied daily to human nail plates for 7 days. Drug absorption was measured by monitoring rate of appearance in each nail layer and the supporting bed. After the multiple day treatment, cumulative concentrations of ketoconazole formulated in novel lacquer in the deep nail layer and the nail bed were significantly greater than cumulative concentrations of commercial ketoconazole (p<0.05), as well as several orders of magnitude greater than the minimal inhibitory concentration (MIC) deemed necessary to inhibit the growth of causative dermatophytic and yeast species. These results suggest that this novel ketoconazole lacquer has the potential to be an effective topical treatment for onychomycosis. PMID:24029171

  7. [Sumac (Rhus chinensis Mill) biomass refinery engineering].

    PubMed

    Wang, Lan; Wang, Ning; Li, Tan; Chen, Hongzhang

    2014-05-01

    Sumac (Rhus chinensis Mill) is an abundant and widely distributed Chinese native plant. Sumac fruit contains low content of vegetable oil, as an atypical oil plants hardly being processed through traditional vegetable oil production technologies. Based on our own studies on the characteristics of sumac fruit and branches, we established a novel model of sumac biomass refinery, and constructed the sumac biomass refinery technology system and eco-industrial chain integration. Steam explosion was the key technology, and several components fractionation technologies were integrated in the sumac biomass refinery system. The fractionated components were converted into different products depending on their functional features. Eight products including sumac fruit oil, biodiesel, protein feed, flavonoids, unbleached facial tissue, phenolic resin, biomass briquette and biogas were produced in the refinery. The extracted sumac fruit oil by steam explosion pretreatment was applied for the new food resource of Ministry of Health, and the permit was approved. This research provides a new model for the development of atypical wild plant resources. PMID:25118393

  8. Galloylglucoses and riccionidin A in Rhus javanica adventitious root cultures.

    PubMed

    Taniguchi, S; Yazaki, K; Yabuuchi, R; Kawakami, K; Ito, H; Hatano, T; Yoshida, T

    2000-02-01

    Adventitious root cultures of Rhus javanica L. produced large amounts of galloylglucoses (gallotannins) and an anthocyanidin, riccionidin A, formerly found only in liverworts. Production of both galloylglucoses and riccionidin A in the adventitious root culture system was suppressed by light. The Rhus root culture showed the highest productivity for those secondary metabolites in a modified Linsmaier-Skoog (LS) liquid medium containing 30 mM NH4+ and 30 mM NO3- as nitrogen sources in the presence of 10(-6) M 3-indoleacetic acid (IAA). PMID:10703057

  9. A bichalcone from the twigs of Rhus pyroides.

    PubMed

    Masesane, I B; Yeboah, S O; Liebscher, J; Mgge, C; Abegaz, B M

    2000-04-01

    The twigs of Rhus pyroides yielded a novel bichalcone 2',4",2"'-trihydroxy-4',4"'-dimethoxy-4-O-5"'-bichalcone. It was identified on the basis of spectroscopic data including 1D and 2D NMR spectroscopy. The name rhuschalcone-1 is proposed. PMID:10820821

  10. Xenoestrogens released from lacquer coatings in food cans.

    PubMed

    Brotons, J A; Olea-Serrano, M F; Villalobos, M; Pedraza, V; Olea, N

    1995-06-01

    We present data showing that some foods preserved in lacquer-coated cans and the liquid in them may acquire estrogenic activity. Hormonal activity was measured using the E-screen bioassay. The biological activity of vegetables packed in cans was a result of plastic monomers used in manufacturing the containers. The plastic monomer bisphenol-A, identified by mass spectrometry, was found as a contaminant not only in the liquid of the preserved vegetables but also in water autoclaved in the cans. The amount of bisphenol-A in the extracts accounted for all the hormonal activity measured. Although the presence of other xenoestrogens cannot be ruled out, it is apparent that all estrogenic activity in these cans was due to bisphenol-A leached from the lacquer coating. The use of plastic in food-packaging materials may require closer scrutiny to determine whether epoxy resins and polycarbonates contribute to human exposure to xenoestrogens. PMID:7556016

  11. Toxicodendron radicans dermatitis with black lacquer deposit on the skin.

    PubMed

    Mallory, S B; Miller OF 3dU; Tyler, W B

    1982-03-01

    Four patients with clinical Toxicodendron dermatitis (poison ivy) presented with dramatic black lacquer-like deposits on several lesions. This black deposit was also observed at sites of injury on poison ivy plants and was reproduced on volunteers by the application of plant sap on the skin. Histologically, the observed material was identified in the stratum corneum. This little-recognized phenomenon has been mentioned in past dermatologic literature. PMID:6461673

  12. Atomic Oxygen Removes Varnish And Lacquer From Old Paintings

    NASA Technical Reports Server (NTRS)

    Rutledge, Sharon K.; Banks, Bruce A.; Cales, Michael

    1996-01-01

    Dry and relatively nondestructive plasma process found effective in removing protective coats from old paintings. Process generates monatomic oxygen, which reacts with varnish, lacquer, polyurethane, acrylic, and other organic coating materials; reactions produce mostly carbon monoxide and water vapor, then simply pumped away by vacuum system in which plasma generated. Does not attack oxide-based pigments in underlying paint layers, and brush-stroke marks remain undisturbed.

  13. Choroidal Thickness and Biometric Markers for the Screening of Lacquer Cracks in Patients with High Myopia

    PubMed Central

    Wang, Nan-Kai; Lai, Chi-Chun; Chou, Chai Lin; Chen, Yen-Po; Chuang, Lan-Hsin; Chao, An-Ning; Tseng, Hsiao-Jung; Chang, Chee-Jen; Wu, Wei-Chi; Chen, Kuan-Jen; Tsang, Stephen H.

    2013-01-01

    Objectives Validation of choroidal thickness and other biometrics measured by spectral domain optical coherence tomography (SD-OCT) in predicting lacquer cracks formation in highly myopic eyes. Methods Patients with a refractive error worse than ?8 diopters and moderate myopic maculopathy were recruited into two groups based on the presence or absence of lacquer cracks (36 eyes without and 33 eyes with lacquer cracks). Choroidal thickness, refractive error, and axial length were measured and subjected to receiver operating characteristic curve analysis to identify the optimal cutoff values at predicting lacquer crack formation. The width of the retinal pigment epithelium (RPE), RPE to the inner segment/outer segment line, RPE to the external limiting membrane were also measured and compared to the subfoveal choroidal thickness to assess their relationships as potential markers of lacquer crack formation. Results Lacquer crack is associated with decreased choroidal thickness, lower best-corrected visual acuity, longer axial length and higher refractive errors. Choroidal thickness has the strongest association with lacquer crack formation versus axial length and refractive error. In eyes with lacquer cracks, stellate lacquer cracks are associated with thinner choroidal thickness compared to eyes with linear lacquer cracks. Subfoveal choroidal thickness less than the width of the retinal pigment epithelium to the inner segment/outer segment line is also associated with lacquer crack formation (sensitivity 78.8%, specificity 88.3%, and accuracy 81.2%). Conclusions This study suggests that choroidal thickness and other SD-OCT measurements could be employed clinically to predict the development and severity of lacquer cracks in patients with high myopia. PMID:23349728

  14. Biochemical and immunological studies of deglycosylated Rhus vernicifera laccase.

    PubMed

    Graziani, M T; Antonilli, L; Sganga, P; Citro, G; Mondovi, B; Rosei, M A

    1990-09-01

    Rhus vernicifera laccase (Japanese) was deglycosylated by treating it with exo- and endoglycosidases. In absence of unfolding agents deglycosylation does not exceed 32% while in denaturating conditions only 10% of saccharides are not digested. In the former case specific activity seems to be directly related to the amount of the residual carbohydrates. After deglycosylation in denaturing conditions the modified enzyme exhibits an electrophoretic component of about 60-65 Kd. A stabilizing effect of saccharide moiety on the catalytic site of native laccase was demonstrated. Antiserum raised against the enzyme recognized native Japanese, Vietnamese as well as deglycosylated laccase indicating that the two isoforms are immunologically similar. PMID:2150479

  15. Tailoring Thin Film-Lacquer Coatings for Space Application

    NASA Technical Reports Server (NTRS)

    Peters, Wanda C.; Harris, George; Miller, Grace; Petro, John

    1998-01-01

    Thin film coatings have the capability of obtaining a wide range of thermal radiative properties, but the development of thin film coatings can sometimes be difficult and costly when trying to achieve highly specular surfaces. Given any space mission's thermal control requirements, there is often a need for a variation of solar absorptance (Alpha(s)), emittance (epsilon) and/or highly specular surfaces. The utilization of thin film coatings is one process of choice for meeting challenging thermal control requirements because of its ability to provide a wide variety of Alpha(s)/epsilon ratios. Thin film coatings' radiative properties can be tailored to meet specific thermal control requirements through the use of different metals and the variation of dielectric layer thickness. Surface coatings can be spectrally selective to enhance radiative coupling and decoupling. The application of lacquer to a surface can also provide suitable specularity for thin film application without the cost and difficulty associated with polishing.

  16. Ingestion of Rhus chicken causing systemic contact dermatitis in a Korean patient.

    PubMed

    Yoo, K H; Seo, S J; Li, K; Hong, C K

    2010-10-01

    Rhus chicken is a common traditional remedy used to cure gastrointestinal diseases and as a health food in Korea. Unfortunately, systemic contact dermatitis (SCD) due to the ingestion of Rhus occasionally occurs. In this study, the clinical and laboratory findings were reviewed and analysed for 30 Korean patients with SCD developing after ingestion of Rhus chicken. Summer was found to be the commonest period for hospital visits because of this condition. The mean period of incubation for SCD, was 4 1.5 days. The commonest skin features were generalized maculopapular eruptions. Of the 30 patients, 10 had a known history of allergy to Rhus chicken. Many of the patients developed neutrophilia and leucocytosis. All the patients responded well to standard treatments. The commonest reason for their ingestion of Rhus chicken was indigestion. We conclude that SCD often occurs in Koreans after ingestion of Rhus chicken. Patients should be educated about the harmful effects of Rhus chicken and advised not to ingest it. PMID:20456389

  17. Copper transfer from Rhus vernicifera laccase.

    PubMed

    Meadows, K A; Morie-Bebel, M M; McMillin, D R

    1991-03-01

    Tree laccase, a multi-copper oxidase, has been studied as a copper donor in conjunction with the demetalated forms of three blue copper proteins. Copper transfer could be observed under reducing conditions in the absence of air. Only about 10% of the total copper in laccase could be transferred regardless of the amount of acceptor present in solution, hence, the laccase is heterogeneous as isolated. Potential sources of the heterogeneity are considered. After transfer, laccase could be partially resolved into copper-deficient and nearly holoprotein fractions that would not donate copper when recombined with acceptor protein. EPR results in conjunction with thiol titrations indicate that there is no net loss of type 1 copper from laccase but that there is loss of type 2 copper as well as a small amount of type 3 copper. Very little transfer is observed when type 2-depleted laccase is used as the donor. Finally, the implications that these results could have in the elucidation of possibly more physiologically relevant processes are briefly summarized. PMID:1647440

  18. Development of microwave absorbing materials prepared from a polymer binder including Japanese lacquer and epoxy resin

    NASA Astrophysics Data System (ADS)

    Iwamaru, T.; Katsumata, H.; Uekusa, S.; Ooyagi, H.; Ishimura, T.; Miyakoshi, T.

    Microwave absorption composites were synthesized from a poly urushiol epoxy resin (PUE) mixed with one of microwave absorbing materials; Ni-Zn ferrite, Soot, Black lead, and carbon nano tube (CNT) to investigate their microwave absorption properties. PUE binders were specially made from Japanese lacquer and epoxy resin, where Japanese lacquer has been traditionally used for bond and paint because it has excellent beauty. Japanese lacquer solidifies with oxygen contained in air's moisture, which has difficulty in making composite, but we improved Japanese lacquer's solidification properties by use of epoxy resin. We made 10 mm thickness composite samples and cut them into toroidal shape to measure permittivity, permeability, and reflection loss in frequencies ranging from 50 Hz to 20 GHz. Electric magnetic absorber's composites synthesized from a PUE binders mixed either with Soot or CNT showed significantly higher wave absorption over -27 dB than the others at frequencies around 18 GHz, although Japanese lacquer itself doesn't affect absorption. This means Japanese lacquer can be used as binder materials for microwave absorbers.

  19. Pharmacokinetic Profile of Eight Phenolic Compounds and Their Conjugated Metabolites after Oral Administration of Rhus verniciflua Extracts in Rats.

    PubMed

    Jin, Ming Ji; Kim, In Sook; Park, Jong Suk; Dong, Mi-Sook; Na, Chun-Soo; Yoo, Hye Hyun

    2015-06-10

    Rhus verniciflua (Toxicodendron vernicifluum) is a medicinal tree popularly used in Asian countries such as China, Japan, and Korea as a food additive or herbal medicine because of its beneficial effects. R. verniciflua extract (RVE) contains diverse phenolic compounds, such as flavonoids, as its major biological active constituents. In this study, the pharmacokinetic profiles of eight phenolic compounds were investigated following oral administration of RVE to rats. The eight phenolic compounds were 2,4-dihydroxybenzoic acid, 3,4-dihydroxybenzoic acid, fisetin, fustin, butin, sulfuretin, taxifolin, and garbanzol. The plasma concentrations of the eight compounds were determined by using a liquid chromatography-triple-quadrupole mass spectrometer before and after treatment with ?-glucuronidase. When 1.5 g/kg RVE was administered, the eight compounds were all detected in plasma, mainly as conjugated forms. These pharmacokinetic data would be useful for understanding the pharmacological effects of RVE. PMID:25998231

  20. In vivo evaluation of antidiarrhoeal activity of Rhus semialata fruit extract in rats.

    PubMed

    Bose, Sekhar K; Dewanjee, Saikat; Sen Gupta, Avijit; Samanta, Kartick C; Kundu, Mintu; Mandal, Subhash C

    2007-01-01

    Rhus semialata Murr. (Anacardiaceae) is a deciduous tree of north eastern India. The fruit of this plant is traditionally used to control diarrhoea and dysentery. The Present study was undertaken to evaluate anti-diarrhoeal potency of methanol extract of fruits of R. semialata using Wister albino rats to substantiate folklore claims. The extract at graded doses (100, 200, 400 and 600 mg/kg body weight) was investigated for anti-diarrhoeal activity in term of reduction in the rate of defecation in castor oil induced diarrhoea. To understand the mechanism of its antidiarrhoeal activity, the gastrointestinal transit and PGE(2)-induced intestinal fluid accumulation (enteropooling) were further evaluated. At graded doses, the extract showed a remarkable anti-diarrhoeal activity evidenced by the reduction in the rate of defecation up to 80.70% of control diarrhoeal animals at the dose of 600 mg/kg body weight. Results are comparable to that of standard drug diphenoxylate (50 mg/kg body weight). Extract produced profound decrease in intestinal transit (8.02-47.05%) at selected doses comparable to that of single intraperitoneal injection of standard drug atropine sulphate at doses of 0.1 mg/kg body weight. It significantly inhibited PGE(2)-induced enteropooling (21.98-56.03%). The results indicated that the methanol extract of the fruits of R. semialata possesses significant anti-diarrhoeal effect and substantiated the use of this herbal remedy as a non-specific treatment for diarrhoea in folk medicine. PMID:20162061

  1. Rhus chinensis and Galla Chinensis--folklore to modern evidence: review.

    PubMed

    Djakpo, Odilon; Yao, Weirong

    2010-12-01

    The species Rhus chinensis Mill. (Anacardiaceae) is an important representative of the genus Rhus, which contains over 250 individual species found in temperate and tropical regions worldwide. Rhus chinensis has long been used by folk medicine practitioners in Asia. Leaves, roots, stem, bark, fruit and particularly the galls on Rhus chinensis leaves, Galla chinensis, are recognized to have preventative and therapeutic effects on different ailments (such as diarrhea, dysentery, rectal and intestinal cancer, diabetes mellitus, sepsis, oral diseases and inflammation). However, it is critical to separate evidence from anecdote. Fortunately, recent scientific research has revealed that Rhus chinensis compounds possess strong antiviral, antibacterial, anticancer, hepatoprotective, antidiarrheal and antioxidant activities. Moreover, compounds isolated from the stem of Rhus chinensis significantly suppressed HIV-1 activity in vitro. Compounds from this plant were also found to inhibit enamel demineralization in vitro and enhance remineralization of dental enamel with fluoride. This review highlights claims from traditional and tribal medicinal lore and makes a contemporary summary of phytochemical, biological and pharmacological findings on this plant material. It aims to show that the pharmaceutical potential of this plant deserves closer attention. PMID:20564459

  2. A controlled trial of clobetasol propionate ointment 0.05% in the treatment of experimentally induced Rhus dermatitis.

    PubMed

    Vernon, H J; Olsen, E A

    1990-11-01

    We studied the effectiveness of clobetasol propionate ointment 0.05% in experimentally induced Rhus dermatitis. Clobetasol rapidly decreased the vesiculation at each treated site, although the effect was most prominent at the site to which clobetasol was applied the earliest, that is, at 12 hours after exposure to Rhus extract. On the basis of this experimental model, clobetasol propionate ointment 0.05% may be effective therapy for naturally occurring Rhus dermatitis. PMID:2147698

  3. Room temperature ESR spectra of Rhus vernicifera laccase and derivatives.

    PubMed

    Sakurai, T; Takahashi, J

    1995-10-01

    Although both the type 1 and type 2 coppers of Rhus vernicifera laccase are fully ESR detectable at 77 K, only 30% of the type 2 copper are in the cupric form at room temperature. The residual 70% of the type 2 copper was easily transformed into the ESR detectable form by irradiating the resting enzyme with microwave of 200 mW. The enzyme activity did not change by the irradiation with high-powered microwave, indicating that the type 2 copper can be in both the ESR detectable and ESR undetectable forms in solution. The room temperature ESR spectra of the type 2 copper-depleted laccase and of the azide-bound type 3 copper signals were also measured at room temperature and compared with those at 77 K. PMID:7575597

  4. Tailoring Thin Film-Lacquer Coatings for Space Applications

    NASA Technical Reports Server (NTRS)

    Peters, Wanda C.; Harris, George; Miller, Grace; Petro, John

    1998-01-01

    Thin film coatings have the capability of obtaining a wide range of thermal radiative properties, but the development of thin film coatings can sometimes be difficult and costly when trying to achieve highly specular surfaces. Given any space mission's then-nal control requirements, there is often a need for a variation of solar absorptance (alpha(sub s)), emittance (epsilon) and/or highly specular surfaces. The utilization of thin film coatings is one process of choice for meeting challenging thermal control requirements because of its ability to provide a wide variety of alpha(sub s)/epsilon ratios. Thin film coatings' radiative properties can be tailored to meet specific thermal control requirements through the use of different metals and the variation of dielectric layer thickness. Surface coatings can be spectrally selective to enhance radiative coupling and decoupling. The application of lacquer to a surface can also provide suitable specularity for thin film application without the cost and difficulty associated with polishing.

  5. Nuclear Magnetic Resonance (NMR) analysis of a Kel-F resin and lacquer

    NASA Astrophysics Data System (ADS)

    Rutenberg, A. C.

    1985-08-01

    Proton, carbon, and fluorine nuclear magnetic resonance (NMR) spectroscopy has been used at the Oak Ridge Y-12 Plant to determine the concentration of various species present in Kel-F 800 resin and its lacquers. Nuclear magnetic resonance (NMR) spectroscopy has been used to characterize Kel-F 800 resin and to measure the various chemical species present in a lacquer based on this resin. Proton NMR spectroscopy was used to measure the ratio of ethyl acetate to xylenes and to estimate the vinylidene fluoride content of the resin. Fluorine NMR spectroscopy was used to determine the water and ethanol content of the lacquer as well as some of its components. Fluorine NMR spectroscopy was also used to estimate the amount of perfluorodecanoate emulsifier present in the Kel-F resin. Carbon-13 NMR spectroscopy was used to determine the isomeric composition of various batches of xylenes and as an alternate method for measuring the vinylidene fluoride content of the resin.

  6. 40 CFR 180.1179 - Plant extract derived from Opuntia lindheimeri, Quercus falcata, Rhus aromatica, and Rhizophoria...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... lindheimeri, Quercus falcata, Rhus aromatica, and Rhizophoria mangle; exemption from the requirement of a... Rhizophoria mangle; exemption from the requirement of a tolerance. The biochemical pesticide plant extract derived from Opuntia lindheimeri, Quercus falcata, Rhus aromatica, and Rhizophoria mangle is exempted...

  7. 40 CFR 180.1179 - Plant extract derived from Opuntia lindheimeri, Quercus falcata, Rhus aromatica, and Rhizophoria...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 24 2011-07-01 2011-07-01 false Plant extract derived from Opuntia... Tolerances 180.1179 Plant extract derived from Opuntia lindheimeri, Quercus falcata, Rhus aromatica, and... derived from Opuntia lindheimeri, Quercus falcata, Rhus aromatica, and Rhizophoria mangle is exempted...

  8. Antioxidant activity of a Rhus verniciflua Stokes ethanol extract.

    PubMed

    Lim, K T; Hu, C; Kitts, D D

    2001-03-01

    A fractionated ethanol extract derived from Rhus Verniciflua Stokes (RVS) was assessed in both organic and aqueous media for the purpose of characterizing the mechanisms of antioxidant activity. RVS, an indigenous plant to Korea, was initially extracted with ethanol and characterized to contain a 90 KDa-ABTS reactive protein possessing 0.662 ng/mg copper. This characterization suggested that a primary component of RVS was Laccase, an oxidase enzyme complex. RVS exhibited a significant (P < 0.01) concentration-dependent inhibition of linoleic acid oxidation in an emulsion system up to 48 hours of incubation. Free radical scavenging activity of both a stable radical (e.g DPPH) and hydroxyl (e.g. *OH) radical followed a concentration-dependent pattern in different model systems. Using a liposome model with peroxyl radicals generated by AAPH, a significant extension of both the lag phase and a reduction of peak propagation of peroxyl radicals by RVS over a concentration range of 1 to 10 microg/ml was observed. RVS ethanol extract was also found to protect human low-density lipoprotein (LDL) from oxidative modification, mediated by cupric ion at 37 degrees C. Finally, RVS was found to be effective at protecting against plasmid DNA strand breakage induced by peroxyl free radicals in an aqueous medium. Our findings show that the ethanol fraction derived from RVS contained significant antioxidant activity in both polar and non-polar mediums. PMID:11278054

  9. Bioactive constituents from Harpephyllum caffrum Bernh. and Rhus coriaria L

    PubMed Central

    Shabana, Marawan M.; El Sayed, Aly M.; Yousif, Miriam F.; El Sayed, Abeer M.; Sleem, Amany A.

    2011-01-01

    Background: The leaf ethanol extract of Harpephyllum caffrum Bernh. has evidenced medicinal value due to its hepatoprotective activity. It demonstrated inhibitory effects on test standard microbes approximated to 40% the potency of ofloxacin and fluconazole. The same extract evidenced in vitro cytotoxicity on human cell lines, liver carcinoma HEPG2, larynx carcinoma HEP2, and colon carcinoma HCT116 cell lines when compared to doxorubicin. Materials and Methods: Fractionation of the leaf ethanol extract led to the isolation of the polyphenols, ethyl gallate, and quercetin-3-O-rhamnoside, a hydrocarbon, hendecane, the fatty acid ester, methyl linoleate, and four triterpenoids, betulonic acid, 3-acetyl-methyl betulinate, lupenone and lupeol for the first time, in addition to the previously reported phenol acids and flavonoids, gallic acid, methyl gallate, quercetin, kaempferol, kaempferol-3-O-rhamnoside, kaempferol-3-O-galactoside, apigenin-7-O-glucoside, and quercetin-3-O-arabinoside. Results: The ethanol extract of the fruit of the genetically related Rhus coriaria L., known as sumac, afforded protocatechuic acid, isoquercitrin, and myricetin-3-O-α-L-rhamnoside from the fruits for the first time, in addition to the previously reported phenol acids and flavonoids, gallic acid, methyl gallate, kaempferol, and quercetin. Conclusion: The leaf ethanol extract of H. caffrum Bernh. exhibited variable anti-inflammatory, analgesic, and antipyretic activities, besides the hepatoprotective, in vitro cytotoxic and anti-microbial activities. PMID:22262932

  10. High Speed Liquid Chromatographic Determination of Total Aromatics in Enamel and Lacquer Solvents.

    ERIC Educational Resources Information Center

    Esposito, G. G.

    Aromatic solvents possess the strongest solvency of the hydrogen types, but various air pollution control districts have established maximum limits on the amount that may be present in organic coatings. In the proposed procedure, high efficiency liquid chromatography is used to determine total aromatics in enamels and lacquer thinners, their…

  11. High Speed Liquid Chromatographic Determination of Total Aromatics in Enamel and Lacquer Solvents.

    ERIC Educational Resources Information Center

    Esposito, G. G.

    Aromatic solvents possess the strongest solvency of the hydrogen types, but various air pollution control districts have established maximum limits on the amount that may be present in organic coatings. In the proposed procedure, high efficiency liquid chromatography is used to determine total aromatics in enamels and lacquer thinners, their

  12. Corrosion behavior of lacquered tinplate cans in contact with cockles (cardium edulis) in brine solution

    SciTech Connect

    Bastidas, J.M.; Cabanes, J.M.; Catala, R.

    2000-04-01

    Tinplate cans internally coated with an epoxyphenolic plus zinc oxide (ZnO) lacquer were studied. The relationship between lacquer adhesion and total chromium, metallic chromium, and chromium oxide (CrO{sub x}) in the passivated layer was analyzed. The thickness of the CrO{sub x} layer is a controlling parameter of adhesion. Electrochemical impedance spectroscopy (EIS), direct current (DC) polarization, and atomic absorption (AA) experiments were conducted at different time periods up to 150 days. EIS, DC, and AA results indicated that the passivation treatment with the lowest chromium content (Type 1) showed slightly worse corrosion behavior, with substantial iron dissolution and sulfur staining of the tinplate, than passivation treatments Types 2 and 3, which behaved similarly to each other. A fully opened can was used as the working electrode and electrolytic cell in contact with canned cockles (a mollusc, Cardium edulis).

  13. Matrix based system of isotretinoin as nail lacquer to enhance transungal delivery across human nail plate.

    PubMed

    Joshi, Monika; Sharma, Vijay; Pathak, Kamla

    2015-01-15

    The project was aimed at development of isotretinoin nail lacquer and assessment of its penetration efficiency across human nail plate. Preliminary studies (hydration enhancement factor and SEM) aided the selection of thioglycolic acid as permeation and eugenol was selected as local anesthetic in the formulation. The nail lacquer was optimized by 3(2) factorial design and a total of nine formulations were prepared and screened. In vitro adhesion and ex vivo permeation (cumulative drug permeation per unit area (CDP/A)=6.610.57mg/cm(2)) across bovine hoof guided the selection of F3 as optimized formulation that was improvised. Viscosity adjustments to improve handling characteristics were affected by incorporation of ethyl cellulose (6%; F3M1) that scaled the viscosity to 312.681?cp and insignificantly (p>0.05) affected CDP/A (6.320.45mg/cm(2)). In comparison to marketed preparation (Retino-A cream) F3M1 afforded two fold increase in CDP/A. The permeation characteristics were defined by Higuchi model (r(2)=0.964) and flux value of 176?g/cm(2)/h. Confocal laser scanning microscopy, after 72h of nail lacquer application, revealed extensive distribution of the fluorescent tracer across the human nail plate in comparison to control that was confined to the top layer. Conclusively, an efficacious and stable nail lacquer of isotretinoin was developed for potential clinical topical use to target the drug to nail bed in treatment of nail psoriasis. PMID:25445993

  14. The removal of the type-2 copper from Rhus vernicifera laccase.

    PubMed

    Li, J; McMillin, D R

    1992-12-28

    We have studied the removal of the type-2 copper from tree laccase (Rhus vernicifera) by treatment with EDTA at pH 5.2 in the presence of a redox buffer containing ferri- and ferrocyanide. The efficiency with which the copper is removed depends on the Fe(CN) 6(4-)/Fe(CN) 6(3-) ratio. We have varied this ratio from approx. 2:1 to about 50:1 and the best results were obtained with the highest ratio, i.e., the most cathodic solution potential. Nevertheless, the presence of Fe(CN) 6(3-) is required for the procedure to be effective. Although we cannot exclude the possibility that a mixed-valence form of laccase is the reactive species, we believe the results are better explained by a model which assumes that the removal of the type-2 copper depends upon an ordered sequence of oxidation-reduction reactions. Specifically, we propose that the copper is released as the monovalent ion from previously reduced laccase and then reoxidized in solution and sequestered with EDTA. The reoxidation step drives the reaction because recombination with the protein is inhibited when copper is in the divalent form. In testing this model, we have also shown that the type-2 copper can be removed under strictly reducing conditions when 4,4'-dicarboxy-2,2'-biquinoline (BCA) is present to complex the copper(I) ion. Although the BCA method is effective, the reaction takes longer, perhaps because of the limited solubility of BCA at the pH values of interest. Finally, we have found that the best results are obtained with either method when a cyanometalate ion such as Fe(CN) 6(3-) or Co(CN) 6(3-) is present in the medium. The exact role of this factor has yet to be established, but there is no indication that free cyanide has a role in the process. The most likely interpretation is that some type of binding interaction with the protein facilitates copper release. PMID:1477094

  15. Natural coniferous resin lacquer in treatment of toenail onychomycosis: an observational study

    PubMed Central

    Sipponen, Pentti; Sipponen, Arno; Lohi, Jouni; Soini, Marjo; Tapanainen, Riikka; Jokinen, Janne J

    2013-01-01

    In in vitro tests, natural coniferous resin from the Norway spruce (Picea abies) is strongly antifungal. In this observational study, we tested the clinical effectiveness of a lacquer composed of spruce resin for topical treatment of onychomycosis. Thirty-seven patients with clinical diagnosis of onychomycosis were enrolled into the study. All patients used topical resin lacquer treatment daily for 9 months. A mycological culture and potassium hydroxide (KOH) stain were done from nail samples in the beginning and in the end of the study. Treatment was considered effective, if a mycological culture was negative and there was an apparent clinical cure. At study entry, 20 patients (20/37; 54%; 95% CI: 3870) had a positive mycological culture and/or positive KOH stain for dermatophytes. At study end, the result of 13 patients was negative (13/19; 68%; 95% CI: 4889). In one case (1/14; 7%; 95% CI: 021) the mycological culture was initially negative, but it turned positive during the study period. By 14 compliant patients (14/32; 44%; 95% CI: 2761), resin lacquer treatment was considered clinically effective: complete healing took place in three cases (9%) and partial healing in 11 cases (85%). The results indicate some evidence of clinical efficacy of the natural coniferous resin used for topical treatment of onychomycosis. PMID:23131104

  16. Nuclear magnetic resonance (NMR) analysis of a Kel-F resin and lacquer

    SciTech Connect

    Rutenberg, A.C.

    1985-08-02

    Proton, carbon, and fluorine nuclear magnetic resonance (NMR) spectroscopy has been used at the Oak Ridge Y-12 Plant to determine the concentration of various species present in Kel-F 800 resin and its lacquers. Nuclear magnetic resonance (NMR) spectroscopy has been used to characterize Kel-F 800 resin and to measure the various chemical species present in a lacquer based on this resin. Proton NMR spectroscopy was used to measure the ratio of ethyl acetate to xylenes and to estimate the vinylidene fluoride content of the resin. Fluorine NMR spectroscopy was used to determine the water and ethanol content of the lacquer as well as some of its components. Fluorine NMR spectroscopy was also used to estimate the amount of perfluorodecanoate emulsifier present in the Kel-F resin. Carbon-13 NMR spectroscopy was used to determine the isomeric composition of various batches of xylenes and as an alternate method for measuring the vinylidene fluoride content of the resin. 3 refs., 12 figs., 1 tab.

  17. The failure of immunotherapy with dinitrochlorobenzene and Rhus extract for recurrent conjunctival squamous papillomas.

    PubMed

    Novick, N L; Bosniak, S L

    1986-06-01

    A 25-year-old white male is described who presented with recurrent conjunctival squamous papillomata. Despite prior reports of successful dinitrochlorobenzene use for tropical immunotherapy, its failure in our patient, and the first documented attempt to employ Rhus oleoresin (poison ivy/oak) extract for topical conjunctival immunotherapy is reported. The role of topical immunotherapy in treating recurrent conjunctival papillomas is discussed. PMID:2940277

  18. 6-Pentadecylsalicylic acid: an antithrombin component isolated from the stem of Rhus semialata var. roxburghii.

    PubMed

    Kuo, S C; Teng, C M; Lee, L G; Chiu, T H; Wu, T S; Huang, S C; Wu, J B; Shieh, T Y; Chang, R J; Chou, T C

    1991-06-01

    Bioassay-directed fractionation of the n-hexane extract of the stem of Rhus semialata Murr. var. roxburghii DC (Anacardiaceae) has led to the isolation of 6-pentadecylsalicylic acid. It showed antithrombin activity at 50 micrograms/ml in the amidolytic method. It also prolonged the clotting time in a dose-dependent manner in the clotting assay of thrombin-fibrinogen interaction. PMID:1896523

  19. Rhusemialins A-C, new cyclolignan esters from the roots of Rhus javanica var. roxburghiana.

    PubMed

    Ouyang, Ming-An; Wein, Yung-Shung; Su, Ren-Kuan; Kuo, Yueh-Hsiung

    2007-05-01

    Three new cyclolignan esters and seven known compounds including two cyclolignan isolariciresinol, lynoiresinol, and five aromatic compounds methyl ferulate, vanillin, 4-hydroxy-3,5-dimethoxybenaldehyde, 4-methoxygallic acid, gallic acid were isolated from n-butanol extract of Rhus semialata (Anacardiaceae). The structural elucidations of rhusemialins A (1), B (2), and C (3) were based on FAB-MS, 1D and 2D NMR spectra. PMID:17473474

  20. Integrating Traditional Medicine into Modern Inflammatory Diseases Care: Multitargeting by Rhus verniciflua Stokes

    PubMed Central

    Kim, Ji Hye; Shin, Yong Cheol; Ko, Seong-Gyu

    2014-01-01

    Despite the fact that numerous researches were performed on prevention and treatment of inflammation related diseases, the overall incidence has not changed remarkably. This requires new approaches to overcome inflammation mediated diseases, and thus traditional medicine could be an efficacious source for prevention and treatment of these diseases. In this review, we discuss the contribution of traditional medicine, especially Rhus verniciflua Stokes, to modern medicine against diverse inflammation mediated diseases. Traditionally, this remedy has been used in Eastern Asia for the treatment of gastric problems, hepatic disorders, infectious diseases, and blood disorders. Modern science has provided the scientific basis for the use of Rhus verniciflua Stokes against such disorders and diseases. Various chemical constituents have been identified from this plant, including phenolic acid, and flavonoids. Cell-based studies have exhibited the potential of this as antibacterial, antioxidant, neuroprotective, anti-inflammatory, growth inhibitory, and anticancer activities. Enormous animal studies have shown the potential of this against proinflammatory diseases, neurodegenerative diseases, diabetes, liver diseases, and chemical insults. At the molecular level, this medicinal plant has been shown to modulate diverse cell-signaling pathways. In clinical studies, Rhus verniciflua Stokes has shown efficacy against various cancer patients such as colorectal, gastric, hepatic, renal, pancreatic, and pulmonary cancers. Thus, this remedy is now exhibiting activities in the clinic. PMID:25024508

  1. Multimodal imaging including spectral-domain optical coherence tomography and confocal near-infrared reflectance for characterization of lacquer cracks in highly myopic eyes

    PubMed Central

    Liu, C-F; Liu, L; Lai, C-C; Chou, J CL; Yeh, L-K; Chen, K-J; Chen, Y-P; Wu, W-C; Chuang, L-H; Sun, C-C; Wang, N-K

    2014-01-01

    Purpose To compare multimodal imaging in detecting lacquer cracks in highly myopic eyes, and to correlate these findings with those of spectral-domain optical coherence tomography (SD-OCT). Methods An observational case series study. Patients with a refractive error worse than ?8 diopters and lacquer cracks were recruited. The rates of detection of the lacquer cracks using multimodal imaging including near-infrared reflectance (NIR) imaging, fundus autofluorescence (FAF) imaging, and fluorescence angiography (FA) were compared. The characteristic findings of multimodal imaging were correlated with those of SD-OCT. Results NIR imaging was more sensitive (92.9%) in detecting lacquer cracks than either FAF (12.5%) or FA (67.9%). Lacquer cracks showed hyperreflectance on NIR, and they were consistently associated with a continuous retinal pigment epithelium-Bruch's membrane complex, thinner choroid, and acoustic shadows on SD-OCT. Conclusions NIR imaging is superior to blue laser light (FAF and FA) imaging in detecting lacquer cracks. SD-OCT in combination with NIR located primary pathological lacquer cracks in the intact retinal pigment epithelium-Bruch's membrane complex as well as thinner choroid. These findings indicate that multimodal cSLO and SD-OCT imaging allow for detecting of lacquer cracks in highly myopic eyes. PMID:25233819

  2. [State of the nervous system of workers engaged in painting with bituminous lacquers].

    PubMed

    Majdecki, T; Miszczak, J

    1985-01-01

    The neurological and electroencephalographic examinations involved a group of 82 workers dealing with the protection of railway carriage assemblies against corrosion. For anamnesis "The Hck and Hess ailments questionnaire" was used to evaluate the neurotic syndrome. The results have been compared in varnishing workers under better and worse toxicological conditions. The evaluation of the varnishing workers' nervous system did not reveal any specific clinical picture. More frequent neurotic ailments and EEG deviations in those working under worse toxicological conditions may be indicative of enhanced neurotoxic effects of organic solvents, used for lacquers dilution, upon the brain disfunction. PMID:4010504

  3. Rhus coriaria suppresses angiogenesis, metastasis and tumor growth of breast cancer through inhibition of STAT3, NFκB and nitric oxide pathways.

    PubMed

    El Hasasna, Hussain; Saleh, Alaaeldin; Samri, Halima Al; Athamneh, Khawlah; Attoub, Samir; Arafat, Kholoud; Benhalilou, Nehla; Alyan, Sofyan; Viallet, Jean; Dhaheri, Yusra Al; Eid, Ali; Iratni, Rabah

    2016-01-01

    Recently, we reported that Rhus coriaria exhibits anticancer activities by promoting cell cycle arrest and autophagic cell death of the metastatic triple negative MDA-MB-231 breast cancer cells. Here, we investigated the effect of Rhus coriaria on the migration, invasion, metastasis and tumor growth of TNBC cells. Our current study revealed that non-cytotoxic concentrations of Rhus coriaria significantly inhibited migration and invasion, blocked adhesion to fibronectin and downregulated MMP-9 and prostaglandin E2 (PgE2). Not only did Rhus coriaria decrease their adhesion to HUVECs and to lung microvascular endothelial (HMVEC-L) cells, but it also inhibited the transendothelial migration of MDA-MB-231 cells through TNF-α-activated HUVECs. Furthermore, we found that Rhus coriaria inhibited angiogenesis, reduced VEGF production in both MDA-MB-231 and HUVECs and downregulated the inflammatory cytokines TNF-α, IL-6 and IL-8. The underlying mechanism for Rhus coriaria effects appears to be through inhibiting NFκB, STAT3 and nitric oxide (NO) pathways. Most importantly, by using chick embryo tumor growth assay, we showed that Rhus coriaria suppressed tumor growth and metastasis in vivo. The results described in the present study identify Rhus coriaria as a promising chemopreventive and therapeutic candidate that modulate triple negative breast cancer growth and metastasis. PMID:26888313

  4. Rhus coriaria suppresses angiogenesis, metastasis and tumor growth of breast cancer through inhibition of STAT3, NFκB and nitric oxide pathways

    PubMed Central

    El Hasasna, Hussain; Saleh, Alaaeldin; Samri, Halima Al; Athamneh, Khawlah; Attoub, Samir; Arafat, Kholoud; Benhalilou, Nehla; Alyan, Sofyan; Viallet, Jean; Dhaheri, Yusra Al; Eid, Ali; Iratni, Rabah

    2016-01-01

    Recently, we reported that Rhus coriaria exhibits anticancer activities by promoting cell cycle arrest and autophagic cell death of the metastatic triple negative MDA-MB-231 breast cancer cells. Here, we investigated the effect of Rhus coriaria on the migration, invasion, metastasis and tumor growth of TNBC cells. Our current study revealed that non-cytotoxic concentrations of Rhus coriaria significantly inhibited migration and invasion, blocked adhesion to fibronectin and downregulated MMP-9 and prostaglandin E2 (PgE2). Not only did Rhus coriaria decrease their adhesion to HUVECs and to lung microvascular endothelial (HMVEC-L) cells, but it also inhibited the transendothelial migration of MDA-MB-231 cells through TNF-α-activated HUVECs. Furthermore, we found that Rhus coriaria inhibited angiogenesis, reduced VEGF production in both MDA-MB-231 and HUVECs and downregulated the inflammatory cytokines TNF-α, IL-6 and IL-8. The underlying mechanism for Rhus coriaria effects appears to be through inhibiting NFκB, STAT3 and nitric oxide (NO) pathways. Most importantly, by using chick embryo tumor growth assay, we showed that Rhus coriaria suppressed tumor growth and metastasis in vivo. The results described in the present study identify Rhus coriaria as a promising chemopreventive and therapeutic candidate that modulate triple negative breast cancer growth and metastasis. PMID:26888313

  5. Antioxidant effect of aqueous extract of sumac (Rhus coriaria L.) in the alloxan-induced diabetic rats.

    PubMed

    Salimi, Zahra; Eskandary, Azade; Headari, Reza; Nejati, Vahid; Moradi, Mojtaba; Kalhori, Zahra

    2015-01-01

    In this experimental study, 30 adult male Wistar rats divided into 5 groups (n=6). Experimental rats were treated with one intraperitoneal injection of 120 mg/kgbw Alloxan monohydrate alone or in combination with 28 days of oral administration with aqueous extract of Rhus coriaria (50, 100 and 250 mg/kgbw) while the control rats received normal saline. At the end of the study, blood glucose, malondialdehyde concentration and catalase activities of kidney and liver tissues were determined. Treatment with Rhus coriaria extract resulted in a significant reduction in blood glucose, and the liver and kidney tissue contents of malondialdehyde in comparison to diabetic group (P<0.05). Furthermore, diabetic group treated with extract showed a significant increase in catalase activities of the liver and kidney (P<0.05). The present study showed that Rhus coriaria could be effective in decreasing diabetic complication and this effect is attributed to the antioxidant activity of the plant. PMID:26571989

  6. In vitro transungual permeation of ciclopirox from a hydroxypropyl chitosan-based, water-soluble nail lacquer.

    PubMed

    Monti, Daniela; Saccomani, L; Chetoni, P; Burgalassi, S; Saettone, M F; Mailland, F

    2005-01-01

    Commercial antimycotic nail lacquers are commonly based on water-insoluble resins. The present study was aimed at evaluating a novel, experimental nail lacquer (P-3051, Polichem SA, Lugano, Switzerland) based on the water-soluble film-forming agent hydroxypropyl chitosan (HPCH). The in vitro permeation of ciclopirox (CPX) from P-3051 and from a commercial, water-insoluble lacquer based on a vinyl resin (Penlac, Aventis Pharma), was investigated using thin membranes obtained from bovine hooves, an accepted model for human nails. Similar CPX permeation fluxes at steady state through the membranes, but significantly different lag times were observed for P-3051 and Penlac, when these were tested as dry films. The formulations thus appeared to influence only the time required by CPX to saturate the membrane, and not the final drug concentration gradient in the membrane. Permeation experiments performed on the same membranes and on hairless mouse skin with P-3051 and with a similar, HPCH-free vehicle (ERV), both tested in liquid form, disproved the possibility that HPCH might act as a permeation enhancer for CPX in either substrate. The possible reasons for the greater efficiency of the HPCH vehicle in terms of CPX transfer from the vehicle itself to the keratin membrane are discussed. This effect might be tentatively attributed to a particular affinity of HPCH for the membrane, resulting in intimate contact and strong adhesion of the HPCH lacquer to the keratin substrate. PMID:15704853

  7. Ozone exposure-response curves for tree species in Great Smoky Mountains National Park: A re-evaluation of how potential impacts may have changed over the past 25 years

    EPA Science Inventory

    Seedlings of tree species native to Great Smoky Mountains National Park were exposed to ozone in open-top chambers for one or two growing seasons. Species used were red maple (Acer rubrum), chestnut oak (Quercus prinus), black locust (Robinia pseudoacadia), winged sumac (Rhus co...

  8. Exposure to airborne particles and volatile organic compounds from polyurethane molding, spray painting, lacquering, and gluing in a workshop.

    PubMed

    Mølgaard, Bjarke; Viitanen, Anna-Kaisa; Kangas, Anneli; Huhtiniemi, Marika; Larsen, Søren Thor; Vanhala, Esa; Hussein, Tareq; Boor, Brandon E; Hämeri, Kaarle; Koivisto, Antti Joonas

    2015-04-01

    Due to the health risk related to occupational air pollution exposure, we assessed concentrations and identified sources of particles and volatile organic compounds (VOCs) in a handcraft workshop producing fishing lures. The work processes in the site included polyurethane molding, spray painting, lacquering, and gluing. We measured total VOC (TVOC) concentrations and particle size distributions at three locations representing the various phases of the manufacturing and assembly process. The mean working-hour TVOC concentrations in three locations studied were 41, 37, and 24 ppm according to photo-ionization detector measurements. The mean working-hour particle number concentration varied between locations from 3000 to 36,000 cm-3. Analysis of temporal and spatial variations of TVOC concentrations revealed that there were at least four substantial VOC sources: spray gluing, mold-release agent spraying, continuous evaporation from various lacquer and paint containers, and either spray painting or lacquering (probably both). The mold-release agent spray was indirectly also a major source of ultrafine particles. The workers' exposure can be reduced by improving the local exhaust ventilation at the known sources and by increasing the ventilation rate in the area with the continuous source. PMID:25849539

  9. Exposure to Airborne Particles and Volatile Organic Compounds from Polyurethane Molding, Spray Painting, Lacquering, and Gluing in a Workshop

    PubMed Central

    Mølgaard, Bjarke; Viitanen, Anna-Kaisa; Kangas, Anneli; Huhtiniemi, Marika; Larsen, Søren Thor; Vanhala, Esa; Hussein, Tareq; Boor, Brandon E.; Hämeri, Kaarle; Koivisto, Antti Joonas

    2015-01-01

    Due to the health risk related to occupational air pollution exposure, we assessed concentrations and identified sources of particles and volatile organic compounds (VOCs) in a handcraft workshop producing fishing lures. The work processes in the site included polyurethane molding, spray painting, lacquering, and gluing. We measured total VOC (TVOC) concentrations and particle size distributions at three locations representing the various phases of the manufacturing and assembly process. The mean working-hour TVOC concentrations in three locations studied were 41, 37, and 24 ppm according to photo-ionization detector measurements. The mean working-hour particle number concentration varied between locations from 3000 to 36,000 cm−3. Analysis of temporal and spatial variations of TVOC concentrations revealed that there were at least four substantial VOC sources: spray gluing, mold-release agent spraying, continuous evaporation from various lacquer and paint containers, and either spray painting or lacquering (probably both). The mold-release agent spray was indirectly also a major source of ultrafine particles. The workers’ exposure can be reduced by improving the local exhaust ventilation at the known sources and by increasing the ventilation rate in the area with the continuous source. PMID:25849539

  10. Alkaline transition of Rhus vernicifera stellacyanin, an unusual blue copper protein.

    PubMed

    Fernndez, C O; Sannazzaro, A I; Vila, A J

    1997-08-26

    Stellacyanin from Rhus vernificera is a blue copper protein in which the metal is coordinated to a Cys, two His, and a Gln residue. It displays a low redox potential, a fast electron exchange rate, and a reversible alkaline transition. We have studied this transition in Cu(II)- and Co(II)-stellacyanin by means of electronic and NMR spectroscopy. The data indicate that a conformational rearrangement of the metal site occurs at high pH. A drastic alteration in the Gln coordination mode, as initially proposed, is discarded. These results show that the metal site in stellacyanin is more flexible than the sites of other blue copper proteins. The present study demonstrates that the paramagnetic shifts of the bound Cys in the Co(II) derivative are sensitive indicators of the electron delocalization and conformational changes experienced by this residue. PMID:9265638

  11. Hinokiflavone, a cytotoxic principle from Rhus succedanea and the cytotoxicity of the related biflavonoids.

    PubMed

    Lin, Y M; Chen, F C; Lee, K H

    1989-04-01

    Hinokiflavone (1) was isolated as the cytotoxic principle from the drupes of Rhus succedanea L. A comparison of the cytotoxicity of 1 and other related biflavonoids, including amentoflavone (2), robustaflavone (3), agathisflavone (4), rhusflavone (5), rhusflavanone (6) and its hexaacetate (7), succedaneaflavanone (8) and its hexaacetate (9), cupressuflavone (10), neorhusflavanone (11), volkensiflavone (12) and its hexamethyl ether (13), spicataside (14) and its nonaacetate (15), morelloflavone (16) and its heptaacetate (17) and heptamethyl ether (18), GB-1a (19) and its hexamethyl ether (20) and 7"-O-beta-glucoside (21), and GB-2a (22), indicates that an ether linkage between two units of apigenin as seen in 1 is structurally required for significant cytotoxicity. Compounds 13 and 20 also demonstrated significant cytotoxicity. PMID:2526343

  12. [Study on the interaction between Pd(II) and Rhus vernicifera laccase].

    PubMed

    Tu, C; Liang, H; Wang, G

    2001-08-01

    The influence of the mixing time of Pd(II) and Rhus vernicifera laccase on the oxidation of 5,6-dibromo-2,3-dicyanohydroquinone (DDBQH2) catalyzed by laccase has been studied through spectrophotometer at pH 4.5 and (30 +/- 0.1 degree C). The activation of Pd(II) on the laccase activity is gradually converted into inhibition and ultimately inactivation with the extension of the mixing time of Pd(II) and laccase, and the rate of such conversion goes up with the increase of Pd(II) concentration. The influence of Pd(II) on the absorption spectrum of laccase suggests that it is the type I site in laccase with which Pd(II) interacts and Pd(II) may gradually and at last substitute Cu(II) from the site. The substitution may be the cause of decrease and disappearance of laccase activity. PMID:12945281

  13. HPLC-DAD-ESI-MS/MS screening of bioactive components from Rhus coriaria L. (Sumac) fruits.

    PubMed

    Abu-Reidah, Ibrahim M; Ali-Shtayeh, Mohammed S; Jamous, Rana M; Arrez-Romn, David; Segura-Carretero, Antonio

    2015-01-01

    Rhus coriaria L. (sumac) is an important crop widely used in the Mediterranean basin as a food spice, and also in folk medicine, due to its health-promoting properties. Phytochemicals present in plant foods are in part responsible for these consequent health benefits. Nevertheless, detailed information on these bioactive compounds is still scarce. Therefore, the present work was aimed at investigating the phytochemical components of sumac fruit epicarp using HPLC-DAD-ESI-MS/MS in two different ionisation modes. The proposed method provided tentative identification of 211 phenolic and other phyto-constituents, most of which have not been described so far in R. coriaria fruits. More than 180 phytochemicals (tannins, (iso)flavonoids, terpenoids, etc.) are reported herein in sumac fruits for the first time. The obtained results highlight the importance of R. coriaria as a promising source of functional ingredients, and boost its potential use in the food and nutraceutical industries. PMID:25053044

  14. Correlation between antibutyrylcholinesterasic and antioxidant activities of three aqueous extracts from Tunisian Rhus pentaphyllum

    PubMed Central

    2011-01-01

    For centuries, plants have been used in traditional medicines and there has been recent interest in the chemopreventive properties of compounds derived from plants. In the present study, we investigated the antibutyrylcholinestrasic (anti-BuChE) and antioxidant (against some free radicals) activities of extracts from Rhus pentaphyllum. Aqueous extracts were prepared from powdered R. pentaphyllum roots, leaves and seeds and characterized for the presence of tannins, flavonoids and coumarins. Seeds aqueous extract contained the highest quantities of both flavonoids and tannins (21.12% and 17.45% respectively). In the same way, seeds extracts displayed remarkable inhibition against BuChE over 95%, at 100 ?g/ml and with IC50 0.74 ?g/ml. In addition, compared to leaves and roots extracts, seeds aqueous extract revealed relatively strong antiradical activity towards the ABTS.+ (IC50 = 0.25 ?g/ml) and DPPH (IC50 = 2.71 ?g/ml) free radicals and decreased significantly the reactive oxygen species such O2.- (IC50 = 2.9 ?g/ml) formation evaluated by the non-enzymatic generating O2.- system (Nitroblue tetrazolium/riboflavine). These data suggest that the anti-BuChE activities mechanism of these extracts occurs through a free radical scavenging capacities. The present study indicates that extracts of Rhus pentaphyllum leaves, seeds and roots are a significant source of compounds, such as tannins, flavonoids and coumarins, with anti-BuChE and antioxidant activities, and thus may be useful for chemoprevention. PMID:21880140

  15. Novel 4-(2-methylphenyl)-flavan, rhusjavanins A and B, from the roots of Rhus semialata.

    PubMed

    Wu, Yan-Bing; Kuo, Yueh-Hsiung; Ouyang, Ming-An

    2010-10-01

    In this study, two novel flavan derivatives, namely, rhusjavanins A and B, along with two known flavans 2,3-trans-3,4-trans-3,4,7,4'-tetrahydroxyflavan and 2,3-trans-3,4-cis-3,4,7,4'-tetrahydroxyflavan, have been isolated from the roots of Rhus javanica. The structures were elucidated on the basis of spectroscopic data. PMID:20954092

  16. The analysis of lacquer crack in the assessment of myopic choroidal neovascularization

    PubMed Central

    Kim, Y M; Yoon, J U; Koh, H J

    2011-01-01

    Objective The aim of this study was to clarify the characteristic findings in myopic choroidal neovascularization (CNV) and the relationship with lacquer crack (LC). Methods In all, 66 consecutive myopic CNV patients treated with photodynamic therapy and/or intravitreal anti-vascular endothelial growth factor injection in one eye were reviewed. Data from fluorescein angiography (FA) and indocyanine green angiography (ICGA), obtained simultaneously using the Heidelberg retina angiograph 2 (HRA2), were analyzed. Results LCs were associated with a relatively large extent (?3000??m) of peripapillary choroidal atrophy and a dark rim, the proliferation of retinal pigment epithelial cells surrounding the neovascular membrane was accompanied by a small extent. Myopic CNV usually developed in the LC area surrounded by tiny crack fragments. In all, 35 patients with LCs received FA and ICGA at least twice during follow-up. LC progression was observed in nine (25.7%) treated eyes and six (23.1%) non-CNV fellow eyes. Crack fragments progressed in three distinct forms such as elongation, branching, or bridging pattern. Newly diagnosed myopic CNV was reported in 18 treated eyes and 3 fellow eyes. Progression of LCs and development of CNV occurred simultaneously in eight eyes. By multivariate Cox's regression, a statistically significant association was observed between recurrence of myopic CNV and the absence of a dark rim on ICGA. Conclusions The HRA2 instrument affords detailed high-resolution images of FA and ICGA. Notably, recurrence of myopic CNV developed in areas surrounded by new small crack fragments and LCs are considered to be important in the development of myopic CNV. PMID:21527958

  17. A Standardized Extract of Rhus verniciflua Stokes Protects Wistar Rats Against Lipopolysaccharide-Induced Acute Inflammation.

    PubMed

    Moon, Ji Eun; Shin, Jae-Ho; Kwon, Oran; Kim, Ji Yeon

    2015-11-01

    Rhus verniciflua stokes (RVS) (Anacardiaceae) has been traditionally used as a folk remedy for gastritis, several cancers, and various metabolic diseases. The present study evaluated the anti-inflammatory effect of RVS extract standardized to fustin content using lipopolysaccharide (LPS)-stimulated rats. The rats were randomly divided into six groups and intragastrically administered 0, 100, 250, or 500?mg/kg body weight (bw) of RVS or 15?mg/kg bw of fustin for 14 days. LPS was intraperitoneally injected 18?h before sacrifice. The nitric oxide levels of RVS extract in either the serum or liver were significantly decreased compared to the LPS-treated rats (P<.05). The treatment with the RVS extract also blunted the rise of malondialdehyde levels in the liver (P<.05). The administration of RVS extract and fustin significantly prevented the elevation of interleukin 6 cytokine, iNOS, and COX-2 mRNA expression in the liver. Inflammatory cell infiltration was also significantly attenuated by the RVS extract or fustin supplementation. These results suggest that our standardized RVS extract has preventive effects on inflammatory reactions. PMID:26501382

  18. In vitro anti-HIV activity of biflavonoids isolated from Rhus succedanea and Garcinia multiflora.

    PubMed

    Lin, Y M; Anderson, H; Flavin, M T; Pai, Y H; Mata-Greenwood, E; Pengsuparp, T; Pezzuto, J M; Schinazi, R F; Hughes, S H; Chen, F C

    1997-09-01

    Eleven biflavonoids, including amentoflavone (1), agathisflavone (2), robustaflavone (3), hinokiflavone (4), volkensiflavone (5), morelloflavone (7), rhusflavanone (9), succedaneaflavanone (10), GB-1a (11), GB-1a 7"-O-beta-glucoside (13), and GB-2a (14) isolated from Rhus succedanea and Garcinia multiflora, as well as their methyl ethers, volkensiflavone hexamethyl ether (6), morelloflavone heptamethyl ether (8), and GB-1a hexamethyl ether (12), were evaluated for their anti-HIV-1 RT activity. The results indicated that compounds 3 and 4 demonstrated similar activity against HIV-1 reverse transcriptase (RT), with IC50 values of 65 microM. Compounds 1, 2, 7, 11, and 14 were moderately active against HIV-1 RT, with IC50 values of 119 microM, 100 microM, 116 microM, 236 microM, and 170 microM, respectively. Morelloflavone (7) also demonstrated significant antiviral activity against HIV-1 (strain LAV-1) in phytohemagglutinin-stimulated primary human peripheral blood mononuclear cells at an EC50 value of 6.9 microM and a selectivity index value of approximately 10. The other biflavonoids were either weakly active, inactive, or not selective against HIV-1 in human lymphocytes. PMID:9322359

  19. Suppression of recurrent genital herpes simplex virus type 2 infection by Rhus javanica in guinea pigs.

    PubMed

    Nakano, M; Kurokawa, M; Hozumi, T; Saito, A; Ida, M; Morohashi, M; Namba, T; Kawana, T; Shiraki, K

    1998-07-01

    Rhus javanica has been shown to exhibit anti-herpes simplex virus (HSV) activity and potentiate the anti-HSV activity of acyclovir in vitro and in vivo. This extract was examined for its suppressive efficacy on recurrent genital infection in guinea pigs. Guinea pigs were primarily infected intravaginally with HSV type 2 (HSV-2). Prophylactic oral administration, at the dose corresponding to human use, of R. javanica significantly reduced the incidence, severity and/or frequency of spontaneous and severe skin lesions as compared with latently infected guinea pigs administered with water. This prophylactic efficacy was confirmed by the crossover administration, for more than 2 months, of R. javanica and water to the infected guinea pigs. Toxicity, such as weight loss, from R. javanica administration was not observed in the guinea pigs. When recurrent HSV-2 disease was induced by ultraviolet irradiation 3 months after primary infection, the prophylaxis with R. javanica was also significantly effective in reducing the severity of ultraviolet-induced skin lesions. Thus, prophylaxis of recurrent genital HSV-2 infection with R. javanica may preserve the efficacy of acyclovir by reducing both the use of acyclovir and the appearance of acyclovir-resistant viruses. PMID:9754947

  20. Phenolic extracts from Rhus verniciflua Stokes bark by decompressing inner ebullition and their antioxidant activities.

    PubMed

    Chen, Hongxia; Wang, Chengzhang; Ye, Jianzhong; Zhou, Hao; Yuan, Jiaojiao

    2014-01-01

    Decompressing inner ebullition (DIE) can reduce the extraction liquid boiling point and polyphenols oxidation in the extraction process. The aim of this study is to optimise the phenolic extraction process by DIE and to examine the antioxidant activities. The extraction process parameters were observed by central composite design. The antioxidant activity was measured using 1,1-diphenyl-2-picrylhydrazyl (DPPH) and ferric reducing power assays. The results showed that the optimal extraction condition is extract time of 90min, temperature of 45C, solid-liquid ratio of 1:20g/mL, vacuum degree of -0.08MPa, ethanol concentration of 60%, while the phenolic content was 5.4%. The phenolic extracts from Rhus verniciflua Stokes bark had better antioxidant activities; the antioxidant activity (IC50) of the DIE was 20?g/mL by the DPPH method. The reducing power of the phenolic extracts was significantly related to their total phenolic content (R=0.9903). The results presented show that the DIE method is an effective method for polyphenols extraction. PMID:24437977

  1. Extract of Rhus verniciflua stokes protects the diet-induced hyperlipidemia in mice.

    PubMed

    Jeong, Se-Jin; Park, Jong-Gil; Kim, Sinai; Kweon, Hyae Yon; Seo, Seungwoon; Na, Dae-Seung; Lee, Dongho; Hong, Cheol Yi; Na, Chun-Soo; Dong, Mi-Sook; Oh, Goo Taeg

    2015-11-01

    Rhus verniciflua stokes (RVS) is a popular medicinal plant in oriental medicines which is commonly used to resolve extravasated blood. To elucidate the molecular mechanism of the role of RVS extracts on the regulation of lipid and cholesterol biosynthesis, we investigated whether RVS extract protect the hyperlipidemia in western diet-induced C57BL6/J mice. Mice fed a western diet and additionally RVS extracts was administered orally at a dose of 0.1 or 1g/kg/day for 2weeks respectively. Group with higher dose of RVS extract showed a significantly decreased body weight compared with western diet fed mice groups. And total cholesterol, LDL-cholesterol levels and fatty liver formation were also improved especially in group of mice fed western diet supplemented high dose RVS extracts. Next, synthesis of hepatic bile acids were significantly increased in RVS extract fed groups. Furthermore, RVS extracts significantly increase promoter activity of Cyp7a1 via up-regulate the transcriptional expression level of LXR?. Our data suggest that RVS extracts could be a potent therapeutic ingredient for prevent a hyperlipidemia via increase of bile acids biosynthesis. PMID:25784057

  2. Antifungal activity, experimental infections and nail permeation of an innovative ciclopirox nail lacquer based on a water-soluble biopolymer.

    PubMed

    Togni, Giuseppe; Mailland, Federico

    2010-05-01

    P-3051 is an innovative 8% ciclopirox nail lacquer, based on hydroxypropyl chitosan (HPCH) as a film-forming agent. The authors' aim was to investigate P-3051's in vitro antifungal activity, as well as its in vitro and in vivo nail permeation. The dilution susceptibility tests performed for Trichophyton rubrum (T. rubrum) and Candida parapsilosis (C. parapsilosis) showed that the minimum inhibitory concentrations (MICs) of P-3051, as percent of ciclopirox, was for both fungi < or = 0.0015% (equivalent to a concentration of 15.6 mg/ ml). In the biological assay of in vitro nail permeation and fungal inhibition, the authors observed that P-3051 permeated well through bovine hoof membranes and produced dose-dependent inhibitory effects on dermatophyte, yeast and mold strains. Moreover, the inhibition effects were higher than those obtained by equal amounts of the ciclopirox reference nail lacquer. P-3051 and the reference showed the same protective activity in experimental infections with strains of dermatophytes isolated from clinical samples. The amount of ciclopirox remained in cut fingernails washed six hours after in vivo application of P-3051 ranged between 18 and 35% of the applied dose. After in vitro application to cut human nails, 40-50% of the applied ciclopirox penetrated during the first six hours, independent of nails being infected or uninfected, intact or filed. In both experiments, the concentration of ciclopirox is largely higher (three to four orders of magnitude) than the MICs for nail pathogens. PMID:20480796

  3. Rhus coriaria ameliorates insulin resistance in non-insulin-dependent diabetes mellitus (NIDDM) rats.

    PubMed

    Anwer, Tarique; Sharma, Manju; Khan, Gyas; Iqbal, Muzaffar; Ali, Mohammad Sajid; Alam, Mohammad Sarfaraz; Safhi, Mohammed Mohsen; Gupta, Nakul

    2013-01-01

    We have investigated the effect of methanolic extract of Rhus coriaria (RC) on hyperinsulinemia, glucose intolerance and insulin sensitivity in non-insulin-dependent diabetes mellitus (NIDDM) rats. NIDDM was induced by single intraperitoneal injection of streptozotocin (STZ, 100 mg/kg) to 2 days old rat pups. RC (200 mg/kg and 400 mg/kg) was administered orally once a day for 5 weeks after the animals were confirmed diabetic (i.e, 90 days after STZ injection). A group of citrate control rats were also maintained which has received citrate buffer on the 2nd day of their birth. There was a significant increase in blood glucose, glycosylated hemoglobin (HbA1c) and serum insulin levels were observed in NIDDM control rats. Treatment with RC reduced the elevated levels of blood glucose, HbA1c and insulin in the NIDDM rats. An oral glucose tolerance test (OGTT) was also performed in the same groups, in which we found a significant improvement in glucose tolerance in the rats treated with RC. The insulin sensitivity was assessed for both peripheral insulin resistance and hepatic insulin resistance. RC treatment significantly improved insulin sensitivity index (K(ITT)) which was significantly decreased in NIDDM control rats. There was significant rise in homeostasis model assessment of insulin resistance (HOMA-R) in NIDDM control rats whereas RC treatment significantly prevented the rise in HOMA-R in NIDDM treated rats. Our data suggest that methanolic extract of RC significantly delayed the onset of hyperinsulinemia and glucose intolerance and improved insulin sensitivity in NIDDM rats. PMID:24147364

  4. Cytotoxicity and antiangiogenic effects of Rhus coriaria, Pistacia vera and Pistacia khinjuk oleoresin methanol extracts.

    PubMed

    Mirian, M; Behrooeian, M; Ghanadian, M; Dana, N; Sadeghi-Aliabadi, H

    2015-01-01

    Angiogenesis, formation of new blood vessels, play an important role in some diseases such as cancer and its metastasis. Using angiogenesis inhibitors, therefore, is one of the ways for cancer treatment and prevention of metastasis. Medicinal plants have been shown to play a major role in the treatment of a variety of cancers. In this direction, cytotoxic and angiogenic effects of oleo gum resin extracts of Rhus coriaria, Pistacia vera and Pistacia khinjuk from Anacardiaceae family were studied. For IC50 values, cytotoxic effects of the plant extracts were evaluated at different concentrations (1, 10, 20, 40, 80,100 μg/ml) against human umbilical vein endothelial normal cell (HUVEC) and Y79 cell lines using 3-(4, 5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay. In vitro tube formation on matrigel base was used to evaluate angiogenic effects in the presence of increasing concentrations (50, 100, 250 μg/ml) of the extracts. Vascular endothelium growth factor was used as angiogenesis stimulator. Gas chromatography results showed that α-pinene and β-pinene were the major essential oils constituents of all plant extracts. According to the MTT assay results, the R. coriaria resin extract was more cytotoxic than those of P. vera and P. khinjuk extracts (IC50, 9.1 ± 1.6 vs 9.8 ± 2.1 and 12.0 ± 1.9, respectively; P<0.05). Cytotoxic effects of all extracts against Y79 cell line was significantly higher than those of HUVEC used as a normal cell line (P<0.05). Tube formation assay also showed that extract of R. coriaria resin inhibited angiogenesis more significantly than other tested extracts (P<0.05). It could be concluded that R. coriaria resin extract possess cytotoxic effect and antiangiogenesis against cancer cells and as an anticancer natural product has a good potential for future studies. PMID:26600850

  5. Cytotoxicity and antiangiogenic effects of Rhus coriaria, Pistacia vera and Pistacia khinjuk oleoresin methanol extracts

    PubMed Central

    Mirian, M.; Behrooeian, M.; Ghanadian, M.; Dana, N.; Sadeghi-Aliabadi, H.

    2015-01-01

    Angiogenesis, formation of new blood vessels, play an important role in some diseases such as cancer and its metastasis. Using angiogenesis inhibitors, therefore, is one of the ways for cancer treatment and prevention of metastasis. Medicinal plants have been shown to play a major role in the treatment of a variety of cancers. In this direction, cytotoxic and angiogenic effects of oleo gum resin extracts of Rhus coriaria, Pistacia vera and Pistacia khinjuk from Anacardiaceae family were studied. For IC50 values, cytotoxic effects of the plant extracts were evaluated at different concentrations (1, 10, 20, 40, 80,100 μg/ml) against human umbilical vein endothelial normal cell (HUVEC) and Y79 cell lines using 3-(4, 5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay. In vitro tube formation on matrigel base was used to evaluate angiogenic effects in the presence of increasing concentrations (50, 100, 250 μg/ml) of the extracts. Vascular endothelium growth factor was used as angiogenesis stimulator. Gas chromatography results showed that α-pinene and β-pinene were the major essential oils constituents of all plant extracts. According to the MTT assay results, the R. coriaria resin extract was more cytotoxic than those of P. vera and P. khinjuk extracts (IC50, 9.1 ± 1.6 vs 9.8 ± 2.1 and 12.0 ± 1.9, respectively; P<0.05). Cytotoxic effects of all extracts against Y79 cell line was significantly higher than those of HUVEC used as a normal cell line (P<0.05). Tube formation assay also showed that extract of R. coriaria resin inhibited angiogenesis more significantly than other tested extracts (P<0.05). It could be concluded that R. coriaria resin extract possess cytotoxic effect and antiangiogenesis against cancer cells and as an anticancer natural product has a good potential for future studies. PMID:26600850

  6. Mechanisms for tolerating freeze-thaw stress of two evergreen chaparral species: Rhus ovata and Malosma laurina (Anacardiaceae).

    PubMed

    Pratt, R B; Ewers, F W; Lawson, M C; Jacobsen, A L; Brediger, M M; Davis, S D

    2005-07-01

    The response to freeze-thaw stress was examined for two co-occurring evergreen species, Malosma laurina and Rhus ovata. Laboratory and field experiments on adults and seedlings were made in the spring and winter in 1996 and again on adults in 2003 and 2004. Laboratory and field results indicated that the stem xylem for adults of M. laurina and R. ovata were similarly susceptible to freezing-induced cavitation (percentage loss of conductivity = 92 ± 2.6% for R. ovata and 90 ± 4.2% for M. laurina at ≤ -6°C). In contrast, leaves of M. laurina were more susceptible to freezing injury than leaves of R. ovata. Among seedlings in the field, leaves of M. laurina exhibited freezing injury at -4°C and total shoot mortality at -7.2°C, whereas co-occurring seedlings of R. ovata were uninjured. Surprisingly, R. ovata tolerates high levels of freezing-induced xylem embolism in the field, an apparently rare condition among evergreen plants. Rhus ovata avoids desiccation when xylem embolism is high by exhibiting low minimum leaf conductance compared to M. laurina. These results suggest a link between minimum leaf conductance and stem hydraulics as a mechanism permitting the persistence of an evergreen leaf habit in freezing environments. PMID:21646132

  7. Ecophysiological evaluation of the potential invasiveness of Rhus typhina in its non-native habitats.

    PubMed

    Zhang, Zhanjiang; Jiang, Chuangdao; Zhang, Jinzheng; Zhang, Huijin; Shi, Lei

    2009-11-01

    Rhus typhina L. (staghorn sumac) is a clonal woody species that is considered potentially invasive in its non-native habitats. It is slow growing as seedlings, but grows fast once established. Its growth in the early stages is limited by many abiotic factors, including light intensity. To evaluate its potential of becoming invasive in areas it has been introduced into, we conducted a field experiment to investigate the effects of light intensity on the physiology and growth of R. typhina. Two-month-old R. typhina seedlings were examined under five light levels, that is, 100% full sunlight (unlimited light), moderate stress (50% or 25% of full sunlight) and severe stress (10% or 5% of full sunlight), for 60 days in Hunshandak Sandland, China. Net photosynthetic rate (PN) was reduced significantly under severe light stress, but PN of the moderately stressed seedlings was unaffected. Light stress also led to a reduction in saturated light intensity of the moderately stressed seedlings by 20% and of the severely stressed seedlings by 40%, although the light saturation points were as high as 800 and 600 micromol m(-2) s(-1) for the moderately and severely stressed seedlings, respectively. Under severe light stress, the maximum quantum yield of Photosystem II (Fv/Fm) decreased significantly, but the minimal fluorescence yield (F0) increased compared to that of the control plants. The number of newly produced leaves and the stem height, however, decreased as the light intensity became lower. Root length and leaf area decreased, whereas specific leaf area significantly increased as light became increasingly lower. Biomass production was significantly reduced by light stress, but the allocation pattern was unaffected. Our results demonstrated that R. typhina seedlings can survive low light and grow well in other light conditions. The physiology and growth of R. typhina will likely enable it to acclimate to varying light conditions in Hunshandak Sandland, where R. typhina has been widely cultivated for sand stabilization and other purposes. Because of its ability to tolerate low light and to compete aggressively for light resource once established, that is, becoming invasive, we urge caution when it comes to introducing R. typhina into its non-native habitats, despite its many ecological benefits. PMID:19734548

  8. Randomized controlled trial of a water-soluble nail lacquer based on hydroxypropyl-chitosan (HPCH), in the management of nail psoriasis

    PubMed Central

    Cantoresi, Franca; Caserini, Maurizio; Bidoli, Antonella; Maggio, Francesca; Marino, Raffaella; Carnevale, Claudia; Sorgi, Paola; Palmieri, Renata

    2014-01-01

    Background Nail psoriasis occurs in up to 50% of patients affected by psoriasis, with a significant impact on quality of life that leads to a real clinical need for new therapeutic options. Aim To confirm whether the strengthening and hardening properties of the hydroxypropyl-chitosan (HPCH) nail lacquer could improve the structure of the nail plates on psoriatic nails. Materials and methods A randomized, double-blind, placebo controlled, parallel-group trial was carried out to evaluate the efficacy and tolerability of a hydrosoluble nail lacquer containing HPCH, Equisetum arvense, and methylsulfonylmethane on nail psoriasis. The test product or a placebo was applied once daily for 24 weeks to all fingernails. Efficacy assessments were performed on the target fingernail by means of the modified Nail Psoriasis Severity Index score. A cut-off score of 4 was considered to define the clinical cure rate (ie, Cure ?4, Failure >4). Results After 24 weeks, the clinical cure rate showed the statistically significant superiority of the HPCH nail lacquer compared to placebo in both the intention-to-treat (Fishers exact test, P=0.0445) and the per protocol population (Fishers exact test, P=0.0437). This superiority was already present after 16 weeks of treatment. Moreover, the analysis of the modified Nail Psoriasis Severity Index-50 showed a statistically significant clinical improvement after 12 weeks of treatment in comparison to the results obtained after 8 weeks (Fishers exact test, P<0.05). Conclusion The trial showed that HPCH nail lacquer could be a new, valid, effective, and safe option for decreasing the signs of nail dystrophy in psoriatic patients. PMID:24904219

  9. A Liquid Chromatography-Tandem Mass Spectrometry Method for Simultaneous Quantitation of 10 Bioactive Components in Rhus verniciflua Extracts.

    PubMed

    Jin, Ming Ji; Kim, In Sook; Rehman, Shaheed Ur; Dong, Mi-Sook; Na, Chun-Soo; Yoo, Hye Hyun

    2016-03-01

    The purpose of this study was to develop a simultaneous method to quantify 10 bioactive compounds in Rhus verniciflua extracts using high-performance liquid chromatography-tandem mass spectrometry. The chromatographic separation was performed using a C18 column under gradient elution with 0.1% formic acid and acetonitrile as the mobile phase solvents. The analytes were detected in the negative-ion mode using multiple-reaction monitoring detection with an electrospray ionization interface. The calibration curves for all the analytes showed good linearity (r(2) >0.997) over the concentration range of 1-1,000 ng/mL. The recovery values were within 89.53-110.14%, and the intra- and interday coefficients of variation were <4.86% for all the tested compounds. The developed method was successfully applied to a quality assessment of the R. verniciflua extract samples. PMID:26499118

  10. EXAFS investigation of the binuclear cupric site in met T2D Rhus laccase and its azide bound derivative.

    PubMed

    Spira, D J; Co, M S; Solomon, E I; Hodgson, K O

    1983-04-29

    EXAFS analysis of met T2D Rhus laccase and its azide bound derivative indicates an average of 0.33 S at 2.09 A and 3-4 N (or O) atoms at 2.00 A per copper atom for the three copper centers. Using the plastocyanin Cu(II) EXAFS spectrum to model the type 1 site in laccase, a difference EXAFS spectrum for the type 3 site is generated; this spectrum enables assignment of the one S ligand in met T2D to the type 1 site and indicates no evidence of a detectable copper scatterer for the coupled binuclear copper site. Implications regarding type 3 optical features and related studies on the hemocyanins are also discussed. PMID:6221725

  11. Matrix effect on leaching of Bisphenol A diglycidyl ether (BADGE) from epoxy resin based inner lacquer of aluminium tubes into semi-solid dosage forms.

    PubMed

    Lipke, Uwe; Haverkamp, Jan Boris; Zapf, Thomas; Lipperheide, Cornelia

    2016-04-01

    To study the impact of different semi-solid dosage form components on the leaching of Bisphenol A (BPA) and Bisphenol A diglycidyl ether (BADGE) from the epoxy resin-based inner lacquer of aluminium tubes, the tubes were filled with different matrix preparations and stored at an elevated temperature. Despite compliance with the European Standards EN 15348 and EN 15766 on porosity and polymerisation of internal coatings of aluminium tubes, the commercially available tubes used in the study contained an increased amount of polymerisation residues, such as unbound BPA, BADGE and BADGE derivatives in the lacquer, as determined by acetonitrile extraction. Storage of Macrogol ointments in these tubes resulted in an almost quantitative migration of the unbound polymerisation residues from the coating into the ointment. In addition, due to alterations observed in the RP-HPLC chromatograms of the matrix spiked with BADGE and BADGE derivatives it is supposed that the leachates can react with formulation components. The contamination of the medicinal product by BPA, BADGE and BADGE derivatives can be precluded by using aluminium tubes with an internal lacquer with a low degree of unbound polymerisation residues. PMID:26724272

  12. Thermogelling hydrogels of cyclodextrin/poloxamer polypseudorotaxanes as aqueous-based nail lacquers: application to the delivery of triamcinolone acetonide and ciclopirox olamine.

    PubMed

    Nogueiras-Nieto, Luis; Begoña Delgado-Charro, M; Otero-Espinar, Francisco J

    2013-04-01

    This work investigated the use of in situ gelling hydrogels based on polypseudorotaxanes of Pluronic F-127 and partially methylated β-cyclodextrin as aqueous nail lacquers. N-acetylcysteine and urea were incorporated as penetration enhancers. The formulations were tested for their ability to deliver ciclopirox and triamcinolone across human nail plate and bovine hoof. Simple aqueous solutions of the drugs with N-acetylcysteine provided measurable fluxes across hoof membranes but became quickly depleted of drug. Further, these solutions would have a short residence time upon nail application. Addition of Pluronic F-127 facilitated drug solubilization and provided the formulations with in situ gelling properties but drug entrapment into the micelles slowed down the delivery process. This was solved by addition of methylated β-cyclodextrin; the formulations retained the thermogelling properties, drug solubilization was further increased, and drug delivery was accelerated. The polymer chains compete with the drugs for the cyclodextrin cavity forming polypseudorotaxanes, which facilitated drug release. The permeability of both drugs was higher across bovine hoof than human nail. The new polypseudorotaxanes formulation delivered more ciclopirox across human nail than a marketed organic lacquer which supports the growing hypothesis that aqueous-based nail lacquers represent a superior formulation strategy in nail topical delivery. PMID:23201053

  13. Anti-herpes simplex virus activity of moronic acid purified from Rhus javanica in vitro and in vivo.

    PubMed

    Kurokawa, M; Basnet, P; Ohsugi, M; Hozumi, T; Kadota, S; Namba, T; Kawana, T; Shiraki, K

    1999-04-01

    Rhus javanica, a medicinal herb, has been shown to exhibit oral therapeutic anti-herpes simplex virus (HSV) activity in mice. We purified two major anti-HSV compounds, moronic acid and betulonic acid, from the herbal extract by extraction with ethyl acetate at pH 10 followed by chromatographic separations and examined their anti-HSV activity in vitro and in vivo. Moronic acid was quantitatively a major anti-HSV compound in the ethyl acetate-soluble fraction. The effective concentrations for 50% plaque reduction of moronic acid and betulonic acid for wild-type HSV type 1 (HSV-1) were 3.9 and 2.6 microgram/ml, respectively. The therapeutic index of moronic acid (10.3-16.3) was larger than that of betulonic acid (6.2). Susceptibility of acyclovir-phosphonoacetic acid-resistant HSV-1, thymidine kinase-deficient HSV-1, and wild-type HSV type 2 to moronic acid was similar to that of the wild-type HSV-1. When this compound was administered orally to mice infected cutaneously with HSV-1 three times daily, it significantly retarded the development of skin lesions and/or prolonged the mean survival times of infected mice without toxicity compared with the control. Moronic acid suppressed virus yields in the brain more efficiently than those in the skin. This was consistent with the prolongation of mean survival times. Thus, moronic acid was purified as a major anti-HSV compound from the herbal extract of Rhus javanica. Mode of the anti-HSV activity was different from that of ACV. Moronic acid showed oral therapeutic efficacy in HSV-infected mice and possessed novel anti-HSV activity that was consistent with that of the extract. PMID:10086989

  14. Clinical Effects of Rhus coriaria Fruits on Dyslipidemia in Adolescents: a Triple-blinded Randomized Placebo-controlled Trial

    PubMed Central

    Sabzghabaee, Ali Mohammad; Kelishadi, Roya; Golshiri, Keivan; Ghannadi, Alireza; Badri, Shirinsadat

    2014-01-01

    ABSTRACT Objective: Children and adolescents are considered as the best target groups for preventing and controlling the cardiovascular diseases risk factors and reducing mortality in adulthood. Alternative medicine and herbal drugs have been taken into account for managing dyslipidemia in this population. The beneficial effects of Sumac (Rhus coriaria L.) on lipid profile have been confirmed in some laboratory and animal studies. This study was designed to investigate the clinical effects of sumac fruits on dyslipidemia in 12-18 years-old adolescents. Methods: This randomized triple-blinded clinical trial was conducted on 72 obese adolescents with dyslipidemia from August 2011 to June 2012 in Isfahan Cardiovascular Research Center, Isfahan, Iran. Eligible adolescents were randomly assigned to two case and control groups. The control group received placebo capsules and the case group received capsules containing 500 mg of powdered sumac fruits, each three times a day for one month. Biochemical parameters including 12-hrs fasting serum levels of total cholesterol (Total-C), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglycerides (TG) were measured before the initiation and after the completion of the study protocol. Statistical analysis was performed using the SPSS software, version 16.0, using Independent Samples T-test, or Paired Samples T-test, for between-group and within-group analysis, respectively. Findings: The plasma levels of Total-C, LDL-C, and TG changed significantly over-time in the case group. Furthermore, between-group analysis showed a statistically significant difference between case and control groups with this regard (P < 0.05, for all statistical comparisons). However, HDL-C levels have not been changed significantly over-time within the case or control group, neither between the two study groups. Conclusion: In this study, the considerable effects of Rhus coriaria (sumac) on reducing serum levels of Total-C, LDL-C, and TG have been noticed during one-month trial. However, probably due to the concise period of sumac consumption, its effect on HDL-C was not statistically significant. PMID:25568560

  15. [A chromatographic method of determining the levels of organic solvents in the air, the components of the offset lacquer LO-2].

    PubMed

    Dobecki, M; Czerczak, S

    1987-01-01

    A gas chromatographic method was worked out to determine the mixture of ethyl acetate, toluene, buthyl acetate, p,m-xylene, o-xylene and ethyl ethylene glycol vapours. These solvents are used as some components of offset lacquer LO-2. Optimum separation conditions were achieved on 3-metre SS column filled with 10% FFAP on Chormosorb W AW DMCS 80-100 mesh. Air samples were collected on activated charcoal placed in glass tubes. The components tested were desorbed from the sorbent material by 10% acetone solution in CS2. The method enables to determine the concentrations of each compound, corresponding to one fifth of their TLVs. PMID:3444421

  16. Inhibitory effects of polyphenols isolated from Rhus verniciflua on Aldo-keto reductase family 1 B10.

    PubMed

    Song, Dae-Geun; Lee, Joo Young; Lee, Eun Ha; Jung, Sang Hoon; Nho, Chu Won; Cha, Kwang Hyun; Koo, Song Yi; Pan, Cheol-Ho

    2010-04-01

    Aldo-keto reductase family 1 B10 (AKR1B10) is a member of the NADPH-dependent aldo-keto reductase (AKR) superfamily, and has been considered to be a potential cancer therapeutic target. Total extract from the bark of Rhus verniciflua (Toxicodendron vernicifluum (Stokes)) showed AKR1B10 inhibitory activity. To identify the active compounds from R. verniciflua responsible for AKR1B10 inhibition, nine compounds were isolated via bioactivity-guided isolation and tested for their effects against recombinant human AKR1B10 (rhAKR1B10). Results showed that butein, isolated from the ethyl acetate fraction, was most able to inhibit rhAKR1B10. The inhibitory rate of butein against rhAKR1B10 was 42.86% at 1 microM with an IC(50) value of 1.47 microM, and enzyme kinetic analysis revealed its inhibition mode to be uncompetitive. PMID:20423612

  17. Anaerobic reactions of Rhus vernicifera laccase and its type-2 copper-depleted derivatives with hexacyanoferrate(II).

    PubMed

    Sakurai, T

    1992-06-15

    Anaerobic reactions of Rhus vernicifera laccase and its type-2 copper-depleted derivatives with hexacyanoferrate(II) were investigated by absorption and e.s.r. spectroscopy. When native laccase was treated with excess hexacyanoferrate(II), the type-1 and type-2 coppers were immediately reduced and the e.s.r. signal due to type-3 copper was transiently observed. After incubation, a novel e.s.r. signal (g parallel = 2.31, g perpendicular = 2.08) developed together with the type-1 copper signal. Only the novel e.s.r. signal was left after the sample had been treated with ascorbate. In the corresponding absorption spectrum, a new band was observed at around 490 nm. A similar new e.s.r. signal did not appear for the type-2-copper-depleted (T2D) laccase, in which the type-3 copper had been reduced during the procedure to deplete the type-2 copper. On the other hand, the novel e.s.r. signal emerged when the type-3 copper in T2D laccase had been previously reoxidized with H2O2. The novel e.s.r. signal was not significantly saturated even by 200 mV microwave power at 4 K. Quantitative estimations and a small molecule study for CuII-FeII(CN)6 and CuII-FeIII(CN)6 systems suggested that the novel e.s.r. signal corresponds to some sort of adduct involving the type-3 copper and hexacyanoferrate(II). PMID:1320374

  18. Anaerobic reactions of Rhus vernicifera laccase and its type-2 copper-depleted derivatives with hexacyanoferrate(II).

    PubMed Central

    Sakurai, T

    1992-01-01

    Anaerobic reactions of Rhus vernicifera laccase and its type-2 copper-depleted derivatives with hexacyanoferrate(II) were investigated by absorption and e.s.r. spectroscopy. When native laccase was treated with excess hexacyanoferrate(II), the type-1 and type-2 coppers were immediately reduced and the e.s.r. signal due to type-3 copper was transiently observed. After incubation, a novel e.s.r. signal (g parallel = 2.31, g perpendicular = 2.08) developed together with the type-1 copper signal. Only the novel e.s.r. signal was left after the sample had been treated with ascorbate. In the corresponding absorption spectrum, a new band was observed at around 490 nm. A similar new e.s.r. signal did not appear for the type-2-copper-depleted (T2D) laccase, in which the type-3 copper had been reduced during the procedure to deplete the type-2 copper. On the other hand, the novel e.s.r. signal emerged when the type-3 copper in T2D laccase had been previously reoxidized with H2O2. The novel e.s.r. signal was not significantly saturated even by 200 mV microwave power at 4 K. Quantitative estimations and a small molecule study for CuII-FeII(CN)6 and CuII-FeIII(CN)6 systems suggested that the novel e.s.r. signal corresponds to some sort of adduct involving the type-3 copper and hexacyanoferrate(II). PMID:1320374

  19. Efficacy of Injections with Disci/Rhus Toxicodendron Compositum for Chronic Low Back Pain A Randomized Placebo-Controlled Trial

    PubMed Central

    Pach, Daniel; Brinkhaus, Benno; Roll, Stephanie; Wegscheider, Karl; Icke, Katja; Willich, Stefan N.; Witt, Claudia M.

    2011-01-01

    Background The effectiveness of injection therapy for low-back pain is still debatable. We compared the efficacy of local injections of the homeopathic preparation Disci/Rhus toxicodendron compositum (verum) with placebo injections and with no treatment in patients with chronic low back pain. Methodology/Principal Findings In a randomized controlled partly double blind multicenter trial patients with chronic low back pain from 9 German outpatient clinics were enrolled and randomly allocated in a 1?1?1 ratio to receive subcutaneous injections (verum or placebo) into painful sites on the lower back over 12 treatment sessions within eight weeks, or no treatment (rescue pain medication with paracetamol or NSAIDs). All trial personnel and participants were masked to treatment allocation. The primary outcome measure was the average pain intensity over the last seven days on a visual analogue scale (0100 mm, 0?=?no pain, 100?=?worst imaginable pain) after eight weeks. Follow-up was 26 weeks. Primary analysis was by intention to treat. Between August 2007 and June 2008, 150 patients were randomly allocated to three groups (51 verum, 48 placebo and 51 no treatment). The mean baseline-adjusted low back pain intensity at week eight was: verum group 37.0 mm (97.5% CI 25.3;48.8), no treatment group 53.0 (41.8;64.2), and placebo group 41.8 (30.1;53.6). The verum was significantly superior to no treatment (P?=?0.001), but not to placebo (P?=?0.350). No significant side effects were reported. Conclusions/Significance The homeopathic preparation was not superior to placebo. Compared to no treatment injections resulted in significant and clinical relevant chronic back pain relief. Trial Registration ClinicalTrials.gov NCT00567736 PMID:22087222

  20. Talking Trees

    ERIC Educational Resources Information Center

    Tolman, Marvin

    2005-01-01

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

  1. Rhus coriaria induces senescence and autophagic cell death in breast cancer cells through a mechanism involving p38 and ERK1/2 activation.

    PubMed

    El Hasasna, Hussain; Athamneh, Khawlah; Al Samri, Halima; Karuvantevida, Noushad; Al Dhaheri, Yusra; Hisaindee, Soleiman; Ramadan, Gaber; Al Tamimi, Nedaa; AbuQamar, Synan; Eid, Ali; Iratni, Rabah

    2015-01-01

    Here, we investigated the anticancer effect of Rhus coriaria on three breast cancer cell lines. We demonstrated that Rhus coriaria ethanolic extract (RCE) inhibits the proliferation of these cell lines in a time- and concentration-dependent manner. RCE induced senescence and cell cycle arrest at G1 phase. These changes were concomitant with upregulation of p21, downregulation of cyclin D1, p27, PCNA, c-myc, phospho-RB and expression of senescence-associated ?-galactosidase activity. No proliferative recovery was detected after RCE removal. Annexin V staining and PARP cleavage analysis revealed a minimal induction of apoptosis in MDA-MB-231 cells. Electron microscopy revealed the presence of autophagic vacuoles in RCE-treated cells. Interestingly, blocking autophagy by 3-methyladenine (3-MA) or chloroquine (CQ) reduced RCE-induced cell death and senescence. RCE was also found to activate p38 and ERK1/2 signaling pathways which coincided with induction of autophagy. Furthermore, we found that while both autophagy inhibitors abolished p38 phosphorylation, only CQ led to significant decrease in pERK1/2. Finally, RCE induced DNA damage and reduced mutant p53, two events that preceded autophagy. Our findings provide strong evidence that R. coriaria possesses strong anti-breast cancer activity through induction of senescence and autophagic cell death, making it a promising alternative or adjunct therapeutic candidate against breast cancer. PMID:26263881

  2. Rhus coriaria induces senescence and autophagic cell death in breast cancer cells through a mechanism involving p38 and ERK1/2 activation

    PubMed Central

    El Hasasna, Hussain; Athamneh, Khawlah; Al Samri, Halima; Karuvantevida, Noushad; Al Dhaheri, Yusra; Hisaindee, Soleiman; Ramadan, Gaber; Al Tamimi, Nedaa; AbuQamar, Synan; Eid, Ali; Iratni, Rabah

    2015-01-01

    Here, we investigated the anticancer effect of Rhus coriaria on three breast cancer cell lines. We demonstrated that Rhus coriaria ethanolic extract (RCE) inhibits the proliferation of these cell lines in a time- and concentration-dependent manner. RCE induced senescence and cell cycle arrest at G1 phase. These changes were concomitant with upregulation of p21, downregulation of cyclin D1, p27, PCNA, c-myc, phospho-RB and expression of senescence-associated β-galactosidase activity. No proliferative recovery was detected after RCE removal. Annexin V staining and PARP cleavage analysis revealed a minimal induction of apoptosis in MDA-MB-231 cells. Electron microscopy revealed the presence of autophagic vacuoles in RCE-treated cells. Interestingly, blocking autophagy by 3-methyladenine (3-MA) or chloroquine (CQ) reduced RCE-induced cell death and senescence. RCE was also found to activate p38 and ERK1/2 signaling pathways which coincided with induction of autophagy. Furthermore, we found that while both autophagy inhibitors abolished p38 phosphorylation, only CQ led to significant decrease in pERK1/2. Finally, RCE induced DNA damage and reduced mutant p53, two events that preceded autophagy. Our findings provide strong evidence that R. coriaria possesses strong anti-breast cancer activity through induction of senescence and autophagic cell death, making it a promising alternative or adjunct therapeutic candidate against breast cancer. PMID:26263881

  3. Keratinocyte intercellular adhesion molecule-1 (ICAM-1) expression precedes dermal T lymphocytic infiltration in allergic contact dermatitis (Rhus dermatitis).

    PubMed Central

    Griffiths, C. E.; Nickoloff, B. J.

    1989-01-01

    The ability of small molecules such as urushiol, present as a wax on the poison ivy leaf surface, to cause allergic contact dermatitis (rhus dermatitis) has fascinated immunologists for decades. Current dogma suggests that these epicutaneously applied catechol-containing molecules serve as haptens to conjugate with larger proteins via reactive o-quinone intermediates. These complexes are then recognized as foreign antigens by the immune system and elicit a hypersensitivity reaction. Phorbol ester can directly induce cultured keratinocyte (KC) intercellular adhesion molecule-1 (ICAM-1) expression via a protein kinase C (PK-C)-dependent mechanism. As urushiol is also a known PK-C agonist, we asked if topical application of a poison ivy/oak mixture could directly induce epidermal KC ICAM-1 expression. During the pre-erythematous phase of this reaction (4 to 20 hours), epidermal KCs expressed ICAM-1; this "initiation phase" preceded the appearance of activated memory T lymphocytes in the papillary dermis, and thus appeared to be nonlymphokine mediated. A near-contiguous cellular-adhesion molecular network was identified by ICAM-1 staining of basal KCs, dermal dendrocytes, and endothelial cells. During the second 24-hour period with the onset of erythema and edema, there was an "amplification phase" of more intense KC ICAM-1 expression coupled with relatively weak KC HLA-DR expression that coincided with dermal and epidermal T-cell infiltration. This suggests the presence of lymphokines, such as gamma interferon, during the amplification phase because of KC HLA-DR expression. On cultured KCs, urushiol directly induced ICAM-1 expression but not HLA-DR. Thus, in addition to functioning as an antigenic hapten, urushiol directly induces KC ICAM-1 expression. The KC ICAM-1 expression may then alter the dynamic trafficking of memory T cells in the epidermis, so as to initiate cutaneous inflammation in a nonantigen specific manner. This initiation phase is followed by T-cell infiltration and consequent lymphokine production that significantly amplifies the original stimulus. Thus much can still be learned about the molecular pathophysiology of this common type of cutaneous inflammation. Images Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 PMID:2574536

  4. Keratinocyte intercellular adhesion molecule-1 (ICAM-1) expression precedes dermal T lymphocytic infiltration in allergic contact dermatitis (Rhus dermatitis).

    PubMed

    Griffiths, C E; Nickoloff, B J

    1989-12-01

    The ability of small molecules such as urushiol, present as a wax on the poison ivy leaf surface, to cause allergic contact dermatitis (rhus dermatitis) has fascinated immunologists for decades. Current dogma suggests that these epicutaneously applied catechol-containing molecules serve as haptens to conjugate with larger proteins via reactive o-quinone intermediates. These complexes are then recognized as foreign antigens by the immune system and elicit a hypersensitivity reaction. Phorbol ester can directly induce cultured keratinocyte (KC) intercellular adhesion molecule-1 (ICAM-1) expression via a protein kinase C (PK-C)-dependent mechanism. As urushiol is also a known PK-C agonist, we asked if topical application of a poison ivy/oak mixture could directly induce epidermal KC ICAM-1 expression. During the pre-erythematous phase of this reaction (4 to 20 hours), epidermal KCs expressed ICAM-1; this "initiation phase" preceded the appearance of activated memory T lymphocytes in the papillary dermis, and thus appeared to be nonlymphokine mediated. A near-contiguous cellular-adhesion molecular network was identified by ICAM-1 staining of basal KCs, dermal dendrocytes, and endothelial cells. During the second 24-hour period with the onset of erythema and edema, there was an "amplification phase" of more intense KC ICAM-1 expression coupled with relatively weak KC HLA-DR expression that coincided with dermal and epidermal T-cell infiltration. This suggests the presence of lymphokines, such as gamma interferon, during the amplification phase because of KC HLA-DR expression. On cultured KCs, urushiol directly induced ICAM-1 expression but not HLA-DR. Thus, in addition to functioning as an antigenic hapten, urushiol directly induces KC ICAM-1 expression. The KC ICAM-1 expression may then alter the dynamic trafficking of memory T cells in the epidermis, so as to initiate cutaneous inflammation in a nonantigen specific manner. This initiation phase is followed by T-cell infiltration and consequent lymphokine production that significantly amplifies the original stimulus. Thus much can still be learned about the molecular pathophysiology of this common type of cutaneous inflammation. PMID:2574536

  5. On the spectral features associated with peroxide reactivity of the coupled binuclear copper active site in type 2 depleted and native Rhus laccase.

    PubMed

    Penner-Hahn, J E; Hedman, B; Hodgson, K O; Spira, D J; Solomon, E I

    1984-03-15

    We report herein an X-ray absorption spectroscopic (XAS) determination of the oxidation state of the copper sites in T2D and native Rhus laccase. The increase in intensity of the 330 nm absorption feature which results from peroxide titration of T2D laccase (T3: [Cu(I)Cu(I)], T1: [Cu(II)]) is found to correlate linearly with the percent of oxidation of the binuclear copper site (determined by XAS analysis). This indicates that peroxide oxidizes but does not bind to the T3 site. We have used this correlation to determine that native laccase, as isolated, contains approximately 25% reduced T3 sites and that all spectral changes observed upon peroxide addition to native laccase can be accounted for by oxidation of these reduced sites. The importance of this result to previous reports of peroxide binding at the laccase active site is discussed. PMID:6231927

  6. 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;

  7. Test tree

    SciTech Connect

    Schwendemann, K. L.

    1985-01-22

    A subsurface test tree so compact in its vertical dimension that the entire tree can be positioned below the blind rams in a blowout preventer stack. When the stinger is removed the remaining valve section of the tree will be below the blind rams in any conventional blowout preventer stack. The valve operators are split, one carried by the stinger and one carried in the valve housing with the arrangement of operator and valve in the housing providing an extremely small vertical dimension. A dome charge is effective on a piston to drive a ball valve to closed position to cut a line extending through the ball valve and to provide sequential operation between the ball valve on bottom and the valve thereabove which may be a flapper valve so that the lower valve closes and the line is cut before the upper valve closes. In one form the invention includes a subsurface safety valve below the test tree operated by one of control or balance pressure fluid.

  8. Rhus (Toxicodendron) dermatitis.

    PubMed

    Tanner, T L

    2000-06-01

    This article reviews the current fund of knowledge on poison ivy, poison oak, and poison sumac dermatitis. It is intended as a global summary to provide the primary care provider with the required information and sources for more esoteric academic pursuits. Toxicodendron characteristics, morphology, and biology are reviewed. The overall medical impact is delineated as well as the clinical manifestations, pathophysiology, prevention, and treatment. Historical perspectives are mentioned throughout, as are future trends in research. PMID:10815057

  9. Tea tree oil

    MedlinePLUS

    Tea tree oil is derived from the leaves of the tea tree. The tea tree was named by eighteenth century sailors, ... to make black and green teas. Tea tree oil is applied to the skin (used topically) for ...

  10. 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

  11. 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)

  12. 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…

  13. Fisetin-Rich Extracts of Rhus verniciflua Stokes Improve Blood Flow Rates in Mice Fed Both Normal and High-Fat Diets.

    PubMed

    Im, Won Kyun; Park, Hyun Jung; Lee, Kwang Soo; Lee, Jung Hoon; Kim, Young Dong; Kim, Kyeong-Hee; Park, Sang-Jae; Hong, Seokmann; Jeon, Sung Ho

    2016-02-01

    Although it has been previously reported that Rhus verniciflua Stokes (RVS) possesses in vitro anti-inflammatory activity, the precise in vivo mechanisms of RVS extracts and a main active component called fisetin have not been well elucidated. In this study, using newly developed protocols, we prepared urushiol-free but fisetin-enriched RVS extracts and investigated their effects on the vascular immune system. We found that the water-soluble fractions of detoxified RVS with the flavonoid fisetin can inhibit lipopolysaccharide-induced production of nitric oxide (NO) and prostaglandin E2 (PGE2). Furthermore, RVS can reduce inducible nitric oxide synthase and COX2 gene expression levels, which are responsible for NO and PGE2 production, respectively, in RAW264.7 macrophage cells. Because inflammation is linked to the activation of the coagulation system, we hypothesized that RVS and its active component fisetin possess anticoagulatory activities. As expected, we found that both RVS and fisetin could inhibit the coagulation of human peripheral blood cells. Moreover, in vivo RVS treatment could return the retarded blood flow elicited by a high-fat diet (HFD) back to the normal level in mice. In addition, RVS treatment has significantly reduced body weight gained by HFD in mice. Taken together, the fisetin-rich RVS extracts have potential antiplatelet and antiobesity activities and could be used as a functional food ingredient to improve blood circulation. PMID:26741654

  14. Protective effect of detoxified Rhus verniciflua stokes on human keratinocytes and dermal fibroblasts against oxidative stress and identification of the bioactive phenolics.

    PubMed

    Liu, Chun-Shan; Nam, Tae-Gyu; Han, Min-Woo; Ahn, Soo-mi; Choi, Han Seok; Kim, Tae Young; Chun, Ock K; Koo, Sung I; Kim, Dae-Ok

    2013-01-01

    Oxidative stress due to the over-production of reactive oxygen species (ROS) is associated with human skin aging. This study was designed to identify the bioactive phenolics in detoxified Rhus verniciflua Stokes (DRVS) that may protect human skin against oxidative stress. Under oxidative stress caused by H?O?, the 40% (v/v) aqueous methanol extract of DRVS protected human keratinocytes in a dose-dependent manner. The expression of matrix metalloproteinase-1 (MMP-1) was also inhibited by the DRVS extract in human dermal fibroblasts-neonatal cells exposed to ultraviolet A. The major bioactive phenolics of DRVS were tentatively identified by LC/Q-TOF-ESI-MS/MS, and included gallic acid, 2-(ethoxymethoxy)-3-hydroxyphenol, fustin, a fustin isomer, tetragalloyl glucose, pentagalloyl glucose, fisetin, sulfuretin, a sulfuretin isomer, and butein. The results suggest that a DRVS extract may be effective in slowing skin aging through its antioxidative properties and by down-regulating MMP-1 expression. Further studies are needed to examine whether this effect would be mediated by the phenolics identified in this study. PMID:23924730

  15. pH and microwave power effects on the electron spin resonance spectra of Rhus vernicifera laccase and Cucumis sativus ascorbate oxidase.

    PubMed

    Sakurai, T; Suzuki, S; Chikira, M

    1990-01-01

    The present study shows that the electron spin resonance (ESR) spectral features of Rhus laccase depend considerably on the pH value of the enzyme solution and the irradiated microwave power. Because of the local protein structure change, the type 1 copper is appreciably autoreduced at alkaline pH as monitored both by the ESR and absorption spectroscopies. In addition, the ESR signal of the type 2 copper, especially its g perpendicular region, becomes prominent at alkaline pH. Protein dissociation from a water or an imidazole group coordinated to the type 2 copper is supposed to be responsible for this behavior. Besides above pH effects, the g perpendicular component of the type 2 copper ESR signal is obscured with rising microwave power level. The power saturation behavior of native laccase and its derivatives reveals that the type 2 copper is more easily saturated than the type 1 copper. Cucumis ascorbate oxidase also exhibits similar behavior upon pH variation and microwave power saturation. PMID:2158983

  16. Observation of Cu-N3- stretching and N3- asymmetric stretching bands for mono-azide adduct of Rhus vernicifera laccase.

    PubMed

    Hirota, S; Matsumoto, H; Huang, H W; Sakurai, T; Kitagawa, T; Yamauchi, O

    1998-02-13

    Mono-azide adduct of Rhus vernicifera laccase, a multicopper oxidase containing one type-1 (blue) copper, one type-2 (non-blue normal) copper, and a pair of type-3 (binuclear and EPR silent) coppers, of which type-2 and type-3 coppers constitute a trinuclear site, was investigated with resonance Raman (RR) and Fourier transform infrared (FT-IR) spectroscopies as a step toward elucidation of the structure and function of the trinuclear site. The Cu-N3- stretching (vCu-N3-) RR band was observed for azide-bound multicopper oxidases for the first time. The vCu-N3- band was located at 400 cm-1 for mono-14N3- laccase, which shifted to 396 cm-1 with the 15N14N14N3- analog. The N3- asymmetric stretching (v(N3-)asym) band was observed by FT-IR spectroscopy at 2035 cm-1 for mono-14N3- laccase and at 2025 cm-1 for the 15N14N14N3- analog. The vCu-N3- and v(N3-)asym frequencies and their 15N14N14N- isotope shifts for azido laccase correspond well with those of metazido hemocyanin, indicating that both derivatives should have a similar binding geometry of azide. PMID:9480826

  17. Spectroscopic and kinetic studies on the oxygen-centered radical formed during the four-electron reduction process of dioxygen by Rhus vernicifera laccase.

    PubMed

    Huang, H; Zoppellaro, G; Sakurai, T

    1999-11-12

    The oxygen-centered radical bound to the trinuclear copper center was detected as an intermediate during the reoxidation process of the reduced Rhus vernicifera laccase with dioxygen and characterized by using absorption, stopped-flow, and electron paramagnetic resonance (EPR) spectroscopies and by super conducting quantum interface devices measurement. The intermediate bands appeared at 370 nm (epsilon approximately 1000), 420 nm (sh), and 670 nm (weak) within 15 ms, and were observable for approximately 2 min at pH 7.4 but for less than 5 s at pH 4.2. The first-order rate constant for the decay of the intermediate has been determined by stopped-flow spectroscopy, showing the isotope effect, k(H)/k(D) of 1.4 in D(2)O. The intermediate was found to decay mainly from the protonated form by analyzing pH dependences. The enthalpy and entropy of activation suggested that a considerable structure change takes place around the active site during the decay of the intermediate. The EPR spectra at cryogenic temperatures (<27 K) showed two broad signals with g approximately 1.8 and 1.6 depending on pH. We propose an oxygen-centered radical in magnetic interaction with the oxidized type III copper ions as the structure of the three-electron reduced form of dioxygen. PMID:10551829

  18. Glycoprotein isolated from Rhus verniciflua Stokes inhibits inflammation-related protein and nitric oxide production in LPS-stimulated RAW 264.7 cells.

    PubMed

    Oh, Phil-Sun; Lee, Sei-Jung; Lim, Kye-Taek

    2007-01-01

    Rhus verniciflua Stokes (RVS) has traditionally been used for medical purpose, such as healing of inflammatory diseases in South Korea. Glycoprotein (36 kDa) was isolated from RVS fruit, purified and used to evaluate the inhibitory effect on inflammatory-related proteins and nitric oxide (NO) production in lipopolysaccharide (LPS, 200 ng/ml)-stimulated RAW 264.7 (murine macrophage cell line). Our results were showed that RVS glycoprotein has a strong antioxidative activity against lipid peroxyl radicals in cell-free system, and inhibits NO production in LPS-stimulated RAW 264.7 cells. To elucidate the inhibitory effect of RVS glycoprotein on activities of inflammatory-related proteins, we firstly evaluated the amount of intracellular reactive oxygen species (ROS), and expression of intracellular protein kinase C (PKC), nuclear factor (NF)-kappaB, and activator protein-1 (AP-1). The results in the present study showed that RVS glycoprotein (200 microg/ml) inhibits ROS production and PKCalpha translocation, and down-regulates the expression of NF-kappaB and AP-1. Such upstream signals consequently inhibited the levels of inducible NO synthase (iNOS) and cyclooxygenase (COX)-2 expression. Therefore, we speculate that RVS glycoprotein inhibits the inflammatory-related protein and can act as an anti-inflammatory agent. PMID:17202669

  19. Heartwood extract of Rhus verniciflua Stokes and its active constituent fisetin attenuate vasoconstriction through calcium-dependent mechanism in rat aorta.

    PubMed

    Park, Jung-Min; Lee, Jun-Hyeong; Na, Chun-Soo; Lee, Dongho; Lee, Jin-Yong; Satoh, Masahiko; Lee, Moo-Yeol

    2016-03-01

    Rhus verniciflua Stokes (RVS) exert cardiovascular protective activity by promoting blood circulation, but its active ingredients and underlying mechanism have yet to be identified. This study investigated the vascular effects of RVS, focusing on vasoconstriction and smooth muscle Ca(2+) signaling. RVS heartwood extract attenuated contraction of aortic rings induced by the vasoconstrictors serotonin and phenylephrine, and inhibited the Ca(2+) signaling evoked by serotonin in vascular smooth muscle cells. Subsequent activity-guided fractionation identified fisetin as an active constituent exerting a Ca(2+) inhibitory effect. Fisetin could inhibit major Ca(2+) mobilization pathways including extracellular Ca(2+) influx mediated by the L-type voltage-gated Ca(2+) channel, Ca(2+) release from the intracellular store and store-operated Ca(2+) entry. In accordance with Ca(2+) inhibitory effect, fisetin attenuated vasoconstriction by serotonin and phenylephrine. These results suggest that the anticontractile effect, which is presumably mediated by inhibition of Ca(2+) signaling, may contribute to the improvement of blood circulation by RVS. PMID:26539820

  20. Fermented Rhus verniciflua Stokes Extract Exerts an Antihepatic Lipogenic Effect in Oleic-Acid-Induced HepG2 Cells via Upregulation of AMP-Activated Protein Kinase.

    PubMed

    Lee, Myoung-Sun; Kim, Joo-Seok; Cho, Sun-Mi; Lee, Seon Ok; Kim, Sung-Hoon; Lee, Hyo-Jeong

    2015-08-19

    Rhus verniciflua Stokes has been used as a traditional medicine and food supplement in Korea. In the present study, fermented R. verniciflua Stokes extract (FRVE), an allergen-free extract of R. verniciflua Stokes fermented with the yeast Saccharomyces carlsbergensis, was assessed for its lipid-lowering potential in an in vitro non-alcoholic fatty liver disease model. FRVE markedly suppressed lipid accumulation and intracellular triglycerides (TGs) in the presence of oleic acid (OA). Additionally, FRVE decreased both mRNA and protein levels of lipid-synthesis- and cholesterol-metabolism-related factors, such as sterol regulatory element-binding protein-1 (SREBP-1), fatty acid synthase (FAS), glycerol-3-phosphate acyltransferase (GPAT), and 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR), in OA-induced HepG2 cells. Moreover, FRVE activated low-density lipoprotein receptor (LDLR), AMP-activated protein kinase (AMPK), and fatty acid oxidation-related factors peroxisome proliferator activated receptor ? (PPAR?) and carnitine palmitoyltransferase 1 (CPT-1). Further, the AMPK inhibitor compound C suppressed the increased expression of AMPK phosphorylation induced by FRVE. Phenolics and cosanols in FRVE increased the phosphorylation of AMPK and decreased that of SREBP-1. Taken together, our findings suggest that FRVE has antilipogenic potential in non-alcoholic fatty livers via AMPK upregulation. PMID:26176317

  1. Additive Similarity Trees

    ERIC Educational Resources Information Center

    Sattath, Shmuel; Tversky, Amos

    1977-01-01

    Tree representations of similarity data are investigated. Hierarchical clustering is critically examined, and a more general procedure, called the additive tree, is presented. The additive tree representation is then compared to multidimensional scaling. (Author/JKS)

  2. Categorizing ideas about trees: a tree of trees.

    PubMed

    Fisler, Marie; Lecointre, Guillaume

    2013-01-01

    The aim of this study is to explore whether matrices and MP trees used to produce systematic categories of organisms could be useful to produce categories of ideas in history of science. We study the history of the use of trees in systematics to represent the diversity of life from 1766 to 1991. We apply to those ideas a method inspired from coding homologous parts of organisms. We discretize conceptual parts of ideas, writings and drawings about trees contained in 41 main writings; we detect shared parts among authors and code them into a 91-characters matrix and use a tree representation to show who shares what with whom. In other words, we propose a hierarchical representation of the shared ideas about trees among authors: this produces a "tree of trees." Then, we categorize schools of tree-representations. Classical schools like "cladists" and "pheneticists" are recovered but others are not: "gradists" are separated into two blocks, one of them being called here "grade theoreticians." We propose new interesting categories like the "buffonian school," the "metaphoricians," and those using "strictly genealogical classifications." We consider that networks are not useful to represent shared ideas at the present step of the study. A cladogram is made for showing who is sharing what with whom, but also heterobathmy and homoplasy of characters. The present cladogram is not modelling processes of transmission of ideas about trees, and here it is mostly used to test for proximity of ideas of the same age and for categorization. PMID:23950877

  3. Tree Tectonics

    NASA Astrophysics Data System (ADS)

    Vogt, Peter R.

    2004-09-01

    Nature often replicates her processes at different scales of space and time in differing media. Here a tree-trunk cross section I am preparing for a dendrochronological display at the Battle Creek Cypress Swamp Nature Sanctuary (Calvert County, Maryland) dried and cracked in a way that replicates practically all the planform features found along the Mid-Oceanic Ridge (see Figure 1). The left-lateral offset of saw marks, contrasting with the right-lateral ``rift'' offset, even illustrates the distinction between transcurrent (strike-slip) and transform faults, the latter only recognized as a geologic feature, by J. Tuzo Wilson, in 1965. However, wood cracking is but one of many examples of natural processes that replicate one or several elements of lithospheric plate tectonics. Many of these examples occur in everyday venues and thus make great teaching aids, ``teachable'' from primary school to university levels. Plate tectonics, the dominant process of Earth geology, also occurs in miniature on the surface of some lava lakes, and as ``ice plate tectonics'' on our frozen seas and lakes. Ice tectonics also happens at larger spatial and temporal scales on the Jovian moons Europa and perhaps Ganymede. Tabletop plate tectonics, in which a molten-paraffin ``asthenosphere'' is surfaced by a skin of congealing wax ``plates,'' first replicated Mid-Oceanic Ridge type seafloor spreading more than three decades ago. A seismologist (J. Brune, personal communication, 2004) discovered wax plate tectonics by casually and serendipitously pulling a stick across a container of molten wax his wife and daughters had used in making candles. Brune and his student D. Oldenburg followed up and mirabile dictu published the results in Science (178, 301-304).

  4. The Needs of Trees

    ERIC Educational Resources Information Center

    Boyd, Amy E.; Cooper, Jim

    2004-01-01

    Tree rings can be used not only to look at plant growth, but also to make connections between plant growth and resource availability. In this lesson, students in 2nd-4th grades use role-play to become familiar with basic requirements of trees and how availability of those resources is related to tree ring sizes and tree growth. These concepts can

  5. The effect of sumac (Rhus coriaria L.) powder on insulin resistance, malondialdehyde, high sensitive C-reactive protein and paraoxonase 1 activity in type 2 diabetic patients

    PubMed Central

    Rahideh, Seyedeh Tayebeh; Shidfar, Farzad; Khandozi, Nafiseh; Rajab, Asadollah; Hosseini, Seyed Payam; Mirtaher, Seyed Mohsen

    2014-01-01

    Background: Sumac (Rhus coriaria L.) has been used in traditional treatment of some diseases. The aim of this study was to determine the effect of sumac (R. coriaria L.) powder on insulin resistance (IR), malondialdehyde (MDA), high sensitive C-reactive protein (hs-CRP), and paraoxonase 1 (PON1) activity in type 2 diabetic patients. Materials and Methods: A double-blind randomized placebo controlled trial on 41 type 2 diabetic volunteers was conducted. Participants randomly assigned into 3 g per day sumac powder (n = 22) or placebo (n = 19) groups for 3 months. IR was assessed using the homeostatic model assessment of IR (HOMA-IR), which including measurement of insulin by immunoassay method and measurement of glucose by enzymatic method. MDA and PON1 activity were measured colorimetrically, hs-CRP turbidimetrically. Results: There were a significant increase in PON1 activity (from 84.72 30.59 to 92.91 32.63) and significant decrease in insulin (from 7.09 4.28 to 5.32 3.22), HOMA-IR (from 2.56 1.58 to 1.67 0.94), MDA (from 2.71 0.73 to 1.97 0.49), and also hs-CRP (from 18.49 16.96 to 15.89 16.70) in the sumac group at the end of study compared with initial values (P < 0.05). Furthermore, there were significant differences in MDA and PON1 between the two groups at the end of the study (P < 0.05). Furthermore, the mean of differences of insulin, HOMA-IR, MDA, hs-CRP and PON1 activity between groups were significant (P < 0.05). Conclusion: We concluded that daily intake of 3 g sumac for 3 months may be beneficial for diabetic patients to make them less susceptible to cardiovascular disease. PMID:25538775

  6. A novel mixed valence form of Rhus vernicifera laccase and its reaction with dioxygen to give a peroxide intermediate bound to the trinuclear center.

    PubMed

    Zoppellaro, G; Sakurai, T; Huang, H

    2001-06-01

    Rhus vernicifera laccase, in a novel mixed valence state [T1oxT23red: type 1 Cu as Cu(II), and type 2 and 3 Cus as Cu(I)], was formed by reacting Cu(I) on the type 2 Cu-depleted laccase [T1oxT3red: type 1 Cu as Cu(II) and type 3 Cus as Cu(I)] under argon. Contrary to T1oxT3red, T1oxT23red was highly reactive with dioxygen, and gave the three transient bands at 340, 475, and 680 nm due to the two-electron reduced form of dioxygen [charge transfer bands from peroxide to Cu(II)]. The first order decays were highly dependent on pH, which led to the successful detection of the intermediate for ca. 2 h at pH 7.5. Another mixed valence derivative, T12oxT3red [type 1 and type 2 Cus as Cu(II), and type 3 Cus as Cu(I)] prepared through the action of Cu(II) on T1oxT3red was not reactive with dioxygen, but showed high enzyme activity as to the oxidation of N,N-dimethyl-p-phenylenediamine. The whole reaction mechanism of the reduction of dioxygen by laccase was proposed based on the present results together with data for the former detection and characterization of the three-electron reduced form of dioxygen [Huang, H. et al. (1999) J. Biol. Chem. 274, 46, 32718-32724]. PMID:11388911

  7. X-ray absorption study of Rhus laccase: evidence for a copper-copper interaction, which disappears on type 2 copper removal.

    PubMed

    Woolery, G L; Powers, L; Peisach, J; Spiro, T G

    1984-07-17

    X-ray absorption spectra are reported for the multi-Cu oxidase Rhus vernicifera laccase in oxidized and fully reduced forms and for laccase from which the type 2 Cu has been depleted (T2D). The structure of the Cu K edge for both preparations shows the presence of CuII and CuI in the oxidized and reduced states, respectively. As previously reported by LuBien et al. (1981), removal of the type 2 Cu leads to reduction of the type 3 center, which can be reoxidized with H2O2. Fourier transforms of the extended X-ray absorption fine structure (EXAFS) give well-defined first and outer shell scattering peaks. Analysis of the first shell peak is complicated by the heterogeneity of the Cu sites. When (imidazole)4CuIISO4 is used as a model of the average Cu-ligand interactions, it is shown that all of the first shell peaks contain 2.7-3.5 near neighbors per Cu, at an average distance of 1.97-1.98 A. For T2D laccase, the fit is improved by inclusion of one-third of a sulfur atom at 2.19 A, corresponding to the presumptive cysteine ligand of the type 1 Cu, which remains in the preparation containing three Cu atoms per molecule. The outer shell region shows two peaks characteristic of scattering from distant imidazole atoms. For T2D laccase the filtered outer shell contribution can be satisfactorily fit by scattering from an average of 2.1-2.4 imidazole groups. For native laccase, however, imidazole alone cannot satisfactorily model the outer shell contribution.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:6235850

  8. Effects of Hydro-Alcoholic Extract of Rhus coriaria (Sumac) Seeds on Reproductive Complications of Nicotinamide-Streptozotocin Induced Type-2 Diabetes in Male Mice

    PubMed Central

    Ahangarpour, Akram; Heidari, Hamid; Ehsan, Ghaedi; Rashidi Nooshabadi, Mohammad Reza

    2014-01-01

    Purpose The purpose of this study was to investigate the effects of the hydro-alcoholic extract of Rhus coriaria seeds on the reproductive system of nicotinamide-streptozotocin-induced type-2 diabetic mice. Materials and Methods In this experimental study, 56 male Naval Medical Research Institute mice were randomly divided into seven groups (n=8): control; diabetic mice; diabetic mice administered glibenclamide (0.25 mg/kg); diabetic mice who received the hydro-alcoholic extract of R. coriaria seeds (200 and 400 mg/kg groups); and normal mice who received this extract (200 and 400 mg/kg groups). Diabetes was induced by intraperitoneal administration of streptozotocin (65 mg/kg) 15 minutes after an injection of nicotinamide (120 mg/kg). Then, glibenclamide and the above mentioned extract were administered orally for 28 consecutive days. Twenty-four hours after the last treatment, serum samples, the testes, and the cauda epididymis were removed immediately for hormonal, testis morphology, and sperm parameter assessments. Results Body and testicular weight, sperm count and viability, and serum luteinizing hormone, follicle-stimulating hormone and testosterone levels were significantly lower in the diabetic mice (p<0.05). The diabetic mice treated with 400 mg/kg of the hydro-alcoholic extract of R. coriaria seeds recovered from these reductions (p<0.05). Further, glibenclamide alleviated hormonal and sperm count depletion in diabetes-induced mice (p<0.05). Conclusions The present results indicated that the hydro-alcoholic extract of R. coriaria seeds has anti-infertility effects in diabetic males. PMID:25606564

  9. The effect of water extract of sumac (Rhus coriaria L.) and lactic acid on decontamination and shelf life of raw broiler wings.

    PubMed

    Gulmez, M; Oral, N; Vatansever, L

    2006-08-01

    In an attempt to improve the bacteriological quality and refrigerated shelf life of broiler meat, 10-min surface wash treatments with sterile distilled water (DW), 8% (wt/vol) water extract of sumac (Rhus coriaria L.) fruits (WES), and 2% (vol/vol) lactic acid (LA) were compared by using a broiler wing model. The aerobic plate counts (log10 cfu/g) of psychrotrophs, mesophilic aerobes, Enterobacteriaceae, coliforms and presumptive fecal coliforms on the samples were determined. Immediately after a 10-min decontaminaton, the mean count of all the bacterial groups was determined to be 3.9, 2.6, and 1.7 (log10 cfu/g) for DW, WES, and LA, respectively. Because the postdecontamination population level of psychrotrophs, mesophiles, and Enterobacteriaceae were low in the LA-treated group compared to the WES group, an equity between the 2 groups in the point of view of the 3 bacterial groups existed at d 10 of cold storage (3 +/- 1 degrees C). Shelf life was 7 and 14 d for wings treated with DW and WES, respectively, whereas the LA-treated wings did not spoil after 14 d of cold storage (3 +/- 1 degrees C). Nevertheless, an undesirable pale color and an acidulous odor occurred in the LA-treated wings. In contrast, a good color appeared on the WES-treated wings, which was also superior to the color of the DW-treated wings. Such advantages of WES may be important for poultry processors and for consumers. However, the immediate decontamination and refrigerated shelf life extension potential of WES should be intensively studied in antimicrobial interventions in poultry processing plants. PMID:16903480

  10. Categorizing Ideas about Trees: A Tree of Trees

    PubMed Central

    Fisler, Marie; Lecointre, Guillaume

    2013-01-01

    The aim of this study is to explore whether matrices and MP trees used to produce systematic categories of organisms could be useful to produce categories of ideas in history of science. We study the history of the use of trees in systematics to represent the diversity of life from 1766 to 1991. We apply to those ideas a method inspired from coding homologous parts of organisms. We discretize conceptual parts of ideas, writings and drawings about trees contained in 41 main writings; we detect shared parts among authors and code them into a 91-characters matrix and use a tree representation to show who shares what with whom. In other words, we propose a hierarchical representation of the shared ideas about trees among authors: this produces a “tree of trees.” Then, we categorize schools of tree-representations. Classical schools like “cladists” and “pheneticists” are recovered but others are not: “gradists” are separated into two blocks, one of them being called here “grade theoreticians.” We propose new interesting categories like the “buffonian school,” the “metaphoricians,” and those using “strictly genealogical classifications.” We consider that networks are not useful to represent shared ideas at the present step of the study. A cladogram is made for showing who is sharing what with whom, but also heterobathmy and homoplasy of characters. The present cladogram is not modelling processes of transmission of ideas about trees, and here it is mostly used to test for proximity of ideas of the same age and for categorization. PMID:23950877

  11. Landscape in a Lacquer Box

    ERIC Educational Resources Information Center

    Savage, Martha

    2010-01-01

    A symbolic dry landscape garden of Eastern origin holds a special fascination for the author's middle-school students, which is why the author chose to create a project exploring this view of nature. A dry landscape garden, or "karesansui," is an arrangement of rocks, worn by nature and surrounded by a "sea" of sand, raked into patterns

  12. Landscape in a Lacquer Box

    ERIC Educational Resources Information Center

    Savage, Martha

    2010-01-01

    A symbolic dry landscape garden of Eastern origin holds a special fascination for the author's middle-school students, which is why the author chose to create a project exploring this view of nature. A dry landscape garden, or "karesansui," is an arrangement of rocks, worn by nature and surrounded by a "sea" of sand, raked into patterns…

  13. Bronchi, Bronchial Tree, & Lungs

    MedlinePLUS

    ... Modules Resources Archived Modules Updates Bronchi, Bronchial Tree, & Lungs Bronchi and Bronchial Tree In the mediastinum , at ... the walls of the alveolar ducts and alveoli. Lungs The two lungs, which contain all the components ...

  14. Chem-Is-Tree.

    ERIC Educational Resources Information Center

    Barry, Dana M.

    1997-01-01

    Provides details on the chemical composition of trees including a definition of wood. Also includes an activity on anthocyanins as well as a discussion of the resistance of wood to solvents and chemicals. Lists interesting products from trees. (DDR)

  15. Tree Classification Software

    NASA Technical Reports Server (NTRS)

    Buntine, Wray

    1993-01-01

    This paper introduces the IND Tree Package to prospective users. IND does supervised learning using classification trees. This learning task is a basic tool used in the development of diagnosis, monitoring and expert systems. The IND Tree Package was developed as part of a NASA project to semi-automate the development of data analysis and modelling algorithms using artificial intelligence techniques. The IND Tree Package integrates features from CART and C4 with newer Bayesian and minimum encoding methods for growing classification trees and graphs. The IND Tree Package also provides an experimental control suite on top. The newer features give improved probability estimates often required in diagnostic and screening tasks. The package comes with a manual, Unix 'man' entries, and a guide to tree methods and research. The IND Tree Package is implemented in C under Unix and was beta-tested at university and commercial research laboratories in the United States.

  16. Tree Nut Allergies

    MedlinePLUS

    ... likelihood of cross-contact with tree nuts during manufacturing and processing. Avoiding Tree Nuts The federal Food ... Word True Stories Stay Informed Newsletters Alerts Alerts Feed Alerts Archive Ingredient Notices Ingredient Notices Feed FARE ...

  17. Evolution of tree nutrition.

    PubMed

    Raven, John A; Andrews, Mitchell

    2010-09-01

    Using a broad definition of trees, the evolutionary origins of trees in a nutritional context is considered using data from the fossil record and molecular phylogeny. Trees are first known from the Late Devonian about 380 million years ago, originated polyphyletically at the pteridophyte grade of organization; the earliest gymnosperms were trees, and trees are polyphyletic in the angiosperms. Nutrient transporters, assimilatory pathways, homoiohydry (cuticle, intercellular gas spaces, stomata, endohydric water transport systems including xylem and phloem-like tissue) and arbuscular mycorrhizas preceded the origin of trees. Nutritional innovations that began uniquely in trees were the seed habit and, certainly (but not necessarily uniquely) in trees, ectomycorrhizas, cyanobacterial, actinorhizal and rhizobial (Parasponia, some legumes) diazotrophic symbioses and cluster roots. PMID:20581011

  18. Pecan tree biomass estimates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Allometric equations were developed for orchard-grown pecan [Carya illinoinensis (Wangenh.) C. Koch] trees. Trees, ranging in size from 22 to 33 cm in trunk diameter 1.4 m above the ground, were destructively harvested from two sites. The entire above-ground portion of the trees was harvested and...

  19. Minnesota's Forest Trees. Revised.

    ERIC Educational Resources Information Center

    Miles, William R.; Fuller, Bruce L.

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

  20. Structural Equation Model Trees

    ERIC Educational Resources Information Center

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

    2013-01-01

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

  1. Illumination Under Trees

    SciTech Connect

    Max, N

    2002-08-19

    This paper is a survey of the author's work on illumination and shadows under trees, including the effects of sky illumination, sun penumbras, scattering in a misty atmosphere below the trees, and multiple scattering and transmission between leaves. It also describes a hierarchical image-based rendering method for trees.

  2. Winter Birch Trees

    ERIC Educational Resources Information Center

    Sweeney, Debra; Rounds, Judy

    2011-01-01

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

  3. The Wish Tree Project

    ERIC Educational Resources Information Center

    Brooks, Sarah DeWitt

    2010-01-01

    This article describes the author's experience in implementing a Wish Tree project in her school in an effort to bring the school community together with a positive art-making experience during a potentially stressful time. The concept of a wish tree is simple: plant a tree; provide tags and pencils for writing wishes; and encourage everyone to

  4. Rhus javanica Linn protects against hydrogen peroxide?induced toxicity in human Chang liver cells via attenuation of oxidative stress and apoptosis signaling.

    PubMed

    Yoon, Chanjin; Koppula, Sushruta; Yoo, Seunghoon; Yum, Munjeong; Kim, Jinseoub; Lee, Jaedong; Song, Mindong

    2016-01-01

    Rhus javanica Linn, a traditional medicinal herb from the family Anacardiaceae, has been used in the treatment of liver diseases, cancer, parasitic infections, malaria and respiratory diseases in China, Korea and other Asian countries for centuries. In the present study, the protective effects of R. javanica ethanolic extract (RJE) on hydrogen peroxide (H2O2)-induced oxidative stress in human Chang liver cells was investigated. The cell cytotoxicity and viability were assessed using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The activities of superoxide dismutase (SOD) and catalase (CAT) were measured using respective enzymatic kits. Cell cycle analysis was performed using flow cytometric analysis. The protein expression levels of p53, B-cell lymphoma (Bcl)-2, Bcl-2-associated X protein (Bax) and caspase-3 were assessed by western blotting. Human Chang liver cells were treated with different concentrations (0.1, 0.3 or 0.5 mg/ml) of RJE, and were subsequently exposed to H2O2 (30 M). Treatment with H2O2 (30 M) significantly induced cytotoxicity (P<0.05) and reduced the viability of the Chang liver cells. However, pretreatment of the cells with RJE (0.1, 0.3 or 0.5 mg/ml) significantly increased the cell viability (P<0.001 at 0.5 mg/ml) in a concentration-dependent manner following H2O2 treatment. Furthermore, pretreatment with RJE increased the enzyme activities of SOD and CAT, and decreased the sub-G1 growth phase of the cell cycle in response to H2O2-induced oxidative stress (P<0.001 at 0.3 and 0.5 mg/ml H2O2). RJE also regulated the protein expression levels of p53, Bax, caspase-3 and Bcl-2. These results suggested that RJE may protect human Chang liver cells against oxidative damage by increasing the levels of antioxidant enzymes and regulating antiapoptotic oxidative stress mechanisms, thereby providing insights into the mechanism which underpins the traditional claims made for RJE in the treatment of liver diseases. PMID:26648020

  5. Distributed Contour Trees

    SciTech Connect

    Morozov, Dmitriy; Weber, Gunther H.

    2014-03-31

    Topological techniques provide robust tools for data analysis. They are used, for example, for feature extraction, for data de-noising, and for comparison of data sets. This chapter concerns contour trees, a topological descriptor that records the connectivity of the isosurfaces of scalar functions. These trees are fundamental to analysis and visualization of physical phenomena modeled by real-valued measurements. We study the parallel analysis of contour trees. After describing a particular representation of a contour tree, called local{global representation, we illustrate how di#11;erent problems that rely on contour trees can be solved in parallel with minimal communication.

  6. 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

  7. Ephedra alte (Joint Pine): An Invasive, Problematic Weedy Species in Forestry and Fruit Tree Orchards in Jordan

    PubMed Central

    Qasem, Jamal R.

    2012-01-01

    A field survey was carried out to record plant species climbed by Ephedra alte in certain parts of Jordan during 20082010. Forty species of shrubs, ornamental, fruit, and forest trees belonging to 24 plant families suffered from the climbing habit of E. alte. Growth of host plants was adversely affected by E. alte growth that extended over their vegetation. In addition to its possible competition for water and nutrients, the extensive growth it forms over host species prevents photosynthesis, smothers growth and makes plants die underneath the extensive cover. However, E. alte did not climb all plant species, indicating a host preference range. Damaged fruit trees included Amygdalus communis, Citrus aurantifolia, Ficus carica, Olea europaea, Opuntia ficus-indica, and Punica granatum. Forestry species that were adversely affected included Acacia cyanophylla, Ceratonia siliqua, Crataegus azarolus, Cupressus sempervirens, Pinus halepensis, Pistacia atlantica, Pistacia palaestina, Quercus coccifera, Quercus infectoria, Retama raetam, Rhamnus palaestina, Rhus tripartita, and Zizyphus spina-christi. Woody ornamentals attacked were Ailanthus altissima, Hedera helix, Jasminum fruticans, Jasminum grandiflorum, Nerium oleander, and Pyracantha coccinea. Results indicated that E. alte is a strong competitive for light and can completely smother plants supporting its growth. A. communis, F. carica, R. palaestina, and C. azarolus were most frequently attacked. PMID:22645486

  8. Oxidant air pollution effects on plants of Joshua Tree National Monument.

    PubMed

    Temple, P J

    1989-01-01

    Joshua Tree National Monument (JOTR) is located about 100 km east of the Los Angeles Basin, site of the heaviest concentration of photochemical oxidant (O(3)) air pollution in the US. This investigation was conducted to measure O(3) concentrations in JOTR and to determine the effects of O(3) on vegetation in the park. Potentially phytotoxic concentrations of O(3) were recorded in JOTR in 1984 and 1985, but peak concentration occurred at night, when most plant species would be less sensitive to O(3). No O(3) effects were observed on permanent vegetation observation plots in JOTR in 1984 or 1985. Controlled exposures of native summer annual and woody perennial species to O(3) showed that most did not develop visible O(3) injury symptoms except at concentrations higher than those expected in the park. However, Rhus trilobata Nutt. was injured at 0.10 ppm O(3), 4 h per day for 4 days. This species would be a useful bioindicator to assess the effects of O(3) on native desert plants. PMID:15092465

  9. Engineering Laccases: In Search for Novel Catalysts

    PubMed Central

    Robert, Viviane; Mekmouche, Yasmina; Pailley, Pierre R; Tron, Thierry

    2011-01-01

    Laccases (p-diphenol oxidase, EC 1.10.3.2) are blue multicopper oxidases that catalyze the reduction of dioxygen to water, with a concomitant oxidation of small organic substrates. Since the description at the end of the nineteenth century of a factor catalyzing the rapid hardening of the latex of the Japanese lacquer trees (Rhus sp.) exposed to air laccases from different origins (plants, fungi bacteria) have been continuously discovered and extensively studied. Nowadays, molecular evolution and other powerful protein modification techniques offer possibilities to develop tailored laccases for a wide array of applications including drug synthesis, biosensors or biofuel cells. Here, we give an overview on strategies and results of our laboratory in the design of new biocatalysts based on laccases. PMID:21966250

  10. Species integrity in trees.

    PubMed

    Ortiz-Barrientos, Daniel; Baack, Eric J

    2014-09-01

    From California sequoia, to Australian eucalyptus, to the outstanding diversity of Amazonian forests, trees are fundamental to many processes in ecology and evolution. Trees define the communities that they inhabit, are host to a multiplicity of other organisms and can determine the ecological dynamics of other plants and animals. Trees are also at the heart of major patterns of biodiversity such as the latitudinal gradient of species diversity and thus are important systems for studying the origin of new plant species. Although the role of trees in community assembly and ecological succession is partially understood, the origin of tree diversity remains largely opaque. For instance, the relative importance of differing habitats and phenologies as barriers to hybridization between closely related species is still largely uncharacterized in trees. Consequently, we know very little about the origin of trees species and their integrity. Similarly, studies on the interplay between speciation and tree community assembly are in their infancy and so are studies on how processes like forest maturation modifies the context in which reproductive isolation evolves. In this issue of Molecular Ecology, Lindtke et al. (2014) and Lagache et al. (2014) overcome some traditional difficulties in studying mating systems and sexual isolation in the iconic oaks and poplars, providing novel insights about the integrity of tree species and on how ecology leads to variation in selection on reproductive isolation over time and space. PMID:25155715

  11. Fragmentation of random trees

    NASA Astrophysics Data System (ADS)

    Kalay, Ziya; Ben-Naim, Eli

    2015-03-01

    We investigate the fragmentation of a random recursive tree by repeated removal of nodes, resulting in a forest of disjoint trees. The initial tree is generated by sequentially attaching new nodes to randomly chosen existing nodes until the tree contains N nodes. As nodes are removed, one at a time, the tree dissolves into an ensemble of separate trees, namely a forest. We study the statistical properties of trees and nodes in this heterogeneous forest. In the limit N --> ? , we find that the system is characterized by a single parameter: the fraction of remaining nodes m. We obtain analytically the size density ?s of trees of size s, which has a power-law tail ?s ~s-? , with exponent ? = 1 + 1 / m . Therefore, the tail becomes steeper as further nodes are removed, producing an unusual scaling exponent that increases continuously with time. Furthermore, we investigate the fragment size distribution in a growing tree, where nodes are added as well as removed, and find that the distribution for this case is much narrower.

  12. Forest tree biotechnology.

    PubMed

    Dean, J F; LaFayette, P R; Eriksson, K E; Merkle, S A

    1997-01-01

    The forest products industry has traditionally viewed trees as merely a raw, and more or less immutable, natural resource. However, unlike such inanimate resources as metallic ores, trees have the potential to be modified genetically, essentially transmuting lead into gold. Increasingly, modern alchemists are applying the tools of biotechnology in efforts to reduce the biological constraints on forest productivity. Several new methodologies being used to address problems in forest biology are described with respect to their potential impact on forest tree improvement. In addition to addressing problems inherent to the current use of trees for production of pulp and paper or solid wood products, genetic manipulation of trees brings with it the potential to create new industries based on the novel characteristics of transgenic trees, e.g. trees containing transgenes to detoxify specific pollutants could be used in the remediation of sites contaminated with hazardous wastes. Efforts to modify trees through biotechnology are in their infancy, and this review seeks to outline the underpinnings of what will undoubtedly be an area of increased emphasis in the next millennium. PMID:9204750

  13. Grizzly Giant Tree

    USGS Multimedia Gallery

    This giant sequoia is named the Grizzly Giant, the oldest sequoia tree in the Mariposa Grove of Big Trees, located within Yosemite National Park. It is believed to be between 1,900 and 2,400 years old. ...

  14. Trees for Mother Earth.

    ERIC Educational Resources Information Center

    Greer, Sandy

    1993-01-01

    Describes Trees for Mother Earth, a program in which secondary students raise funds to buy fruit trees to plant during visits to the Navajo Reservation. Benefits include developing feelings of self-worth among participants, promoting cultural exchange and understanding, and encouraging self-sufficiency among the Navajo. (LP)

  15. Tree nut oils

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The major tree nuts include almonds, Brazil nuts, cashew nuts, hazelnuts, macadamia nuts, pecans, pine nuts, pistachio nuts, and walnuts. Tree nut oils are appreciated in food applications because of their flavors and are generally more expensive than other gourmet oils. Research during the last de...

  16. Structural Equation Model Trees

    ERIC Educational Resources Information Center

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

    2013-01-01

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

  17. Trees Are Terrific!

    ERIC Educational Resources Information Center

    Braus, Judy, Ed.

    1992-01-01

    Ranger Rick's NatureScope is a creative education series dedicated to inspiring in children an understanding and appreciation of the natural world while developing the skills they will need to make responsible decisions about the environment. Contents are organized into the following sections: (1) "What Makes a Tree a Tree?," including information…

  18. CSI for Trees

    ERIC Educational Resources Information Center

    Rubino, Darrin L.; Hanson, Deborah

    2009-01-01

    The circles and patterns in a tree's stem tell a story, but that story can be a mystery. Interpreting the story of tree rings provides a way to heighten the natural curiosity of students and help them gain insight into the interaction of elements in the environment. It also represents a wonderful opportunity to incorporate the nature of science.…

  19. Fragmentation of random trees

    NASA Astrophysics Data System (ADS)

    Kalay, Z.; Ben-Naim, E.

    2015-01-01

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

  20. CSI for Trees

    ERIC Educational Resources Information Center

    Rubino, Darrin L.; Hanson, Deborah

    2009-01-01

    The circles and patterns in a tree's stem tell a story, but that story can be a mystery. Interpreting the story of tree rings provides a way to heighten the natural curiosity of students and help them gain insight into the interaction of elements in the environment. It also represents a wonderful opportunity to incorporate the nature of science.

  1. Trees in Our Lives.

    ERIC Educational Resources Information Center

    NatureScope, 1986

    1986-01-01

    Provides: (1) background information on how trees have influenced human history and how trees affect people today; (2) four activities dealing with these topics; and (3) a ready-to-copy page related to paper and plastics. Activities include an objective, recommended age level(s), subject area(s), list of materials needed, and procedures. (JN)

  2. Tea Tree Oil

    MedlinePLUS

    ... the arms and legs causing a lack of balance and coordination. One patient went into a coma after drinking half a cup of tea tree oil. Topical use of diluted tea tree oil is generally considered safe for most adults. However, one case study did report a young ...

  3. From Family Trees to Decision Trees.

    ERIC Educational Resources Information Center

    Trobian, Helen R.

    This paper is a preliminary inquiry by a non-mathematician into graphic methods of sequential planning and ways in which hierarchical analysis and tree structures can be helpful in developing interest in the use of mathematical modeling in the search for creative solutions to real-life problems. Highlights include a discussion of hierarchical

  4. Lazy decision trees

    SciTech Connect

    Friedman, J.H.; Yun, Yeogirl; Kohavi, R.

    1996-12-31

    Lazy learning algorithms, exemplified by nearest-neighbor algorithms, do not induce a concise hypothesis from a given training set; the inductive process is delayed until a test instance is given. Algorithms for constructing decision trees, such as C4.5, ID3, and CART create a single {open_quotes}best{close_quotes} decision tree during the training phase, and this tree is then used to classify test instances. The tests at the nodes of the constructed tree are good on average, but there may be better tests for classifying a specific instance. We propose a lazy decision tree algorithm-LazyDT-that conceptually constructs the {open_quotes}best{close_quote} decision tree for each test instance. In practice, only a path needs to be constructed, and a caching scheme makes the algorithm fast. The algorithm is robust with respect to missing values without resorting to the complicated methods usually seen in induction of decision trees. Experiments on real and artificial problems are presented.

  5. Phylogenetic trees in bioinformatics

    SciTech Connect

    Burr, Tom L

    2008-01-01

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

  6. Wounded forests, starving trees

    SciTech Connect

    Shigo, A.L.

    1985-11-01

    Acid rain, insects, and fungi are real problems that can kill trees. Wounded and starving trees are also realities and part of the total picture. Forest decline is a many-sided problem, yet recent attention has focused on only a few visible factors. The blame for diebacks and declines can not always be placed on well-publicized short-term agents. Forestry practices may also play an important part in today's current tree problems. This paper examined past forestry practices to see if they could have predisposed forests to stress and therefore been a major factor in current forest problems. 8 references, 10 figures.

  7. The gravity apple tree

    NASA Astrophysics Data System (ADS)

    Espinosa Aldama, Mariana

    2015-04-01

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

  8. Learning classification trees

    NASA Technical Reports Server (NTRS)

    Buntine, Wray

    1991-01-01

    Algorithms for learning classification trees have had successes in artificial intelligence and statistics over many years. How a tree learning algorithm can be derived from Bayesian decision theory is outlined. This introduces Bayesian techniques for splitting, smoothing, and tree averaging. The splitting rule turns out to be similar to Quinlan's information gain splitting rule, while smoothing and averaging replace pruning. Comparative experiments with reimplementations of a minimum encoding approach, Quinlan's C4 and Breiman et al. Cart show the full Bayesian algorithm is consistently as good, or more accurate than these other approaches though at a computational price.

  9. Evolutionary tree reconstruction

    NASA Technical Reports Server (NTRS)

    Cheeseman, Peter; Kanefsky, Bob

    1990-01-01

    It is described how Minimum Description Length (MDL) can be applied to the problem of DNA and protein evolutionary tree reconstruction. If there is a set of mutations that transform a common ancestor into a set of the known sequences, and this description is shorter than the information to encode the known sequences directly, then strong evidence for an evolutionary relationship has been found. A heuristic algorithm is described that searches for the simplest tree (smallest MDL) that finds close to optimal trees on the test data. Various ways of extending the MDL theory to more complex evolutionary relationships are discussed.

  10. Generalized constructive tree weights

    SciTech Connect

    Rivasseau, Vincent E-mail: adrian.tanasa@ens-lyon.org; Tanasa, Adrian E-mail: adrian.tanasa@ens-lyon.org

    2014-04-15

    The Loop Vertex Expansion (LVE) is a quantum field theory (QFT) method which explicitly computes the Borel sum of Feynman perturbation series. This LVE relies in a crucial way on symmetric tree weights which define a measure on the set of spanning trees of any connected graph. In this paper we generalize this method by defining new tree weights. They depend on the choice of a partition of a set of vertices of the graph, and when the partition is non-trivial, they are no longer symmetric under permutation of vertices. Nevertheless we prove they have the required positivity property to lead to a convergent LVE; in fact we formulate this positivity property precisely for the first time. Our generalized tree weights are inspired by the Brydges-Battle-Federbush work on cluster expansions and could be particularly suited to the computation of connected functions in QFT. Several concrete examples are explicitly given.

  11. Leonardo's Tree Theory.

    ERIC Educational Resources Information Center

    Werner, Suzanne K.

    2003-01-01

    Describes a series of activities exploring Leonardo da Vinci's tree theory that are designed to strengthen 8th grade students' data collection and problem solving skills in physical science classes. (KHR)

  12. Structural Equation Model Trees

    PubMed Central

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

    2015-01-01

    In the behavioral and social sciences, structural equation models (SEMs) have become widely accepted as a modeling tool for the relation between latent and observed variables. SEMs can be seen as a unification of several multivariate analysis techniques. SEM Trees combine the strengths of SEMs and the decision tree paradigm by building tree structures that separate a data set recursively into subsets with significantly different parameter estimates in a SEM. SEM Trees provide means for finding covariates and covariate interactions that predict differences in structural parameters in observed as well as in latent space and facilitate theory-guided exploration of empirical data. We describe the methodology, discuss theoretical and practical implications, and demonstrate applications to a factor model and a linear growth curve model. PMID:22984789

  13. Tree-bank grammars

    SciTech Connect

    Charniak, E.

    1996-12-31

    By a {open_quotes}tree-bank grammar{close_quotes} we mean a context-free grammar created by reading the production rules directly from hand-parsed sentences in a tree bank. Common wisdom has it that such grammars do not perform well, though we know of no published data on the issue. The primary purpose of this paper is to show that the common wisdom is wrong. In particular, we present results on a tree-bank grammar based on the Penn Wall Street Journal tree bank. To the best of our knowledge, this grammar outperforms all other non-word-based statistical parsers/grammars on this corpus. That is, it outperforms parsers that consider the input as a string of tags and ignore the actual words of the corpus.

  14. Trees as energy crops

    SciTech Connect

    Standiford, R.B.; Donaldson, D.R.

    1982-01-01

    A report is presented of studies on the energy production of forest trees in California. The volume yield of the fastest growing species (Eucalyptus) was 23 cubic metres per hectare and energy yield 20 million kcal per hectare per annum.

  15. Tea tree oil.

    PubMed

    Larson, David; Jacob, Sharon E

    2012-01-01

    Tea tree oil is an increasingly popular ingredient in a variety of household and cosmetic products, including shampoos, massage oils, skin and nail creams, and laundry detergents. Known for its potential antiseptic properties, it has been shown to be active against a variety of bacteria, fungi, viruses, and mites. The oil is extracted from the leaves of the tea tree via steam distillation. This essential oil possesses a sharp camphoraceous odor followed by a menthol-like cooling sensation. Most commonly an ingredient in topical products, it is used at a concentration of 5% to 10%. Even at this concentration, it has been reported to induce contact sensitization and allergic contact dermatitis reactions. In 1999, tea tree oil was added to the North American Contact Dermatitis Group screening panel. The latest prevalence rates suggest that 1.4% of patients referred for patch testing had a positive reaction to tea tree oil. PMID:22653070

  16. Generalized constructive tree weights

    NASA Astrophysics Data System (ADS)

    Rivasseau, Vincent; Tanasa, Adrian

    2014-04-01

    The Loop Vertex Expansion (LVE) is a quantum field theory (QFT) method which explicitly computes the Borel sum of Feynman perturbation series. This LVE relies in a crucial way on symmetric tree weights which define a measure on the set of spanning trees of any connected graph. In this paper we generalize this method by defining new tree weights. They depend on the choice of a partition of a set of vertices of the graph, and when the partition is non-trivial, they are no longer symmetric under permutation of vertices. Nevertheless we prove they have the required positivity property to lead to a convergent LVE; in fact we formulate this positivity property precisely for the first time. Our generalized tree weights are inspired by the Brydges-Battle-Federbush work on cluster expansions and could be particularly suited to the computation of connected functions in QFT. Several concrete examples are explicitly given.

  17. Tree Topology Estimation

    PubMed Central

    Estrada, Rolando; Tomasi, Carlo; Schmidler, Scott C.; Farsiu, Sina

    2015-01-01

    Tree-like structures are fundamental in nature, and it is often useful to reconstruct the topology of a tree—what connects to what—from a two-dimensional image of it. However, the projected branches often cross in the image: the tree projects to a planar graph, and the inverse problem of reconstructing the topology of the tree from that of the graph is ill-posed. We regularize this problem with a generative, parametric tree-growth model. Under this model, reconstruction is possible in linear time if one knows the direction of each edge in the graph—which edge endpoint is closer to the root of the tree—but becomes NP-hard if the directions are not known. For the latter case, we present a heuristic search algorithm to estimate the most likely topology of a rooted, three-dimensional tree from a single two-dimensional image. Experimental results on retinal vessel, plant root, and synthetic tree datasets show that our methodology is both accurate and efficient. PMID:26353004

  18. Oscillation damping in trees.

    PubMed

    Spatz, Hanns-Christof; Theckes, Benoit

    2013-06-01

    Oscillation damping is of vital importance for trees to withstand strong gusty winds. Tree adaptation to wind loading takes place over a long time and during a storm only passive damping mechanisms can reduce the impact of the wind on trunk and roots. Structural damping, a phenomenon, which is associated with the conspicuous movements of the branches relative to the trunk is of particular importance. Primary and higher order branches can be seen as multiple tuned mass dampers. Moreover, as the frequency bands overlap within branches and between primary branches and the entire tree, resonance energy transfer can distribute mechanical energy over the entire tree, such that it is dissipated more effectively than in a tree with stiff branches and not so much focused on the tree trunk and the roots. Theoretical studies using modal analysis and finite element methods have supported these assertions. Next to "multiple mass damping" and "multiple resonance damping", both characterized by linear coupling between the elements, a third non linear mode, operative at large amplitudes has been identified: "damping by branching". In all these not mutually exclusive concepts frequency tuning between the elements appears to be a fundamental requisite. PMID:23602100

  19. How Trees Can Save Energy.

    ERIC Educational Resources Information Center

    Fazio, James R., Ed.

    1991-01-01

    This document might easily have been called "How To Use Trees To Save Energy". It presents the energy saving advantages of landscaping the home and community with trees. The discussion includes: (1) landscaping advice to obtain the benefits of tree shade; (2) the heat island phenomenon in cities; (3) how and where to properly plant trees for…

  20. The inference of gene trees with species trees.

    PubMed

    Szll?si, 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

  1. Measuring inconsistency in phylogenetic trees.

    PubMed

    Willson, S J

    1998-01-01

    Suppose that we seek a tree T giving the phylogenetic relationships among the species in a set S. A common method selects for such a tree a maximum parsimony tree using the genome of the species in S. Suppose that K is a proper subset of S. Then T induces a tree U which gives the same relationships among the species in K but omits the species of S which are not in K. Unfortunately, when T is a maximum parsimony tree for the species in S, then U need not be a maximum parsimony tree for the species in K. This phenomenon exhibits an inconsistency in the criterion of maximum parsimony-maximum parsimony trees for different groups of species may be "inconsistent". It implies that the addition of a new species scan change relationships already "established" for prior species if the trees are obtained by the criterion of maximum parsimony. The phenomenon occurs both in artificial examples and with real data. An alternative method for generating phylogenetic trees seeks to minimize such inconsistencies. For each group J consisting of four of the species, we find a tree T(J) describing the relationship only among the four species in J, for example by the use of maximum parsimony on those four species alone. In favorable cases one may combine all the trees T(J) into a single tree T that is consistent with all the trees T(J). If such a tree T exists, then it is unique, and there is a computationally efficient algorithm for finding the tree T. In unfavorable bases such a tree T does not exist, but there may still be a tree containing only "mild" inconsistencies with the trees T(J). A numerical measure is given for the inconsistency I(T) of a tree T in terms of the treelengths of the various trees with set J of leaves in comparison with the tree T. We may then seek a "minimally inconsistent tree T" that minimizes the inconsistency I(T). We describe procedures which find a tree T with low inconsistency I(T). Examples are provided using both artificial strings and data from the complete mitochondrial DNA sequences for 16 species. In particular, minimally inconsistent trees are identified for the 16 species. The definition permits a proof that the trees are in fact minimally inconsistent. The criterion can be applied in both a relative and an absolute sense. PMID:9473388

  2. Tree nut allergens.

    PubMed

    Roux, Kenneth H; Teuber, Suzanne S; Sathe, Shridhar K

    2003-08-01

    Allergic reactions to tree nuts can be serious and life threatening. Considerable research has been conducted in recent years in an attempt to characterize those allergens that are most responsible for allergy sensitization and triggering. Both native and recombinant nut allergens have been identified and characterized and, for some, the IgE-reactive epitopes described. Some allergens, such as lipid transfer proteins, profilins, and members of the Bet v 1-related family, represent minor constituents in tree nuts. These allergens are frequently cross-reactive with other food and pollen homologues, and are considered panallergens. Others, such as legumins, vicilins, and 2S albumins, represent major seed storage protein constituents of the nuts. The allergenic tree nuts discussed in this review include those most commonly responsible for allergic reactions such as hazelnut, walnut, cashew, and almond as well as those less frequently associated with allergies including pecan, chestnut, Brazil nut, pine nut, macadamia nut, pistachio, coconut, Nangai nut, and acorn. PMID:12915766

  3. 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

  4. The gene tree delusion.

    PubMed

    Springer, Mark S; Gatesy, John

    2016-01-01

    Higher-level relationships among placental mammals are mostly resolved, but several polytomies remain contentious. Song et al. (2012) claimed to have resolved three of these using shortcut coalescence methods (MP-EST, STAR) and further concluded that these methods, which assume no within-locus recombination, are required to unravel deep-level phylogenetic problems that have stymied concatenation. Here, we reanalyze Song et al.'s (2012) data and leverage these re-analyses to explore key issues in systematics including the recombination ratchet, gene tree stoichiometry, the proportion of gene tree incongruence that results from deep coalescence versus other factors, and simulations that compare the performance of coalescence and concatenation methods in species tree estimation. Song et al. (2012) reported an average locus length of 3.1 kb for the 447 protein-coding genes in their phylogenomic dataset, but the true mean length of these loci (start codon to stop codon) is 139.6 kb. Empirical estimates of recombination breakpoints in primates, coupled with consideration of the recombination ratchet, suggest that individual coalescence genes (c-genes) approach ∼12 bp or less for Song et al.'s (2012) dataset, three to four orders of magnitude shorter than the c-genes reported by these authors. This result has general implications for the application of coalescence methods in species tree estimation. We contend that it is illogical to apply coalescence methods to complete protein-coding sequences. Such analyses amalgamate c-genes with different evolutionary histories (i.e., exons separated by >100,000 bp), distort true gene tree stoichiometry that is required for accurate species tree inference, and contradict the central rationale for applying coalescence methods to difficult phylogenetic problems. In addition, Song et al.'s (2012) dataset of 447 genes includes 21 loci with switched taxonomic names, eight duplicated loci, 26 loci with non-homologous sequences that are grossly misaligned, and numerous loci with >50% missing data for taxa that are misplaced in their gene trees. These problems were compounded by inadequate tree searches with nearest neighbor interchange branch swapping and inadvertent application of substitution models that did not account for among-site rate heterogeneity. Sixty-six gene trees imply unrealistic deep coalescences that exceed 100 million years (MY). Gene trees that were obtained with better justified models and search parameters show large increases in both likelihood scores and congruence. Coalescence analyses based on a curated set of 413 improved gene trees and a superior coalescence method (ASTRAL) support a Scandentia (treeshrews)+Glires (rabbits, rodents) clade, contradicting one of the three primary systematic conclusions of Song et al. (2012). Robust support for a Perissodactyla+Carnivora clade within Laurasiatheria is also lost, contradicting a second major conclusion of this study. Song et al.'s (2012) MP-EST species tree provided the basis for circular simulations that led these authors to conclude that the multispecies coalescent accounts for 77% of the gene tree conflicts in their dataset, but many internal branches of their MP-EST tree are stunted by an order of magnitude or more due to wholesale gene tree reconstruction errors. An independent assessment of branch lengths suggests the multispecies coalescent accounts for ⩽ 15% of the conflicts among Song et al.'s (2012) 447 gene trees. Unfortunately, Song et al.'s (2012) flawed phylogenomic dataset has been used as a model for additional simulation work that suggests the superiority of shortcut coalescence methods relative to concatenation. Investigator error was passed on to the subsequent simulation studies, which also incorporated further logical errors that should be avoided in future simulation studies. Illegitimate branch length switches in the simulation routines unfairly protected coalescence methods from their Achilles' heel, high gene tree reconstruction error at short internodes. These simulations therefore provide no evidence that shortcut coalescence methods out-compete concatenation at deep timescales. In summary, the long c-genes that are required for accurate reconstruction of species trees using shortcut coalescence methods do not exist and are a delusion. Coalescence approaches based on SNPs that are widely spaced in the genome avoid problems with the recombination ratchet and merit further pursuit in both empirical systematic research and simulations. PMID:26238460

  5. Lava trees and tree molds ("cannon stones") of Mt. Etna

    NASA Astrophysics Data System (ADS)

    Carveni, Pietro; Mele, Giuliana; Benfatto, Santo; Imposa, Sebastiano; Salleo Puntillo, Maria

    2011-08-01

    Unique volcanic structures, known in the literature as "lava trees" and "tree molds", have formed at several sites on Mt. Etna volcano (northeastern Sicily, Italy). They form when a fluid lava flow runs over a tree, wraps around it and, while the wood burns off, solidifies forming a hollow cast of the tree. The inhabitants of the Etna area call these formations "pietre cannone" ("cannon stones") because of their cylindrical shape. The first documentation of lava trees is from Hawaii, but the first eye-witnessed accounts of their formation are, to our knowledge, from Etna's 1865 eruption. Although many of the literature examples of lava trees and tree molds formed in pahoehoe, many of those reported in this work formed in a'a. The sites where we have found the lava tree molds are located within the territory of the Etna Regional Park; most occur next to walking trails and have a high potential for geotourism.

  6. 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

  7. Tree-Ties.

    ERIC Educational Resources Information Center

    Gresczyk, Rick

    Created to help students understand how plants were used for food, for medicine, and for arts and crafts among the Ojibwe (Chippewa) Indians, the game Tree-Ties combines earth and social sciences within a specific culture. The game requires mutual respect, understanding, and agreement to succeed. Sounding like the word "treaties", the title is a

  8. Tree of pain.

    PubMed

    Newnham, David

    2016-01-20

    I like trees as much as anyone. But, thanks to the graceful ash outside our kitchen window, I have now joined the merry band of tennis elbow sufferers who, at any one time, make up one third of the population. PMID:26786443

  9. Christmas Tree Category Manual.

    ERIC Educational Resources Information Center

    Bowman, James S.; Turmel, Jon P.

    This manual provides information needed to meet the standards for pesticide applicator certification. Pests and diseases of christmas tree plantations are identified and discussed. Section one deals with weeds and woody plants and the application, formulation and effects of herbicides in controlling them. Section two discusses specific diseases

  10. Phylogenics & Tree-Thinking

    ERIC Educational Resources Information Center

    Baum, David A.; Offner, Susan

    2008-01-01

    Phylogenetic trees, which are depictions of the inferred evolutionary relationships among a set of species, now permeate almost all branches of biology and are appearing in increasing numbers in biology textbooks. While few state standards explicitly require knowledge of phylogenetics, most require some knowledge of evolutionary biology, and many

  11. Digging Deeper with Trees.

    ERIC Educational Resources Information Center

    Growing Ideas, 2001

    2001-01-01

    Describes hands-on science areas that focus on trees. A project on leaf pigmentation involves putting crushed leaves in a test tube with solvent acetone to dissolve pigment. In another project, students learn taxonomy by sorting and classifying leaves based on observable characteristics. Includes a language arts connection. (PVD)

  12. Tree-Ties.

    ERIC Educational Resources Information Center

    Gresczyk, Rick

    Created to help students understand how plants were used for food, for medicine, and for arts and crafts among the Ojibwe (Chippewa) Indians, the game Tree-Ties combines earth and social sciences within a specific culture. The game requires mutual respect, understanding, and agreement to succeed. Sounding like the word "treaties", the title is a…

  13. Christmas Tree Category Manual.

    ERIC Educational Resources Information Center

    Bowman, James S.; Turmel, Jon P.

    This manual provides information needed to meet the standards for pesticide applicator certification. Pests and diseases of christmas tree plantations are identified and discussed. Section one deals with weeds and woody plants and the application, formulation and effects of herbicides in controlling them. Section two discusses specific diseases…

  14. MPI File Tree Walk

    Energy Science and Technology Software Center (ESTSC)

    2007-04-30

    MPI-FTW is a scalable MPI based software application that navigates a directory tree by dynamically allocating processes to navigate sub-directories found. Upon completion, MPI-FTW provides statistics on the number of directories found, files found, and time to complete. Inaddition, commands can be executed at each directory level.

  15. Arbutus unedo, Strawberry Tree

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Encylopedia of Fruit and Nuts is designed as a research reference source on temperate and tropical fruit and nut crops. Strawberry tree or madrone is native to the Mediterranean region of southern Europe (Arbutus unedo L., Ericaceae) with a relict population in Ireland, as well as in North Ameri...

  16. Sizing Up Trees.

    ERIC Educational Resources Information Center

    Nelson, Don

    1995-01-01

    Presents a way for teachers to capitalize on children's intrinsic fascination with big things by measuring the world's largest living plants--trees. Students develop an appreciation of nature, work together cooperatively, and practice science process skills. Outlines the procedure and equipment including pencils, metersticks, and string. (NB)

  17. Multiquarks and Steiner trees

    NASA Astrophysics Data System (ADS)

    Richard, Jean-Marc

    2010-10-01

    A brief review review is presented of models tentatively leading to stable multiquarks. A new attempt is presented, based on a Steiner-tree model of confinement, which is inspired by by QCD. It leads to more attraction than the empirical colour-additive model used in earlier multiquark calculations, and predict several multiquark states in configurations with different flavours.

  18. Flat Tree Oyster (Isognomon alatus)

    USGS Multimedia Gallery

    At high tide, the red bark of the Red Mangrove Trees is submerged, creating a brilliant reflection at the water's surface. Flat Tree Oysters (Isognomon alatus) grow on the upper portions of the roots....

  19. Rate of tree carbon accumulation increases continuously with tree size

    USGS Publications Warehouse

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

    2014-01-01

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

  20. Building up rhetorical structure trees

    SciTech Connect

    Marcu, D.

    1996-12-31

    I use the distinction between the nuclei and the satellites that pertain to discourse relations to introduce a compositionality criterion for discourse trees. I provide a first-order formalization of rhetorical structure trees and, on its basis, I derive an algorithm that constructs all the valid rhetorical trees that can be associated with a given discourse.

  1. The Hopi Fruit Tree Book.

    ERIC Educational Resources Information Center

    Nyhuis, Jane

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

  2. Our Air: Unfit for Trees.

    ERIC Educational Resources Information Center

    Dochinger, Leon S.

    To help urban, suburban, and rural tree owners know about air pollution's effects on trees and their tolerance and intolerance to pollutants, the USDA Forest Service has prepared this booklet. It answers the following questions about atmospheric pollution: Where does it come from? What can it do to trees? and What can we do about it? In addition,

  3. New Life From Dead Trees

    ERIC Educational Resources Information Center

    DeGraaf, Richard M.

    1978-01-01

    There are numerous bird species that will nest only in dead or dying trees. Current forestry practices include clearing forests of these snags, or dead trees. This practice is driving many species out of the forests. An illustrated example of bird succession in and on a tree is given. (MA)

  4. Our Air: Unfit for Trees.

    ERIC Educational Resources Information Center

    Dochinger, Leon S.

    To help urban, suburban, and rural tree owners know about air pollution's effects on trees and their tolerance and intolerance to pollutants, the USDA Forest Service has prepared this booklet. It answers the following questions about atmospheric pollution: Where does it come from? What can it do to trees? and What can we do about it? In addition,…

  5. The Re-Think Tree.

    ERIC Educational Resources Information Center

    Gear, Jim

    1993-01-01

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

  6. The Tree Worker's Manual. [Revised.

    ERIC Educational Resources Information Center

    Lilly, S. J.

    This manual acquaints readers with the general operations of the tree care industry. The manual covers subjects important to a tree worker and serves as a training aid for workers at the entry level as tree care professionals. Each chapter begins with a set of objectives and may include figures, tables, and photographs. Ten chapters are included:…

  7. The Hopi Fruit Tree Book.

    ERIC Educational Resources Information Center

    Nyhuis, Jane

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

  8. Rate of tree carbon accumulation increases continuously with tree size.

    PubMed

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

    2014-03-01

    Forests are major components of the global carbon cycle, providing substantial feedback to atmospheric greenhouse gas concentrations. Our ability to understand and predict changes in the forest carbon cycle--particularly net primary productivity and carbon storage--increasingly relies on models that represent biological processes across several scales of biological organization, from tree leaves to forest stands. Yet, despite advances in our understanding of productivity at the scales of leaves and stands, no consensus exists about the nature of productivity at the scale of the individual tree, in part because we lack a broad empirical assessment of whether rates of absolute tree mass growth (and thus carbon accumulation) decrease, remain constant, or increase as trees increase in size and age. Here we present a global analysis of 403 tropical and temperate tree species, showing that for most species mass growth rate increases continuously with tree size. Thus, large, old trees do not act simply as senescent carbon reservoirs but actively fix large amounts of carbon compared to smaller trees; at the extreme, a single big tree can add the same amount of carbon to the forest within a year as is contained in an entire mid-sized tree. The apparent paradoxes of individual tree growth increasing with tree size despite declining leaf-level and stand-level productivity can be explained, respectively, by increases in a tree's total leaf area that outpace declines in productivity per unit of leaf area and, among other factors, age-related reductions in population density. Our results resolve conflicting assumptions about the nature of tree growth, inform efforts to undertand and model forest carbon dynamics, and have additional implications for theories of resource allocation and plant senescence. PMID:24429523

  9. Gene tree correction for reconciliation and species tree inference

    PubMed Central

    2012-01-01

    Background Reconciliation is the commonly used method for inferring the evolutionary scenario for a gene family. It consists in embedding inferred gene trees into a known species tree, revealing the evolution of the gene family by duplications and losses. When a species tree is not known, a natural algorithmic problem is to infer a species tree from a set of gene trees, such that the corresponding reconciliation minimizes the number of duplications and/or losses. The main drawback of reconciliation is that the inferred evolutionary scenario is strongly dependent on the considered gene trees, as few misplaced leaves may lead to a completely different history, with significantly more duplications and losses. Results In this paper, we take advantage of certain gene trees properties in order to preprocess them for reconciliation or species tree inference. We flag certain duplication vertices of a gene tree, the non-apparent duplication (NAD) vertices, as resulting from the misplacement of leaves. In the case of species tree inference, we develop a polynomial-time heuristic for removing the minimum number of species leading to a set of gene trees that exhibit no NAD vertices with respect to at least one species tree. In the case of reconciliation, we consider the optimization problem of removing the minimum number of leaves or species leading to a tree without any NAD vertex. We develop a polynomial-time algorithm that is exact for two special classes of gene trees, and show a good performance on simulated data sets in the general case. PMID:23167951

  10. Rate of tree carbon accumulation increases continuously with tree size

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  11. Global value trees.

    PubMed

    Zhu, Zhen; Puliga, Michelangelo; Cerina, Federica; Chessa, Alessandro; Riccaboni, Massimo

    2015-01-01

    The fragmentation of production across countries has become an important feature of the globalization in recent decades and is often conceptualized by the term "global value chains" (GVCs). When empirically investigating the GVCs, previous studies are mainly interested in knowing how global the GVCs are rather than how the GVCs look like. From a complex networks perspective, we use the World Input-Output Database (WIOD) to study the evolution of the global production system. We find that the industry-level GVCs are indeed not chain-like but are better characterized by the tree topology. Hence, we compute the global value trees (GVTs) for all the industries available in the WIOD. Moreover, we compute an industry importance measure based on the GVTs and compare it with other network centrality measures. Finally, we discuss some future applications of the GVTs. PMID:25978067

  12. Global Value Trees

    PubMed Central

    Zhu, Zhen; Puliga, Michelangelo; Cerina, Federica; Chessa, Alessandro; Riccaboni, Massimo

    2015-01-01

    The fragmentation of production across countries has become an important feature of the globalization in recent decades and is often conceptualized by the term “global value chains” (GVCs). When empirically investigating the GVCs, previous studies are mainly interested in knowing how global the GVCs are rather than how the GVCs look like. From a complex networks perspective, we use the World Input-Output Database (WIOD) to study the evolution of the global production system. We find that the industry-level GVCs are indeed not chain-like but are better characterized by the tree topology. Hence, we compute the global value trees (GVTs) for all the industries available in the WIOD. Moreover, we compute an industry importance measure based on the GVTs and compare it with other network centrality measures. Finally, we discuss some future applications of the GVTs. PMID:25978067

  13. How To Write a Municipal Tree Ordinance.

    ERIC Educational Resources Information Center

    Fazio, James R., Ed.

    1990-01-01

    At the heart of the Tree City USA program are four basic requirements: The community must have the following: (1) a tree board or department; (2) an annual community forestry program with financial provisions for trees and tree care; (3) an annual Arbor Day proclamation and observance; and (4) a tree ordinance. Sections of a model tree ordinance…

  14. Structural regression trees

    SciTech Connect

    Kramer, S.

    1996-12-31

    In many real-world domains the task of machine learning algorithms is to learn a theory for predicting numerical values. In particular several standard test domains used in Inductive Logic Programming (ILP) are concerned with predicting numerical values from examples and relational and mostly non-determinate background knowledge. However, so far no ILP algorithm except one can predict numbers and cope with nondeterminate background knowledge. (The only exception is a covering algorithm called FORS.) In this paper we present Structural Regression Trees (SRT), a new algorithm which can be applied to the above class of problems. SRT integrates the statistical method of regression trees into ILP. It constructs a tree containing a literal (an atomic formula or its negation) or a conjunction of literals in each node, and assigns a numerical value to each leaf. SRT provides more comprehensible results than purely statistical methods, and can be applied to a class of problems most other ILP systems cannot handle. Experiments in several real-world domains demonstrate that the approach is competitive with existing methods, indicating that the advantages are not at the expense of predictive accuracy.

  15. Insert tree completion system

    SciTech Connect

    Brands, K.W.; Ball, I.G.; Cegielski, E.J.; Gresham, J.S.; Saunders, D.N.

    1982-09-01

    This paper outlines the overall project for development and installation of a low-profile, caisson-installed subsea Christmas tree. After various design studies and laboratory and field tests of key components, a system for installation inside a 30-in. conductor was ordered in July 1978 from Cameron Iron Works Inc. The system is designed to have all critical-pressure-containing components below the mudline and, with the reduced profile (height) above seabed, provides for improved safety of satellite underwater wells from damage by anchors, trawl boards, and even icebergs. In addition to the innovative nature of the tree design, the completion includes improved 3 1/2-in. through flowline (TFL) pumpdown completion equipment with deep set safety valves and a dual detachable packer head for simplified workover capability. The all-hydraulic control system incorporates a new design of sequencing valve for both Christmas tree control and remote flowline connection. A semisubmersible drilling rig was used to initiate the first end flowline connection at the wellhead for subsequent tie-in to the prelaid, surface-towed, all-welded subsea pipeline bundle.

  16. The Effect of Sumac (Rhus coriaria L.)Powder on Serum Glycemic Status, ApoB, ApoA-I and Total Antioxidant Capacity in Type 2 Diabetic Patients

    PubMed Central

    Shidfar, Farzad; Rahideh, Seyedeh Tayebeh; Rajab, Asadollah; Khandozi, Nafise; Hosseini, Sharieh; Shidfar, Shahrzad; Mojab, Faraz

    2014-01-01

    Sumac (Rhus coriaria L.) is used as an herbal remedy in traditional medicine. The aim of this study was to determine the effects of sumac (R. coriaria) on serum glycemic status, apolipoprotein (apo) B, apoA-I and total antioxidant capacity (TAC) in type 2 diabetic patients. This double blind randomized controlled clinical trial was conducted on 41type 2 diabetic volunteers randomly assigned into 3g/day sumac powder (n=22) or placebo (n=19) groups over 3 months. Blood samples were collected before and after the intervention. Serum glucose and HbA1c were measured using enzymatic and turbidimetric inhibition immunoassay methods, respectively. ApoB, apoA-I and TAC were determined using turbidimetric immunoassay and spectrophotometric methods, respectively. There were signi?cant decreases in serum glucose and HbA1c and also apoB levels at the end of study compared with initial values (P< 0.0001, P= 0.002 and P< 0.0001,respectively). Also, there was a significant difference in HbA1c and TAC levels between placebo and sumac groups at the end of study (P< 0.05).In sumac group, there were significant increase in apoA-I and TAC(P< 0.0001) compared with initial values. The mean of differences of serum glucose, HbA1c, apoB, apoA-I, apoB/apoA-I ratio and TAC between groups were significant (P< 0.05). In conclusion, these results showed the favorite effect of sumac consumption on serum glycemic status, apoB, apoA-I and TAC levels in in type 2 diabetic patients. PMID:25587314

  17. The Effect of Sumac (Rhus coriaria L.)Powder on Serum Glycemic Status, ApoB, ApoA-I and Total Antioxidant Capacity in Type 2 Diabetic Patients.

    PubMed

    Shidfar, Farzad; Rahideh, Seyedeh Tayebeh; Rajab, Asadollah; Khandozi, Nafise; Hosseini, Sharieh; Shidfar, Shahrzad; Mojab, Faraz

    2014-01-01

    Sumac (Rhus coriaria L.) is used as an herbal remedy in traditional medicine. The aim of this study was to determine the effects of sumac (R. coriaria) on serum glycemic status, apolipoprotein (apo) B, apoA-I and total antioxidant capacity (TAC) in type 2 diabetic patients. This double blind randomized controlled clinical trial was conducted on 41type 2 diabetic volunteers randomly assigned into 3g/day sumac powder (n=22) or placebo (n=19) groups over 3 months. Blood samples were collected before and after the intervention. Serum glucose and HbA1c were measured using enzymatic and turbidimetric inhibition immunoassay methods, respectively. ApoB, apoA-I and TAC were determined using turbidimetric immunoassay and spectrophotometric methods, respectively. There were signi?cant decreases in serum glucose and HbA1c and also apoB levels at the end of study compared with initial values (P< 0.0001, P= 0.002 and P< 0.0001,respectively). Also, there was a significant difference in HbA1c and TAC levels between placebo and sumac groups at the end of study (P< 0.05).In sumac group, there were significant increase in apoA-I and TAC(P< 0.0001) compared with initial values. The mean of differences of serum glucose, HbA1c, apoB, apoA-I, apoB/apoA-I ratio and TAC between groups were significant (P< 0.05). In conclusion, these results showed the favorite effect of sumac consumption on serum glycemic status, apoB, apoA-I and TAC levels in in type 2 diabetic patients. PMID:25587314

  18. From event-labeled gene trees to species trees

    PubMed Central

    2012-01-01

    Background Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x represents a speciation or a duplication. This problem appears in the context of analyzing orthology data. Results We show that S is a species tree for T if and only if S displays all rooted triples of T that have three distinct species as their leaves and are rooted in a speciation vertex. A valid reconciliation map can then be found in polynomial time. Simulated data shows that the event-labeled gene trees convey a large amount of information on underlying species trees, even for a large percentage of losses. Conclusions The knowledge of event labels in a gene tree strongly constrains the possible species tree and, for a given species tree, also the possible reconciliation maps. Nevertheless, many degrees of freedom remain in the space of feasible solutions. In order to disambiguate the alternative solutions additional external constraints as well as optimization criteria could be employed.

  19. Save a Tree

    NASA Astrophysics Data System (ADS)

    Williams, Kathryn R.

    1999-10-01

    Starting in September 1925, JCE reproduced pictures of famous chemists or chemistry-related works of art as frontispieces. Often, the Journal included a biography or other article about the picture. The August 1945 frontispiece featured the largest cork oak in the United States. An accompanying article described the goals of the Cork Project to plant cork trees in suitable locations in the U.S., to compensate for uncertain European and African sources during World War II. The final frontispiece appeared in December 1956. To view supplementary material, please refer to JCE Online's supplementary links.

  20. Barking up the Right Tree

    ERIC Educational Resources Information Center

    Houston, Paul D.

    2006-01-01

    There is a childhood saying about a confused dog who thinks he sees a possum in a tree. The problem is that the possum is actually in a different tree so the dog barks up the wrong tree. American education is constantly playing both dog and possum. Sometimes they are the prey, and sometimes they are just confused about what and where the prey is.

  1. Human decision error (HUMDEE) trees

    SciTech Connect

    Ostrom, L.T.

    1993-08-01

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

  2. Tree Modeling and Dynamics Simulation

    NASA Astrophysics Data System (ADS)

    Tian-shuang, Fu; Yi-bing, Li; Dong-xu, Shen

    This paper introduces the theory about tree modeling and dynamic movements simulation in computer graphics. By comparing many methods we choose Geometry-based rendering as our method. The tree is decomposed into branches and leaves, under the rotation and quaternion methods we realize the tree animation and avoid the Gimbals Lock in Euler rotation. We take Orge 3D as render engine, which has good graphics programming ability. By the end we realize the tree modeling and dynamic movements simulation, achieve realistic visual quality with little computation cost.

  3. Distributed Merge Trees

    SciTech Connect

    Morozov, Dmitriy; Weber, Gunther

    2013-01-08

    Improved simulations and sensors are producing datasets whose increasing complexity exhausts our ability to visualize and comprehend them directly. To cope with this problem, we can detect and extract significant features in the data and use them as the basis for subsequent analysis. Topological methods are valuable in this context because they provide robust and general feature definitions. As the growth of serial computational power has stalled, data analysis is becoming increasingly dependent on massively parallel machines. To satisfy the computational demand created by complex datasets, algorithms need to effectively utilize these computer architectures. The main strength of topological methods, their emphasis on global information, turns into an obstacle during parallelization. We present two approaches to alleviate this problem. We develop a distributed representation of the merge tree that avoids computing the global tree on a single processor and lets us parallelize subsequent queries. To account for the increasing number of cores per processor, we develop a new data structure that lets us take advantage of multiple shared-memory cores to parallelize the work on a single node. Finally, we present experiments that illustrate the strengths of our approach as well as help identify future challenges.

  4. DIF Trees: Using Classification Trees to Detect Differential Item Functioning

    ERIC Educational Resources Information Center

    Vaughn, Brandon K.; Wang, Qiu

    2010-01-01

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

  5. Relating phylogenetic trees to transmission trees of infectious disease outbreaks.

    PubMed

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

    2013-11-01

    Transmission events are the fundamental building blocks of the dynamics of any infectious disease. Much about the epidemiology of a disease can be learned when these individual transmission events are known or can be estimated. Such estimations are difficult and generally feasible only when detailed epidemiological data are available. The genealogy estimated from genetic sequences of sampled pathogens is another rich source of information on transmission history. Optimal inference of transmission events calls for the combination of genetic data and epidemiological data into one joint analysis. A key difficulty is that the transmission tree, which describes the transmission events between infected hosts, differs from the phylogenetic tree, which describes the ancestral relationships between pathogens sampled from these hosts. The trees differ both in timing of the internal nodes and in topology. These differences become more pronounced when a higher fraction of infected hosts is sampled. We show how the phylogenetic tree of sampled pathogens is related to the transmission tree of an outbreak of an infectious disease, by the within-host dynamics of pathogens. We provide a statistical framework to infer key epidemiological and mutational parameters by simultaneously estimating the phylogenetic tree and the transmission tree. We test the approach using simulations and illustrate its use on an outbreak of foot-and-mouth disease. The approach unifies existing methods in the emerging field of phylodynamics with transmission tree reconstruction methods that are used in infectious disease epidemiology. PMID:24037268

  6. 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.

  7. Paint, lacquer, and varnish remover poisoning

    MedlinePLUS

    ... and monitor the person's vital signs, including temperature, pulse, breathing rate, and blood pressure. Symptoms will be treated as appropriate. The person may receive: Breathing support, including tube through the mouth into the lungs, and breathing ...

  8. Looking/Learning Drawing: Trees.

    ERIC Educational Resources Information Center

    Hurwitz, Al; Blume, Sharon

    1985-01-01

    Secondary students are asked to study and compare three reproductions--Van Gogh's "Grove of Cypresses," Da Vinci's "Study of a Tree," and Mondrian's "Tree II." The activity will help students develop their powers of observation and analysis, powers that can be applied to their own drawings. (RM)

  9. The limits to tree height.

    PubMed

    Koch, George W; Sillett, Stephen C; Jennings, Gregory M; Davis, Stephen D

    2004-04-22

    Trees grow tall where resources are abundant, stresses are minor, and competition for light places a premium on height growth. The height to which trees can grow and the biophysical determinants of maximum height are poorly understood. Some models predict heights of up to 120 m in the absence of mechanical damage, but there are historical accounts of taller trees. Current hypotheses of height limitation focus on increasing water transport constraints in taller trees and the resulting reductions in leaf photosynthesis. We studied redwoods (Sequoia sempervirens), including the tallest known tree on Earth (112.7 m), in wet temperate forests of northern California. Our regression analyses of height gradients in leaf functional characteristics estimate a maximum tree height of 122-130 m barring mechanical damage, similar to the tallest recorded trees of the past. As trees grow taller, increasing leaf water stress due to gravity and path length resistance may ultimately limit leaf expansion and photosynthesis for further height growth, even with ample soil moisture. PMID:15103376

  10. Mixtures of (Constrained) Ultrametric Trees.

    ERIC Educational Resources Information Center

    Wedel, Michel; DeSarbo, Wayne S.

    1998-01-01

    Presents a method for the estimation of ultrametric trees calibrated on subjects' pairwise proximity judgments of stimuli, capturing subject heterogeneity using a finite mixture formulation. An empirical example from published data shows the ability to deal with external constraints on the tree topology. (Author/SLD)

  11. Hazard Tree Management for Camps.

    ERIC Educational Resources Information Center

    Kong, Earl

    2002-01-01

    The principles behind a camp's hazard tree program are, first, identifying and removing those hazards that offer a clear, immediate threat, and then creating a management plan for the other trees. The plan should be written and contain goals and objectives, field evaluations, and treatments. Follow-up evaluations should be done annually and after

  12. Hydrocarbons from plants and trees

    SciTech Connect

    Calvin, M.

    1982-07-01

    The way energy was used in the US in 1980 was examined. A diagram shows the development of energy from its source to its end use. The following are described: the carbon dioxide problem - the greenhouse effect, sugar cane as an energy source, hydrocarbon-producing plants and trees, and isoprenoids from plants and trees. (MHR)

  13. Genome Trees from Conservation Profiles

    PubMed Central

    Tekaia, Fredj; Yeramian, Edouard

    2005-01-01

    The concept of the genome tree depends on the potential evolutionary significance in the clustering of species according to similarities in the gene content of their genomes. In this respect, genome trees have often been identified with species trees. With the rapid expansion of genome sequence data it becomes of increasing importance to develop accurate methods for grasping global trends for the phylogenetic signals that mutually link the various genomes. We therefore derive here the methodological concept of genome trees based on protein conservation profiles in multiple species. The basic idea in this derivation is that the multi-component presence-absence protein conservation profiles permit tracking of common evolutionary histories of genes across multiple genomes. We show that a significant reduction in informational redundancy is achieved by considering only the subset of distinct conservation profiles. Beyond these basic ideas, we point out various pitfalls and limitations associated with the data handling, paving the way for further improvements. As an illustration for the methods, we analyze a genome tree based on the above principles, along with a series of other trees derived from the same data and based on pair-wise comparisons (ancestral duplication-conservation and shared orthologs). In all trees we observe a sharp discrimination between the three primary domains of life: Bacteria, Archaea, and Eukarya. The new genome tree, based on conservation profiles, displays a significant correspondence with classically recognized taxonomical groupings, along with a series of departures from such conventional clusterings. PMID:16362074

  14. The tree of one percent

    PubMed Central

    Dagan, Tal; Martin, William

    2006-01-01

    Two significant evolutionary processes are fundamentally not tree-like in nature - lateral gene transfer among prokaryotes and endosymbiotic gene transfer (from organelles) among eukaryotes. To incorporate such processes into the bigger picture of early evolution, biologists need to depart from the preconceived notion that all genomes are related by a single bifurcating tree. PMID:17081279

  15. Tree Hydraulics: How Sap Rises

    ERIC Educational Resources Information Center

    Denny, Mark

    2012-01-01

    Trees transport water from roots to crown--a height that can exceed 100 m. The physics of tree hydraulics can be conveyed with simple fluid dynamics based upon the Hagen-Poiseuille equation and Murray's law. Here the conduit structure is modelled as conical pipes and as branching pipes. The force required to lift sap is generated mostly by

  16. Tree Hydraulics: How Sap Rises

    ERIC Educational Resources Information Center

    Denny, Mark

    2012-01-01

    Trees transport water from roots to crown--a height that can exceed 100 m. The physics of tree hydraulics can be conveyed with simple fluid dynamics based upon the Hagen-Poiseuille equation and Murray's law. Here the conduit structure is modelled as conical pipes and as branching pipes. The force required to lift sap is generated mostly by…

  17. Tree preserving embedding.

    PubMed

    Shieh, Albert D; Hashimoto, Tatsunori B; Airoldi, Edoardo M

    2011-10-11

    The goal of dimensionality reduction is to embed high-dimensional data in a low-dimensional space while preserving structure in the data relevant to exploratory data analysis such as clusters. However, existing dimensionality reduction methods often either fail to separate clusters due to the crowding problem or can only separate clusters at a single resolution. We develop a new approach to dimensionality reduction: tree preserving embedding. Our approach uses the topological notion of connectedness to separate clusters at all resolutions. We provide a formal guarantee of cluster separation for our approach that holds for finite samples. Our approach requires no parameters and can handle general types of data, making it easy to use in practice and suggesting new strategies for robust data visualization. PMID:21949369

  18. 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...

  19. 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...

  20. 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...

  1. 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...

  2. Tree reconstruction from partial orders

    SciTech Connect

    Kannan, S.K.; Warnow, T.J.

    1993-03-01

    The problem of constructing trees given a matrix of interleaf distances is motivated by applications in computational evolutionary biology and linguistics. The general problem is to find an edge-weighted tree which most closely approximates the distance matrix. Although the construction problem is easy when the tree exactly fits the distance matrix, optimization problems under all popular criteria are either known or conjectured to be NP-complete. In this paper we consider the related problem where we are given a partial order on the pairwise distances, and wish to construct (if possible) an edge-weighted tree realizing the partial order. In particular we are interested in partial orders which arise from experiments on triples of species, which determine either a linear ordering of the three pairwise distances (called Total Order Model or TOM experiments) or only the pair(s) of minimum distance apart (called Partial Order Model or POM experiments). The POM and TOM experimental model is inspired by the model proposed by Kannan, Lawler, and Warnow for constructing trees from experiments which determine the rooted topology for any triple of species. We examine issues of construction of trees and consistency of TOM and POM experiments, where the trees may either be weighted or unweighted. Using these experiments to construct unweighted trees without nodes of degree two is motivated by a similar problem studied by Winkler, called the Discrete Metric Realization problem, which he showed to be strongly NP-hard. We have the following results: Determining consistency of a set of TOM or POM experiments is NP-Complete whether the tree is weighted or constrained to be unweighted and without degree two nodes. We can construct unweighted trees without degree two nodes from TOM experiments in optimal O(n{sup 3}) time and from POM experiments in O(n{sup 4}) time.

  3. Tree reconstruction from partial orders

    SciTech Connect

    Kannan, S.K. ); Warnow, T.J. )

    1993-01-01

    The problem of constructing trees given a matrix of interleaf distances is motivated by applications in computational evolutionary biology and linguistics. The general problem is to find an edge-weighted tree which most closely approximates the distance matrix. Although the construction problem is easy when the tree exactly fits the distance matrix, optimization problems under all popular criteria are either known or conjectured to be NP-complete. In this paper we consider the related problem where we are given a partial order on the pairwise distances, and wish to construct (if possible) an edge-weighted tree realizing the partial order. In particular we are interested in partial orders which arise from experiments on triples of species, which determine either a linear ordering of the three pairwise distances (called Total Order Model or TOM experiments) or only the pair(s) of minimum distance apart (called Partial Order Model or POM experiments). The POM and TOM experimental model is inspired by the model proposed by Kannan, Lawler, and Warnow for constructing trees from experiments which determine the rooted topology for any triple of species. We examine issues of construction of trees and consistency of TOM and POM experiments, where the trees may either be weighted or unweighted. Using these experiments to construct unweighted trees without nodes of degree two is motivated by a similar problem studied by Winkler, called the Discrete Metric Realization problem, which he showed to be strongly NP-hard. We have the following results: Determining consistency of a set of TOM or POM experiments is NP-Complete whether the tree is weighted or constrained to be unweighted and without degree two nodes. We can construct unweighted trees without degree two nodes from TOM experiments in optimal O(n[sup 3]) time and from POM experiments in O(n[sup 4]) time.

  4. A Cost Benefit Analysis of Urban Trees

    SciTech Connect

    Akbari, Hashem

    1997-09-01

    Urban shade trees offer significant benefits in reducing building air- conditioning and improving urban air quality by reducing smog. The savings associated with these benefits varies by climate regions and can be up to $200 per tree. The cost of planting trees and maintaining them can vary from $10 to $500 per tree. Tree planting programs can be designed offer savings to communities that plant trees.

  5. Through bore subsea christmas trees

    SciTech Connect

    Huber, D.S.; Simmers, G.F.C.; Johnson, C.S.

    1985-01-01

    The workovers of subsea completed wells are expensive and time consuming as even the most routine tasks must be carried out by a semi-submersible. This paper describes the economic, safety and operational advantages which led to the development and successful first installation of 'through bore' subsea production trees. The conventional wet subsea trees have proved to be very reliable over the past ten years of operation in the Argyll, Duncan and Innes fields, however the completion strings require pulling on the average about once every three to five years. The conventional subsea tree/tubing hanger set up design requires the tree to be tripped and a rig BOP stack run to pull the tubing. This operation is time consuming, very weather sensitive and leaves the well temporarily without a well control stack on the wellhead. The 7 1/16'' 'through bore' subsea tree was developed to minimize the tubing pulling workover time and several trees have been run successfully since the latter part of 1984. The time saving on a tubing pulling workover is three days. In addition, the design considerably reduces the hazards and equipment damage risk inherent in the conventional design. Hamilton Brothers and National Supply Company in Aberdeen designed the equipment which must be considered a new generation of subsea production trees.

  6. Terrestrial apes and phylogenetic trees

    PubMed Central

    Arsuaga, Juan Luis

    2010-01-01

    The image that best expresses Darwins thinking is the tree of life. However, Darwins human evolutionary tree lacked almost everything because only the Neanderthals were known at the time and they were considered one extreme expression of our own species. Darwin believed that the root of the human tree was very deep and in Africa. It was not until 1962 that the root was shown to be much more recent in time and definitively in Africa. On the other hand, some neo-Darwinians believed that our family tree was not a tree, because there were no branches, but, rather, a straight stem. The recent years have witnessed spectacular discoveries in Africa that take us close to the origin of the human tree and in Spain at Atapuerca that help us better understand the origin of the Neanderthals as well as our own species. The final form of the tree, and the number of branches, remains an object of passionate debate. PMID:20445090

  7. Falls from trees and tree associated injuries in rural Melanesians.

    PubMed

    Barss, P; Dakulala, P; Doolan, M

    Falls from trees and other tree related injuries are the most common cause of trauma in some parts of rural Melanesia. A four year review of all admissions for trauma to the Provincial Hospital at Alotau, Milne Bay Province, Papua New Guinea, showed that 27% were due to falls from trees, and a further 10% were due to related injuries, such as being struck by a falling branch or a coconut. A questionnaire distributed to rural health centres showed that during the study period at least 28 villagers died from falls from trees before reaching hospital. Head and chest trauma were common causes of death. Many injured patients were boys. Forearm fractures were the most common injuries, but more serious injuries were also frequently encountered. Trees responsible for most deaths and injuries included the coconut palm, betel palm, mango, and breadfruit. There are many strategies for preventing such injuries; perhaps the most important is to stop small boys climbing tall trees. Such falls are a serious occupational hazard for many subsistence farmers. PMID:6440619

  8. Implementing Municipal Tree Planting: Los Angeles Million-Tree Initiative

    NASA Astrophysics Data System (ADS)

    Pincetl, Stephanie

    2010-02-01

    Urban forests are increasingly being seen as an important infrastructure that can help cities remediate their environmental impacts. This work reports on the first steps in implementing a million tree program in Los Angeles and the ways such a biogeniclivinginfrastructure has been approached. Numbers of studies have been done to quantify the benefits of urban forests, but little has been written on the process of implementing urban tree planting programs. The investigative methods were primarily qualitative, involving interviews, attending meetings and conducting literature reviews. Results indicate that multiple nonprofit and city agency programs are involved in planting and maintaining trees and this has required coordination among groups that here-to-fore were unaccustomed to having to collaborate. The main finding that emerge from this research is that the implementation of such a program in Los Angeles is more complicated than it may seem due to several interacting factors: the need to rely on multiple public and private organizations to put trees into the ground and to maintain them; coordination of these multiple efforts must be centralized, but requires a great deal of time and effort and maybe resisted by some of the partners; funding for planting and long term maintenance must be pieced together from multiple sources; acceptance of trees by residents varies by neighborhood as does tree canopy cover; appropriate nursery supply can be limited; the location of the program within the city administration is determined by who initiates the program.

  9. A valuable tree by gum!

    PubMed

    Forrest, M

    2000-06-01

    Which majestic ornamental tree, conspicuous in the Australian landscape, has ten million hectares in cultivation worldwide--yielding timber, fuel, essential oil and cut foliage? It could only be eucalyptus. PMID:11190248

  10. Fault Tree Analysis: A Bibliography

    NASA Technical Reports Server (NTRS)

    2000-01-01

    Fault tree analysis is a top-down approach to the identification of process hazards. It is as one of the best methods for systematically identifying an graphically displaying the many ways some things can go wrong. This bibliography references 266 documents in the NASA STI Database that contain the major concepts. fault tree analysis, risk an probability theory, in the basic index or major subject terms. An abstract is included with most citations, followed by the applicable subject terms.

  11. Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies.

    PubMed

    Leach, Adam D; Banbury, Barbara L; Felsenstein, Joseph; de Oca, Adrin Nieto-Montes; Stamatakis, Alexandros

    2015-11-01

    Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practises for using these data in phylogenetics is lacking. We use computer simulations, and new double digest RADseq (ddRADseq) data for the lizard family Phrynosomatidae, to investigate the accuracy of RAD loci for phylogenetic inference. We compare the two primary ways RAD loci are used during phylogenetic analysis, including the analysis of full sequences (i.e., SNPs together with invariant sites), or the analysis of SNPs on their own after excluding invariant sites. We find that using full sequences rather than just SNPs is preferable from the perspectives of branch length and topological accuracy, but not of computational time. We introduce two new acquisition bias corrections for dealing with alignments composed exclusively of SNPs, a conditional likelihood method and a reconstituted DNA approach. The conditional likelihood method conditions on the presence of variable characters only (the number of invariant sites that are unsampled but known to exist is not considered), while the reconstituted DNA approach requires the user to specify the exact number of unsampled invariant sites prior to the analysis. Under simulation, branch length biases increase with the amount of missing data for both acquisition bias correction methods, but branch length accuracy is much improved in the reconstituted DNA approach compared to the conditional likelihood approach. Phylogenetic analyses of the empirical data using concatenation or a coalescent-based species tree approach provide strong support for many of the accepted relationships among phrynosomatid lizards, suggesting that RAD loci contain useful phylogenetic signal across a range of divergence times despite the presence of missing data. Phylogenetic analysis of RAD loci requires careful attention to model assumptions, especially if downstream analyses depend on branch lengths. PMID:26227865

  12. Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies

    PubMed Central

    Leaché, Adam D.; Banbury, Barbara L.; Felsenstein, Joseph; de Oca, Adrián nieto-Montes; Stamatakis, Alexandros

    2015-01-01

    Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing in part to their ubiquity throughout the genome and ease of collection. Restriction site associated DNA sequencing (RADseq) methods are becoming increasingly popular for SNP data collection, but an assessment of the best practises for using these data in phylogenetics is lacking. We use computer simulations, and new double digest RADseq (ddRADseq) data for the lizard family Phrynosomatidae, to investigate the accuracy of RAD loci for phylogenetic inference. We compare the two primary ways RAD loci are used during phylogenetic analysis, including the analysis of full sequences (i.e., SNPs together with invariant sites), or the analysis of SNPs on their own after excluding invariant sites. We find that using full sequences rather than just SNPs is preferable from the perspectives of branch length and topological accuracy, but not of computational time. We introduce two new acquisition bias corrections for dealing with alignments composed exclusively of SNPs, a conditional likelihood method and a reconstituted DNA approach. The conditional likelihood method conditions on the presence of variable characters only (the number of invariant sites that are unsampled but known to exist is not considered), while the reconstituted DNA approach requires the user to specify the exact number of unsampled invariant sites prior to the analysis. Under simulation, branch length biases increase with the amount of missing data for both acquisition bias correction methods, but branch length accuracy is much improved in the reconstituted DNA approach compared to the conditional likelihood approach. Phylogenetic analyses of the empirical data using concatenation or a coalescent-based species tree approach provide strong support for many of the accepted relationships among phrynosomatid lizards, suggesting that RAD loci contain useful phylogenetic signal across a range of divergence times despite the presence of missing data. Phylogenetic analysis of RAD loci requires careful attention to model assumptions, especially if downstream analyses depend on branch lengths. PMID:26227865

  13. Parallel TreeSPH

    NASA Astrophysics Data System (ADS)

    Dav, Romeel; Dubinski, John; Hernquist, Lars

    1997-08-01

    We describe PTreeSPH, a gravity treecode combined with an SPH hydrodynamics code designed for parallel supercomputers having distributed memory. Our computational algorithm is based on the popular TreeSPH code of Hernquist & Katz (1989)[ApJS, 70, 419]. PTreeSPH utilizes a domain decomposition procedure and a synchronous hypercube communication paradigm to build self-contained subvolumes of the simulation on each processor at every timestep. Computations then proceed in a manner analogous to a serial code. We use the Message Passing Interface (MPI) communications package, making our code easily portable to a variety of parallel systems. PTreeSPH uses individual smoothing lengths and timesteps, with a communication algorithm designed to minimize exchange of information while still providing all information required to accurately perform SPH computations. We have incorporated periodic boundary conditions with forces calculated using a quadrupole Ewald summation method, and comoving integration under a variety of cosmologies. Following algorithms presented in Katz et al. (1996)[ApJS, 105, 19], we have also included radiative cooling, heating from a parameterized ionizing background, and star formation. A cosmological simulation from z = 49 to z = 2 with 64 3 gas particles and 64 3 dark matter particles requires 1800 node-hours on a Cray T3D, with a communications overhead of 8%, load balanced to ? 95% level. When used on the new Cray T3E, this code will be capable of performing cosmological hydrodynamical simulations down to z = 0 with 2 10 6 particles, or to z = 2 with 10 7 particles, in a reasonable amount of time. Even larger simulations will be practical in situations where the matter is not highly clustered or when periodic boundaries are not required.

  14. Generic physical protection logic trees

    SciTech Connect

    Paulus, W.K.

    1981-10-01

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

  15. Tunnel of the California Tunnel Tree

    USGS Multimedia Gallery

    In this image, the tunnel through the California Tunnel Tree may be seen. The tunnel was cut through the giant sequoia tree in 1895 to allow coaches, and eventually cars, to drive through the tree as part of a marketing stunt. The California Tunnel Tree is the only living giant sequoia with a t...

  16. Critical wind speed at which trees break

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  17. How To Select and Plant a Tree.

    ERIC Educational Resources Information Center

    Fazio, James R., Ed.

    1991-01-01

    This bulletin furnishes information about selecting and planting trees. The tree selection process includes being aware of the physical characteristics of bare root seedlings, containerized seedlings, balled and burlapped, or potted trees and determining the proper size and root ball proportions. The section on tree planting discusses how to: (1)…

  18. Growing a Forest for the Trees.

    ERIC Educational Resources Information Center

    Growing Ideas, 2001

    2001-01-01

    Describes a tree studies program in a fourth-grade classroom. Students collected local tree seeds and seeds from supermarket fruits, researched growing conditions, and grew seeds under various conditions. Students kept journals on local trees, observing seed dispersal mechanisms and examining rings on trunk slices. Inquiry-based tree studies

  19. Tree Growth Rings: What They Tell Us.

    ERIC Educational Resources Information Center

    Sunal, Dennis W.; Sunal, Cynthia Szymanski

    1991-01-01

    Activities in which students can learn to determine the history of a tree from the growth pattern recorded in the rings of a cross-section of a tree are described. Activities include background information, objectives, a list of needed materials per group, and procedures. Cross-sections of four different tree types are included if real tree

  20. Microwave sensing of tree trunks

    NASA Astrophysics Data System (ADS)

    Jezova, Jana; Mertens, Laurence; Lambot, Sebastien

    2015-04-01

    The main subject of this research is the observation of the inner part of living tree trunks using ground-penetrating radar (GPR). Trees are everyday part of human life and therefore it is important to pay attention to the tree conditions. The most obvious consequence of the poor tree condition is dead or injury caused by falling tree. The trunk internal structure is divided into three main parts: heartwood, sapwood and bark, which make this medium highly anisotropic and heterogeneous. Furthermore, the properties of the wood are not only specie-dependent but also depend on genetic and on environmental conditions. In urban areas the main problem for the stability of the trees relies in the apparition of decays provoked by fungi, insect or birds. This results in cavities or decreasing of the support capacity of the tree. GPR has proved itself to be a very powerful electromagnetic tool for non-destructive detection of buried objects. Since the beginning of the 20th century it has been used in several different areas (archaeology, landmine detection, civil engineering, ...). GPR uses the principle of the scattering of the electromagnetic waves that are radiated from a transmitting antenna. Then the waves propagate through the medium and are reflected from the object and then they are received by a receiving antenna. The velocity of the scattered signal is determined primarily by the permittivity of the material. The optimal functionality of the GPR was investigated using the numerical simulation tool gprMax2D. This tool is based on a Finite-Difference Time-Domain (FDTD) numerical model. Subsequently, the GPR functionality was tested using the laboratory model of a decayed tree trunk. Afterwards, the results and lessons learnt in the simplified tests will be used in the processing of the real data and will help to achieve deeper understanding of them. The laboratory model of the tree trunk was made by plastic or carton pipes and filled by sand. Space inside the model was divided into three sections to separate parts with different moisture (heartwood and sapwood) or empty space (decays). For easier manipulation with the antenna we developed a special ruler for measuring the distance along the scans. Instead of the surveying wheel we read the distance with a camera, which was fixed on the antenna and focused on the ruler with a binary pattern. Hence, during whole measurement and the data processing we were able to identify an accurate position on the tree in view of the scan. Some preliminary measurements on the trees were also conducted. They were performed using a GSSI 900 MHz antenna. Several tree species (beech, horse-chestnut, birch, ...) in Louvain-la-Neuve and Brussels, Belgium, have been investigated to see the internal structure of the tree decays. The measurements were carried out mainly by circumferential measurement around the trunk and also by vertical measurement along the trunk for approximate detection of the cavity. The comparison between the numerical simulations, simplified tree trunk model and real data from trees is presented. This research is funded by the Fonds de la Recherche Scientifique (FNRS, Belgium) and benefits from networking activities carried out within the EU COST Action TU1208 "Civil Engineering Applications of Ground Penetrating Radar".

  1. Sussing Merger Trees: The Merger Trees Comparison Project

    NASA Astrophysics Data System (ADS)

    Srisawat, Chaichalit; Knebe, Alexander; Pearce, Frazer R.; Schneider, Aurel; Thomas, Peter A.; Behroozi, Peter; Dolag, Klaus; Elahi, Pascal J.; Han, Jiaxin; Helly, John; Jing, Yipeng; Jung, Intae; Lee, Jaehyun; Mao, Yao-Yuan; Onions, Julian; Rodriguez-Gomez, Vicente; Tweed, Dylan; Yi, Sukyoung K.

    2013-11-01

    Merger trees follow the growth and merger of dark-matter haloes over cosmic history. As well as giving important insights into the growth of cosmic structure in their own right, they provide an essential backbone to semi-analytic models of galaxy formation. This paper is the first in a series to arise from the Sussing Merger Trees Workshop in which 10 different tree-building algorithms were applied to the same set of halo catalogues and their results compared. Although many of these codes were similar in nature, all algorithms produced distinct results. Our main conclusions are that a useful merger-tree code should possess the following features: (i) the use of particle IDs to match haloes between snapshots; (ii) the ability to skip at least one, and preferably more, snapshots in order to recover subhaloes that are temporarily lost during merging; (iii) the ability to cope with (and ideally smooth out) large, temporary fluctuations in halo mass. Finally, to enable different groups to communicate effectively, we defined a common terminology that we used when discussing merger trees and we encourage others to adopt the same language. We also specified a minimal output format to record the results.

  2. Genealogical trees from genetic distances

    NASA Astrophysics Data System (ADS)

    Prignano, L.; Serva, M.

    2009-06-01

    In a population with haploid reproduction any individual has a single parent in the previous generation. If all genealogical distances among pairs of individuals (generations from the closest common ancestor) are known it is possible to exactly reconstruct their genealogical tree. Unfortunately, in most cases, genealogical distances are unknown and only genetic distances are available. The genetic distance between two individuals is measurable from differences in mtDNA (mitochondrial DNA) since in the case of humans or other complex organisms mtDNA is transmitted in a haploid manner. An analogous distance can be also computed for languages where it may be measured from lexical differences, in this case, nevertheless, haploid reproduction is only a raw approximation. Assuming a constant rate of mutation, these genetic distances are random and proportional only on average to genealogical ones. The reconstruction of the genealogical tree from the available genetic distances is forceful imprecise. In this paper we try to quantify the error one may commit in the reconstruction of the tree for different degrees of randomness. The errors may concern both topology of the tree (the branching hierarchy) and, in case of correct topology, the proportions of the tree (length of various branches).

  3. New program controls tree management

    SciTech Connect

    Beaty, W.

    1995-02-01

    Senior management of TransAlta Utilities Corp. (TAU) Calgary, Alberta, Canada, was highly dissatisfied with the fact that even though the distribution line clearance budget had been increased an average 35 percent a year between 1978 and 1984, there were few if any discernible positive results. Tree-related power outages kept increasing and budget requests from the field kept increasing. In searching for a solution TAU had to deal with the concept that the right level of funding can only be determined through an inventory of tree work. This inventory is comprised of two factors, the number of trees in proximity to the power lines and the local growth rates. Based on the inventory of a hired consultant, a 12-year budget projection was established. The period covered entailed a six-year, first-cycle or catch up phase, and a six-year, second-cycle maintenance phase. In implementing the new vegetation management program in 1986, TAU decided to contact each landowner directly to obtain consent to undertake the tree work. The intent was to reduce the risk of claims while maximizing tree removals. Complaints and claims were dramatically reduced and currently run at about one per 1,000 landowners and budgets have dropped back to the 1985 levels as predicted for the maintenance phase.

  4. Tree Growth Stage and Environment after Pathogen Inoculation Alters Susceptibility of Pear Trees to Phytophthora Canker

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We investigated whether growth stage of pear (Pyrus communis) tree rootstock and environment after inoculation with Phytophthora syringae influences tree susceptibility to infection. Trees at different stages of dormancy development were inoculated with the pathogen and maintained in different condi...

  5. Mapping tree density at a global scale.

    PubMed

    Crowther, T W; Glick, H B; Covey, K R; Bettigole, C; Maynard, D S; Thomas, S M; Smith, J R; Hintler, G; Duguid, M C; Amatulli, G; Tuanmu, M-N; Jetz, W; Salas, C; Stam, C; Piotto, D; Tavani, R; Green, S; Bruce, G; Williams, S J; Wiser, S K; Huber, M O; Hengeveld, G M; Nabuurs, G-J; Tikhonova, E; Borchardt, P; Li, C-F; Powrie, L W; Fischer, M; Hemp, A; Homeier, J; Cho, P; Vibrans, A C; Umunay, P M; Piao, S L; Rowe, C W; Ashton, M S; Crane, P R; Bradford, M A

    2015-09-10

    The global extent and distribution of forest trees is central to our understanding of the terrestrial biosphere. We provide the first spatially continuous map of forest tree density at a global scale. This map reveals that the global number of trees is approximately 3.04 trillion, an order of magnitude higher than the previous estimate. Of these trees, approximately 1.39 trillion exist in tropical and subtropical forests, with 0.74 trillion in boreal regions and 0.61 trillion in temperate regions. Biome-level trends in tree density demonstrate the importance of climate and topography in controlling local tree densities at finer scales, as well as the overwhelming effect of humans across most of the world. Based on our projected tree densities, we estimate that over 15 billion trees are cut down each year, and the global number of trees has fallen by approximately 46% since the start of human civilization. PMID:26331545

  6. Mapping tree density at a global scale

    NASA Astrophysics Data System (ADS)

    Crowther, T. W.; Glick, H. B.; Covey, K. R.; Bettigole, C.; Maynard, D. S.; Thomas, S. M.; Smith, J. R.; Hintler, G.; Duguid, M. C.; Amatulli, G.; Tuanmu, M.-N.; Jetz, W.; Salas, C.; Stam, C.; Piotto, D.; Tavani, R.; Green, S.; Bruce, G.; Williams, S. J.; Wiser, S. K.; Huber, M. O.; Hengeveld, G. M.; Nabuurs, G.-J.; Tikhonova, E.; Borchardt, P.; Li, C.-F.; Powrie, L. W.; Fischer, M.; Hemp, A.; Homeier, J.; Cho, P.; Vibrans, A. C.; Umunay, P. M.; Piao, S. L.; Rowe, C. W.; Ashton, M. S.; Crane, P. R.; Bradford, M. A.

    2015-09-01

    The global extent and distribution of forest trees is central to our understanding of the terrestrial biosphere. We provide the first spatially continuous map of forest tree density at a global scale. This map reveals that the global number of trees is approximately 3.04 trillion, an order of magnitude higher than the previous estimate. Of these trees, approximately 1.39 trillion exist in tropical and subtropical forests, with 0.74 trillion in boreal regions and 0.61 trillion in temperate regions. Biome-level trends in tree density demonstrate the importance of climate and topography in controlling local tree densities at finer scales, as well as the overwhelming effect of humans across most of the world. Based on our projected tree densities, we estimate that over 15 billion trees are cut down each year, and the global number of trees has fallen by approximately 46% since the start of human civilization.

  7. Measurement of tree canopy architecture

    NASA Technical Reports Server (NTRS)

    Martens, S. N.; Ustin, S. L.; Norman, J. M.

    1991-01-01

    The lack of accurate extensive geometric data on tree canopies has retarded development and validation of radiative transfer models. A stratified sampling method was devised to measure the three-dimensional geometry of 16 walnut trees which had received irrigation treatments of either 100 or 33 per cent of evapotranspirational (ET) demand for the previous two years. Graphic reconstructions of the three-dimensional geometry were verified by 58 independent measurements. The distributions of stem- and leaf-size classes, lengths, and angle classes were determined and used to calculate leaf area index (LAI), stem area, and biomass. Reduced irrigation trees have lower biomass of stems, leaves and fruit, lower LAI, steeper leaf angles and altered biomass allocation to large stems. These data can be used in ecological models that link canopy processes with remotely sensed measurements.

  8. Coalescent Histories for Lodgepole Species Trees.

    PubMed

    Disanto, Filippo; Rosenberg, Noah A

    2015-10-01

    Coalescent histories are combinatorial structures that describe for a given gene tree and species tree the possible lists of branches of the species tree on which the gene tree coalescences take place. Properties of the number of coalescent histories for gene trees and species trees affect a variety of probabilistic calculations in mathematical phylogenetics. Exact and asymptotic evaluations of the number of coalescent histories, however, are known only in a limited number of cases. Here we introduce a particular family of species trees, the lodgepole species trees (?n)n ? 0, in which tree ?n has m = 2n+1 taxa. We determine the number of coalescent histories for the lodgepole species trees, in the case that the gene tree matches the species tree, showing that this number grows with m!! in the number of taxa m. This computation demonstrates the existence of tree families in which the growth in the number of coalescent histories is faster than exponential. Further, it provides a substantial improvement on the lower bound for the ratio of the largest number of matching coalescent histories to the smallest number of matching coalescent histories for trees with m taxa, increasing a previous bound of [Formula: see text] to [Formula: see text]. We discuss the implications of our enumerative results for phylogenetic computations. PMID:25973633

  9. Attention trees and semantic paths

    NASA Astrophysics Data System (ADS)

    Giusti, Christian; Pieroni, Goffredo G.; Pieroni, Laura

    2007-02-01

    In the last few decades several techniques for image content extraction, often based on segmentation, have been proposed. It has been suggested that under the assumption of very general image content, segmentation becomes unstable and classification becomes unreliable. According to recent psychological theories, certain image regions attract the attention of human observers more than others and, generally, the image main meaning appears concentrated in those regions. Initially, regions attracting our attention are perceived as a whole and hypotheses on their content are formulated; successively the components of those regions are carefully analyzed and a more precise interpretation is reached. It is interesting to observe that an image decomposition process performed according to these psychological visual attention theories might present advantages with respect to a traditional segmentation approach. In this paper we propose an automatic procedure generating image decomposition based on the detection of visual attention regions. A new clustering algorithm taking advantage of the Delaunay- Voronoi diagrams for achieving the decomposition target is proposed. By applying that algorithm recursively, starting from the whole image, a transformation of the image into a tree of related meaningful regions is obtained (Attention Tree). Successively, a semantic interpretation of the leaf nodes is carried out by using a structure of Neural Networks (Neural Tree) assisted by a knowledge base (Ontology Net). Starting from leaf nodes, paths toward the root node across the Attention Tree are attempted. The task of the path consists in relating the semantics of each child-parent node pair and, consequently, in merging the corresponding image regions. The relationship detected in this way between two tree nodes generates, as a result, the extension of the interpreted image area through each step of the path. The construction of several Attention Trees has been performed and partial results will be shown.

  10. Transport of Methane in Trees

    NASA Astrophysics Data System (ADS)

    Kutschera, E.; Khalil, A. K.; Shearer, M. J.; Rosenstiel, T.; Rice, A. L.

    2011-12-01

    Although overall methane (CH4) emissions for croplands, wetlands, and forests have been measured, the exact dynamics of CH4 transport through trees is not well understood. What roles transport mechanisms play in emission rates has been thoroughly investigated for rice, but is fairly unknown for trees. Better defined plant transport mechanisms yield more accurate determination of greenhouse gas flux and its variations, contributing to a comprehensive theory quantifying greenhouse gas emissions globally. CH4 emissions from the common wetland tree species black cottonwood (Populus trichocarpa) native to the Pacific Northwest have been measured under hydroponic conditions in order to separate plant transport processes from the influence of soil processes. Canopy emissions of CH4 have been measured via canopy enclosure. Measurements of CH4 flux from each of 16 trees have indicated that emissions are normally constant over the half-hour sampling period. Samples for stable carbon isotope composition have been taken during these experiments and measured on a mass spectrometer. Compared to the isotopic composition of root water CH4, canopy CH4 is depleted in 13C; this indicates that CH4 moving through the tree is not following a bulk flow pathway (where no depletion would occur), but instead moves either diffusively or through other cell or tissue barriers. No correlation was found to exist between leaf area and CH4 emission; this is vital to upscaling tree-level emissions to the global scale since leaf area index (LAI) cannot be treated as an appropriate parameter to upscale flux. Correctly informing global-scale CH4 fluxes from plants requires an association between the role plant physiology plays in the production and transport of CH4 and magnitudes of flux. This research was supported by the Office of Science (BER), U. S. Department of Energy, Grant No. DE-FG02-08ER64515. Supported in part through NASA / Oregon Space Grant Consortium, grant NNG05GJ85H.

  11. Interpreting the universal phylogenetic tree.

    PubMed

    Woese, C R

    2000-07-18

    The universal phylogenetic tree not only spans all extant life, but its root and earliest branchings represent stages in the evolutionary process before modern cell types had come into being. The evolution of the cell is an interplay between vertically derived and horizontally acquired variation. Primitive cellular entities were necessarily simpler and more modular in design than are modern cells. Consequently, horizontal gene transfer early on was pervasive, dominating the evolutionary dynamic. The root of the universal phylogenetic tree represents the first stage in cellular evolution when the evolving cell became sufficiently integrated and stable to the erosive effects of horizontal gene transfer that true organismal lineages could exist. PMID:10900003

  12. Interpreting the universal phylogenetic tree

    NASA Technical Reports Server (NTRS)

    Woese, C. R.

    2000-01-01

    The universal phylogenetic tree not only spans all extant life, but its root and earliest branchings represent stages in the evolutionary process before modern cell types had come into being. The evolution of the cell is an interplay between vertically derived and horizontally acquired variation. Primitive cellular entities were necessarily simpler and more modular in design than are modern cells. Consequently, horizontal gene transfer early on was pervasive, dominating the evolutionary dynamic. The root of the universal phylogenetic tree represents the first stage in cellular evolution when the evolving cell became sufficiently integrated and stable to the erosive effects of horizontal gene transfer that true organismal lineages could exist.

  13. Peanut and tree nut allergy.

    PubMed

    Cox, Amanda; Sicherer, Scott H

    2015-01-01

    Allergy to peanut and tree nuts is a major worldwide health concern. The prevalence of these allergies may be increasing, but the reasons for these increases remain unclear. This group of foods accounts for a large proportion of severe and fatal food-allergic reactions. These allergies present most often during childhood but can occur at any age. Resolution is possible but uncommon, and frequent lifetime reactions caused by accidental ingestion are a serious problem. The major allergens of peanut and most tree nuts have been identified, allowing for insights into patient diagnoses, clinical outcomes, and potential future immunotherapies. PMID:26022873

  14. Dating the tree of life.

    PubMed

    Benton, Michael J; Ayala, Francisco J

    2003-06-13

    The relative merits of molecular and paleontological dates of major branching points in the tree of life are currently debated. In some cases, molecular date estimates are up to twice as old as paleontological dates. However, although it is true that paleontological dates are often too young (missing fossils), molecular dates are often too old (statistical bias). Intense study of the dating of major splits in the tree of mammals has shown rapprochement as fossil dates become older and molecular dates become younger. PMID:12805535

  15. Tree hydraulics: how sap rises

    NASA Astrophysics Data System (ADS)

    Denny, Mark

    2012-01-01

    Trees transport water from roots to crowna height that can exceed 100 m. The physics of tree hydraulics can be conveyed with simple fluid dynamics based upon the Hagen-Poiseuille equation and Murray's law. Here the conduit structure is modelled as conical pipes and as branching pipes. The force required to lift sap is generated mostly by transpiration or capillary action; we investigate the effectiveness of both these forces for the two conduit architectures considered. The level of analysis is appropriate for undergraduates. The subject is of broad interest because it provides a naturally-occurring example of an unusual metastable state of matter: liquid under tension.

  16. Tree Height Calculator: An Android App for Estimating Tree Height

    NASA Astrophysics Data System (ADS)

    Burca, V. S.; Htet, N. M.; Huang, X.; de Lanerolle, T. R.; Morelli, R.; Gourley, J. R.

    2011-12-01

    Conventionally, measuring tree height requires a collection of different tools - clinometer, transit, pencil, paper, laptop computer. Results are recorded manually and entered into a spreadsheet or database for future calculation and analysis. Tree Height Calculator is a mobile Android app the integrates the various steps in this process thereby improving the accuracy and dramatically reducing the time required to go from taking measurements to analyzing data. Given the user's height and the distance from the base of the tree (which can be downloaded into the app from a server), the app uses the phone's orientation sensor to calculate the angle of elevation. A simple trigonometric formula is then used to calculate and record the tree's height in the phone's database. When the phone has a WiFi connection, the data are transmitted to a server, from where they can be downloaded directly into a spreadsheet. The application was first tested in an Environmental Science laboratory at Trinity College. On the first trial, 103 data samples were collected, stored, and uploaded to the online database with only couple of dropped data points. On the second trial, 98 data samples were gathered with no loss of data. The app combined the individual measurements taken by the students in the lab, reducing the time required to produce a graph of the class's results from days to hours.

  17. Water Transport in Trees--An Artificial Laboratory Tree

    ERIC Educational Resources Information Center

    Susman, K.; Razpet, N.; Cepic, M.

    2011-01-01

    Water transport in tall trees is an everyday phenomenon, seldom noticed and not completely understood even by scientists. As a topic of current research in plant physiology it has several advantages for presentation within school physics lectures: it is interdisciplinary and clearly shows the connection between physics and biology; the

  18. Water Transport in Trees--An Artificial Laboratory Tree

    ERIC Educational Resources Information Center

    Susman, K.; Razpet, N.; Cepic, M.

    2011-01-01

    Water transport in tall trees is an everyday phenomenon, seldom noticed and not completely understood even by scientists. As a topic of current research in plant physiology it has several advantages for presentation within school physics lectures: it is interdisciplinary and clearly shows the connection between physics and biology; the…

  19. AncesTrees: ancestry estimation with randomized decision trees.

    PubMed

    Navega, David; Coelho, Catarina; Vicente, Ricardo; Ferreira, Maria Teresa; Wasterlain, Sofia; Cunha, Eugnia

    2015-09-01

    In forensic anthropology, ancestry estimation is essential in establishing the individual biological profile. The aim of this study is to present a new program--AncesTrees--developed for assessing ancestry based on metric analysis. AncesTrees relies on a machine learning ensemble algorithm, random forest, to classify the human skull. In the ensemble learning paradigm, several models are generated and co-jointly used to arrive at the final decision. The random forest algorithm creates ensembles of decision trees classifiers, a non-linear and non-parametric classification technique. The database used in AncesTrees is composed by 23 craniometric variables from 1,734 individuals, representative of six major ancestral groups and selected from the Howells' craniometric series. The program was tested in 128 adult crania from the following collections: the African slaves' skeletal collection of Valle da Gafaria; the Medical School Skull Collection and the Identified Skeletal Collection of 21st Century, both curated at the University of Coimbra. The first step of the test analysis was to perform ancestry estimation including all the ancestral groups of the database. The second stage of our test analysis was to conduct ancestry estimation including only the European and the African ancestral groups. In the first test analysis, 75% of the individuals of African ancestry and 79.2% of the individuals of European ancestry were correctly identified. The model involving only African and European ancestral groups had a better performance: 93.8% of all individuals were correctly classified. The obtained results show that AncesTrees can be a valuable tool in forensic anthropology. PMID:25053239

  20. The Education of Little Tree.

    ERIC Educational Resources Information Center

    Carter, Forrest

    First published in 1976, this autobiography contains Forrest Carter's--Little Tree's--remembrances of life with his Eastern Cherokee Hill country grandparents in the 1930s. There are 21 chapters, recounting humorous and serious episodes from a 5-year period and dealing with the themes of growing up, Indian life and values, family relationships,

  1. Cedar Tree in Bryce Canyon

    USGS Multimedia Gallery

    A cedar tree in Bryce Canyon National Park. Bryce Canyon is a unique sandstone formation in southern Utah. It is home to a large number of hoodoos, which are oddly shaped pillars of rock that formed due to different erosion rates for the dolomite that caps them and the sandstone that forms their ba...

  2. Compartmentalization of Decay in Trees.

    ERIC Educational Resources Information Center

    Shigo, Alex L.

    1985-01-01

    Unlike animals, which heal, trees compartmentalize by setting boundaries that resist the spread of invading microorganisms. Discusses the creation of new walls by anatomical and chemical means in response to death of a branch or pruning. Points out that genetic control of compartmentalization has resulted from evolution of resistant species. (DH)

  3. The Trees that surround us

    NASA Astrophysics Data System (ADS)

    Costa, M. E. G.; Rodrigues, M. A. S.

    2012-04-01

    In our school the activities linked with sciences are developed in a partnership with other school subjects. Interdisciplinary projects are always valued from beginning to end of a project. It is common for teachers of different areas to work together in a Science project. Research of English written articles is very important not only for the development of our students' scientific literacy but also as a way of widening knowledge and a view on different perspectives of life instead of being limited to research of any articles in Portuguese language. In this study we are going to collect data about the predominant tree species in the region, especially the invasive trees from the acacia species, the native tree species and the commercial species. We are going to study the reasons for the appearance of each species and draw a chart of soil occupation in the council. This chart will also allow the study of the distribution and use of land for each tree species. This research work is the first stage for a contribution to warn the town council of the dangers of the invasive species to the future economy of the council.

  4. Not Just a Fall Tree

    ERIC Educational Resources Information Center

    Miller-Hewes, Kathy A.

    2004-01-01

    Trees burst with color in the northern states. Autumn leaves dust the ground. Painting the fall landscape is nothing new. Teachers have been doing it in classrooms for decades. The approach, however, can make the difference between whether the fall landscape is simply painting for fun, or a real learning experience. Students learn best when they…

  5. Can Children Read Evolutionary Trees?

    ERIC Educational Resources Information Center

    Ainsworth, Shaaron; Saffer, Jessica

    2013-01-01

    Representations of the "tree of life" such as cladograms show the history of lineages and their relationships. They are increasingly found in formal and informal learning settings. Unfortunately, there is evidence that these representations can be challenging to interpret correctly. This study explored the question of whether children aged 7-11…

  6. The Tree of Animal Life

    ERIC Educational Resources Information Center

    Braude, Stan

    2007-01-01

    In this article, the author describes a short activity which introduces third- to fifth-grade students to animal classification. The Tree of Animal Life activity is a simple, sorting exercise that can help them see a bigger picture. The activity sets the stage for learning about animal taxonomy and introduces the characteristics of various animal

  7. Support Vector Machine Classification Trees.

    PubMed

    de Boves Harrington, Peter

    2015-11-01

    Proteomic and metabolomic studies based on chemical profiling require powerful classifiers to model accurately complex collections of data. Support vector machines (SVMs) are advantageous in that they provide a maximum margin of separation for the classification hyperplane. A new method for constructing classification trees, for which the branches comprise SVMs, has been devised. The novel feature is that the distribution of the data objects is used to determine the SVM encoding. The variance and covariance of the data objects are used for determining the bipolar encoding required for the SVM. The SVM that yields the lowest entropy of classification becomes the branch of the tree. The SVM-tree classifier has the added advantage that nonlinearly separable data may be accurately classified without optimization of the cost parameter C or searching for a correct higher dimensional kernel transform. It compares favorably to a regularized linear discriminant analysis, SVMs in a one against all multiple classifier, and a fuzzy rule-building expert system, a tree classifier with a fuzzy margin of separation. SVMs offer a speed advantage, especially for data sets that have more measurements than objects. PMID:26461495

  8. Key for Trees of Iowa.

    ERIC Educational Resources Information Center

    Coder, Kim D.; Wray, Paul H.

    This key is designed to help identify the most common trees found in Iowa. It is based on vegetative characteristics such as leaves, fruits, and bark and is illustrated with black and white line drawings. Since vegetative characteristics vary due to climate, age, soil fertility, and other conditions, the numerical sizes listed, such as length and

  9. The Gift of the Tree

    ERIC Educational Resources Information Center

    Jones, Marla Wagner

    2009-01-01

    A piece of children's literature can be a powerful tool for teaching and learning science; however, it takes more than reading about a topic to qualify as "doing science." Inspired by the book, "The Gift of the Tree", the author developed an in-depth interdisciplinary lesson for her sixth-grade students without diluting the science. Through this

  10. Electric Trees and Pond Creatures.

    ERIC Educational Resources Information Center

    Weaver, Helen; Hounshell, Paul B.

    1978-01-01

    Two learning activities are presented to develop observation and classification skills at the elementary level. The first is an electric box that associates tree names with leaf and bark specimens, and the second is a pond water observation and slide preparation activity. (BB)

  11. Chopping Down the Cherry Tree.

    ERIC Educational Resources Information Center

    Griswold, Jerry

    1995-01-01

    Attempts once again to put to rest the infamous "I cannot tell a lie" episode involving George Washington and a downed cherry tree. Appends an editor's note that states that William Bennett's "The Children's Book of Virtues" which perpetuates this infamous piece of "fakelore." (RS)

  12. The Gift of the Tree

    ERIC Educational Resources Information Center

    Jones, Marla Wagner

    2009-01-01

    A piece of children's literature can be a powerful tool for teaching and learning science; however, it takes more than reading about a topic to qualify as "doing science." Inspired by the book, "The Gift of the Tree", the author developed an in-depth interdisciplinary lesson for her sixth-grade students without diluting the science. Through this…

  13. Proceedings: Water treeing and aging

    SciTech Connect

    Bulinski, A.T.

    1991-10-01

    This report presents the record of the workshop Water Treeing and Aging.'' The workshop was held in Phoenix, Arizona on December 9--11, 1990 and was sponsored by the Distribution Program of the Electrical Systems Division of the Electric Power Research Institute (EPRI). Attendance at the workshop was by invitation only. Twenty two attendees from seven countries, from universities, research organizations, electric utilities and polymeric materials suppliers took part in this workshop. The workshop was designed to assess progress in the understanding of water treeing phenomena and polymeric cable insulation aging since the last meeting of a similar forum of experts, which was organized by the Office of Exploratory Research of EPRI in December 1985. The objective of the present workshop was to assess progress and to provide direction for further studies in this field. The discussions covered a wide range of subjects including water tree structure, initiation, growth and breakdown mechanisms, accelerated aging tests for new materials and cables, diagnostic tests, detection of deterioration, tree retardants, field repairs and preventive measures. The workshop discussions were recorded, transcribed, edited and included in this report. The records of the discussions within the breakout groups are also included (Appendices A and B) as they contain information regarding experience from different labs which may be valuable to the reader.

  14. GumTree: Data reduction

    NASA Astrophysics Data System (ADS)

    Rayner, Hugh; Hathaway, Paul; Hauser, Nick; Fei, Yang; Franceschini, Ferdi; Lam, Tony

    2006-11-01

    Access to software tools for interactive data reduction, visualisation and analysis during a neutron scattering experiment enables instrument users to make informed decisions regarding the direction and success of their experiment. ANSTO aims to enhance the experiment experience of its facility's users by integrating these data reduction tools with the instrument control interface for immediate feedback. GumTree is a software framework and application designed to support an Integrated Scientific Experimental Environment, for concurrent access to instrument control, data acquisition, visualisation and analysis software. The Data Reduction and Analysis (DRA) module is a component of the GumTree framework that allows users to perform data reduction, correction and basic analysis within GumTree while an experiment is running. It is highly integrated with GumTree, able to pull experiment data and metadata directly from the instrument control and data acquisition components. The DRA itself uses components common to all instruments at the facility, providing a consistent interface. It features familiar ISAW-based 1D and 2D plotting, an OpenGL-based 3D plotter and peak fitting performed by fityk. This paper covers the benefits of integration, the flexibility of the DRA module, ease of use for the interface and audit trail generation.

  15. Can Children Read Evolutionary Trees?

    ERIC Educational Resources Information Center

    Ainsworth, Shaaron; Saffer, Jessica

    2013-01-01

    Representations of the "tree of life" such as cladograms show the history of lineages and their relationships. They are increasingly found in formal and informal learning settings. Unfortunately, there is evidence that these representations can be challenging to interpret correctly. This study explored the question of whether children aged 7-11

  16. Trees of Our National Forests.

    ERIC Educational Resources Information Center

    Forest Service (USDA), Washington, DC.

    Presented is a description of the creation of the National Forests system, how trees grow, managing the National Forests, types of management systems, and managing for multiple use, including wildlife, water, recreation and other uses. Included are: (1) photographs; (2) line drawings of typical leaves, cones, flowers, and seeds; and (3)

  17. The Tree of Life Project

    ERIC Educational Resources Information Center

    Milbrath, Sherry

    2009-01-01

    Middle-school students are just beginning to recognize their place in the world. That is why this author believes it is important to incorporate their world into their art. In this article, the author discusses the "Tree of Life" project, which she developed for her students in order to make them aware of various environmental issues, and how to…

  18. MYCOTOXINS IN EDIBLE TREE NUTS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tree nuts (almonds, pistachios, and walnuts) are an exceptionally valuable crop, especially in California, with an aggregate value approaching $3.5 billion. Much of this economic value comes from overseas markets, with up to 60% of the crop being exported. The product can be contaminated with aflat...

  19. The Tree of Life Project

    ERIC Educational Resources Information Center

    Milbrath, Sherry

    2009-01-01

    Middle-school students are just beginning to recognize their place in the world. That is why this author believes it is important to incorporate their world into their art. In this article, the author discusses the "Tree of Life" project, which she developed for her students in order to make them aware of various environmental issues, and how to

  20. Wellhead and tree standards updated

    SciTech Connect

    Dach, A.J. Jr.; Haeberle, T.

    1996-03-11

    Revisions in the API 6A, 17th Edition, have resolved a number of long-term problems and expanded its scope and coverage of wellhead and christmas tree equipment. The 17th Edition, Feb. 1, 1996, represents the state-of-the-art in international requirements for wellhead and christmas tree equipment. The design, materials, and quality control aspects of API 6A have all been improved with an emphasis on making the document more acceptable around the world. However, there are unresolved issues that raise many questions about the future direction of efforts aimed at international standardization of wellhead and christmas tree equipment. Unfortunately, these unresolved issues confuse both manufacturers and companies purchasing this equipment. This ultimately increases wellhead and christmas tree costs, so it is to everyone`s advantage to resolve these issues. This article describes the significant revisions that are included in API 6A, 17th Edition. Also discussed are the regulatory, standardization, and customer acceptance issues that cloud the future of API 6A, 17th Edition.

  1. Feathered Hollow in Living Tree

    USGS Multimedia Gallery

    Hollow in living tree in gallery forest of tributary to Tebicuary river. Grey feathers stuck along bottom of entrance suggest that it may be used by a bird. Paraguay is home to at least 589 breeding bird species and 120 migratory bird species. The Ñeembucú Region is typified by extensi...

  2. The Tree of Animal Life

    ERIC Educational Resources Information Center

    Braude, Stan

    2007-01-01

    In this article, the author describes a short activity which introduces third- to fifth-grade students to animal classification. The Tree of Animal Life activity is a simple, sorting exercise that can help them see a bigger picture. The activity sets the stage for learning about animal taxonomy and introduces the characteristics of various animal…

  3. Secondhand Trees, Firsthand Learning. Holiday Evergreens Revitalized.

    ERIC Educational Resources Information Center

    Graves, C. John

    1990-01-01

    Described is an activity that uses discarded evergreen trees from Christmas. Tree age and growth characteristics are investigated by looking at the number of whorls and rings of the trunks. Extensions and follow-up activities are included. (KR)

  4. Modelling Stem Cells Lineages with Markov Trees

    NASA Astrophysics Data System (ADS)

    Olariu, Victor; Coca, Daniel; Billings, Stephen A.; Kadirkamanathan, Visakan

    A variational Bayesian EM with smoothed probabilities algorithm for hidden Markov trees (HMT) is proposed for incomplete tree structured data. The full posterior of the HMT parameters is determined and the underflow problems associated with previous algorithms are eliminated. Example results for the prediction of the types of cells in real stem cell lineage trees are presented.

  5. Genomics of Tropical Fruit Tree Crops

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic improvement of tropical fruit trees is limited when compared to progress achieved in temperate fruit trees and annual crops. Tropical fruit tree breeding programs require significant resources to develop new cultivars that are adapted to modern shipping and storage requirements. The use...

  6. Data multiplexer using a tree switch

    NASA Technical Reports Server (NTRS)

    Easton, R. A.; Hilbert, E. E.

    1973-01-01

    Self-decoding FET-hybrid or integrated-circuit tree configuration uses minimum number of components and can be sequenced by clock or computer. Redundancy features can readily be incorporated into tree configuration; as tree grows in size and more sensors are included, percentage of parts that will affect given percentage of sensors steadily decreases.

  7. 7 CFR 1214.3 - Christmas tree.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 10 2013-01-01 2013-01-01 false Christmas tree. 1214.3 Section 1214.3 Agriculture... AND ORDERS; MISCELLANEOUS COMMODITIES), DEPARTMENT OF AGRICULTURE CHRISTMAS TREE PROMOTION, RESEARCH, AND INFORMATION ORDER Christmas Tree Promotion, Research, and Information Order Definitions ...

  8. 7 CFR 1214.3 - Christmas tree.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 10 2014-01-01 2014-01-01 false Christmas tree. 1214.3 Section 1214.3 Agriculture... AND ORDERS; MISCELLANEOUS COMMODITIES), DEPARTMENT OF AGRICULTURE CHRISTMAS TREE PROMOTION, RESEARCH, AND INFORMATION ORDER Christmas Tree Promotion, Research, and Information Order Definitions ...

  9. 7 CFR 1214.3 - Christmas tree.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 10 2012-01-01 2012-01-01 false Christmas tree. 1214.3 Section 1214.3 Agriculture... AND ORDERS; MISCELLANEOUS COMMODITIES), DEPARTMENT OF AGRICULTURE CHRISTMAS TREE PROMOTION, RESEARCH, AND INFORMATION ORDER Christmas Tree Promotion, Research, and Information Order Definitions ...

  10. Neighborhoods of trees in circular orderings.

    PubMed

    Bastkowski, Sarah; Baskowski, Sarah; Moulton, Vincent; Spillner, Andreas; Wu, Taoyang

    2015-01-01

    In phylogenetics, a common strategy used to construct an evolutionary tree for a set of species [Formula: see text] is to search in the space of all such trees for one that optimizes some given score function (such as the minimum evolution, parsimony or likelihood score). As this can be computationally intensive, it was recently proposed to restrict such searches to the set of all those trees that are compatible with some circular ordering of the set [Formula: see text]. To inform the design of efficient algorithms to perform such searches, it is therefore of interest to find bounds for the number of trees compatible with a fixed ordering in the neighborhood of a tree that is determined by certain tree operations commonly used to search for trees: the nearest neighbor interchange (NNI), the subtree prune and regraft (SPR) and the tree bisection and reconnection (TBR) operations. We show that the size of such a neighborhood of a binary tree associated with the NNI operation is independent of the tree's topology, but that this is not the case for the SPR and TBR operations. We also give tight upper and lower bounds for the size of the neighborhood of a binary tree for the SPR and TBR operations and characterize those trees for which these bounds are attained. PMID:25477080

  11. Totally Tree-mendous Activities: Projects To Discover the Beauty and Benefits of Trees.

    ERIC Educational Resources Information Center

    Hollister, Sarah

    This teacher's guide supplies information and hands-on activities to teach about trees from several disciplines. Activities are grouped into six areas that cover botany, social studies, arts and literature (aesthetics), and trees as a resource. Sections include: (1) Tree Identification, which defines trees and leaves and presents activities that

  12. Trees Outside Forest In Poland

    NASA Astrophysics Data System (ADS)

    Zajączkowski, Jacek; Zajączkowski, Kazimierz

    2015-01-01

    Increasing environmental threats to agricultural production and the stability of ecosystems have been observed on the Polish lowlands since the 1970s. Several hundred million trees and shrubs have been planted on farmland, mostly along roads and with the involvement of public agencies, with a view to timber being produced, and soil erosion and the water deficit mitigated. On the basis of over 50 years of practical observations and scientific experiments, recommendations have been drawn up as regards the structural and spatial features of new tree planting outside forests that maximize environmental, production-related and social benefits. This paper gives a brief description of the history of the active establishment of woody vegetation across agricultural landscapes in Poland, along with best practices elaborated for this at several scientific centres.

  13. Tree decline in North America.

    PubMed

    Chevone, B I; Linzon, S N

    1988-01-01

    Air-borne, phytotoxic pollutants are known to adversely affect forest tree growth in North America. On a local scale, exposure to high concentrations of toxic gases, such as sulphur dioxide and fluoride, result in foliar injury, branch dieback, reduced radial growth and increased mortality in a variety of tree species. On a regional scale, the photochemical oxidant, ozone, is responsible for growth decline of pollutant-sensitive eastern white pine genotypes in the eastern United States, and of ponderosa and Jeffrey pines in the mountains of southern and central California. The etiology associated with the reported declines of high elevation red spruce in the Appalachian Mountains and of sugar maple in the northeastern United States and southeastern Canada is incompletely known at present. A complex of predisposing and inciting factors, including temperature and moisture stress, edaphic conditions, aluminium toxicity, insect depredation, and air-borne pollutants are probably involved in these declines. PMID:15092654

  14. Real Trees in the Classroom

    ERIC Educational Resources Information Center

    Fernandes, Francisca Maria; de Carvalho, Luis Mendonca; Silveira, Margarida

    2006-01-01

    At home, children often have pets that they take care of and play with; even in the classroom it is not uncommon to find a wormery, an aquarium or an ant farm. However, children rarely have the opportunity to own and care for a plant over a lengthy period of time, let alone a tree. The authors describe a project in Portugal aimed at improving

  15. Real Trees in the Classroom

    ERIC Educational Resources Information Center

    Fernandes, Francisca Maria; de Carvalho, Luis Mendonca; Silveira, Margarida

    2006-01-01

    At home, children often have pets that they take care of and play with; even in the classroom it is not uncommon to find a wormery, an aquarium or an ant farm. However, children rarely have the opportunity to own and care for a plant over a lengthy period of time, let alone a tree. The authors describe a project in Portugal aimed at improving…

  16. 7 CFR 1437.306 - Christmas tree crops.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... measure for all Christmas tree crops is a plant. (c) A Christmas tree having any value as a Christmas tree... 7 Agriculture 10 2010-01-01 2010-01-01 false Christmas tree crops. 1437.306 Section 1437.306... Determining Coverage Using Value 1437.306 Christmas tree crops. (a) A Christmas tree is a value loss...

  17. Anatomical modeling of the bronchial tree

    NASA Astrophysics Data System (ADS)

    Hentschel, Gerrit; Klinder, Tobias; Blaffert, Thomas; Blow, Thomas; Wiemker, Rafael; Lorenz, Cristian

    2010-02-01

    The bronchial tree is of direct clinical importance in the context of respective diseases, such as chronic obstructive pulmonary disease (COPD). It furthermore constitutes a reference structure for object localization in the lungs and it finally provides access to lung tissue in, e.g., bronchoscope based procedures for diagnosis and therapy. This paper presents a comprehensive anatomical model for the bronchial tree, including statistics of position, relative and absolute orientation, length, and radius of 34 bronchial segments, going beyond previously published results. The model has been built from 16 manually annotated CT scans, covering several branching variants. The model is represented as a centerline/tree structure but can also be converted in a surface representation. Possible model applications are either to anatomically label extracted bronchial trees or to improve the tree extraction itself by identifying missing segments or sub-trees, e.g., if located beyond a bronchial stenosis. Bronchial tree labeling is achieved using a nave Bayesian classifier based on the segment properties contained in the model in combination with tree matching. The tree matching step makes use of branching variations covered by the model. An evaluation of the model has been performed in a leaveone- out manner. In total, 87% of the branches resulting from preceding airway tree segmentation could be correctly labeled. The individualized model enables the detection of missing branches, allowing a targeted search, e.g., a local rerun of the tree-segmentation segmentation.

  18. Inference of fitness from genealogical trees

    NASA Astrophysics Data System (ADS)

    Vucelja, Marija; Dayarian, Adel; Shraiman, Boris

    2013-03-01

    Natural populations are fitness diverse and can have numerous genes under selection. The genealogical trees, that one obtains by sampling, often bear hallmarks of selection, such multiple mergers, asymmetric tree branches and long terminal branches (the trees are squished towards the root). These are qualitative differences compared to trees in the absence of selection. We propose a theoretical model that links the morphology of a tree with the fitness of the leaves. We obtain multipoint correlation functions of the fitness along the tree. In this way we are able extract some quantitative information about the strength of selection from data-reconstructed trees. The extensions of this approach can potentially be useful for inferring relative fitness of sequenced genomes of tumors and for predicting viral outbreaks.

  19. On finding minimum-diameter clique trees

    SciTech Connect

    Blair, J.R.S. . Dept. of Computer Science); Peyton, B.W. )

    1991-08-01

    It is well-known that any chordal graph can be represented as a clique tree (acyclic hypergraph, join tree). Since some chordal graphs have many distinct clique tree representations, it is interesting to consider which one is most desirable under various circumstances. A clique tree of minimum diameter (or height) is sometimes a natural candidate when choosing clique trees to be processed in a parallel computing environment. This paper introduces a linear time algorithm for computing a minimum-diameter clique tree. The new algorithm is an analogue of the natural greedy algorithm for rooting an ordinary tree in order to minimize its height. It has potential application in the development of parallel algorithms for both knowledge-based systems and the solution of sparse linear systems of equations. 31 refs., 7 figs.

  20. Colloquium paper: terrestrial apes and phylogenetic trees.

    PubMed

    Arsuaga, Juan Luis

    2010-05-11

    The image that best expresses Darwin's thinking is the tree of life. However, Darwin's human evolutionary tree lacked almost everything because only the Neanderthals were known at the time and they were considered one extreme expression of our own species. Darwin believed that the root of the human tree was very deep and in Africa. It was not until 1962 that the root was shown to be much more recent in time and definitively in Africa. On the other hand, some neo-Darwinians believed that our family tree was not a tree, because there were no branches, but, rather, a straight stem. The recent years have witnessed spectacular discoveries in Africa that take us close to the origin of the human tree and in Spain at Atapuerca that help us better understand the origin of the Neanderthals as well as our own species. The final form of the tree, and the number of branches, remains an object of passionate debate. PMID:20445090

  1. Dendrochemistry: Seeing the forest through the trees

    NASA Astrophysics Data System (ADS)

    Hauck, Danielle K.

    Dendrochemistry is a term used to describe the compositional analysis of tree-rings and its application to biomonitoring of the tree's environment. The central hypothesis of this study is that the concentrations of silver and gold in tree-rings in the Mediterranean region record the history of African dust storms. Although there have been previous studies of tree-ring composition using both NAA and other analytical techniques, to the author's knowledge, this is the first dendrochemical study to consider the effects of dust storms on tree-ring chemistry. However, the results, as with many other dendrochemical studies, are promising at best. The tree-ring concentrations in a single tree in west-central Turkey were highly correlated with the local aerosol index obtained from the Total Ozone Mapping Spectrometer (TOMS). This suggests that silver and gold concentrations in carefully selected trees may serve as a proxy indicator of dust storm activity and indirectly, the phase of the North Atlantic Oscillation. Three other trees from the same forest did not have any silver or gold concentration peaks and possible reasons for this discrepancy are discussed. The correlation with dust storms is still uncertain because it was impossible to gather appropriate information about soil characteristics or additional trees for sampling to prove or disprove the hypothesis. However, the chemistries of silver and gold are discussed to elucidate why they may be uniquely good at recording environmental signals in tree-rings. Some promising results for detecting volcanic eruptions in tree-rings were obtained on tree samples of a shorter duration (20-30 years) from Catacik Turkey that were prepared for irradiation under improved conditions of cleanliness. These tree samples were analyzed later in the project after sample preparation procedures were altered to reduce the possibility of sample contamination. Concentration peaks in the Catacik samples were correlated with the timing of the Pinatubo eruption (1991) and the El Chichon eruption in 1982. However, many of the concentration peaks were in single trees and could not be verified by comparison to other trees that grew nearby. The relative success of correlating concentration peaks in these shorter tree sequences may have been due to the improved sample preparation procedures. Another possible explanation is that concentration peaks do not remain in the tree-rings over time due to diffusion or mobilization by the tree. This would make it more difficult to find or identify possible environmental signals in the older rings of a long tree sequence. Unfortunately, this study contributes to the overwhelming number of feasibility studies that have been performed since the 1950s. There is still no consensus regarding the mechanisms responsible for recording environmental events in tree-rings beyond passive uptake. The feasibility of dendrochemistry will be more firmly established by moving forward with thoughtfully planned control studies. The refined NAA procedures developed here are necessary for future experiments which should strive to understand the actual mechanisms responsible for uptake. There are several different aspects of dendrochemistry that could be tested with control studies and that would be useful for interpreting tree-ring chemistry. For instance, dendrochemical studies could focus on the variation in specific elements between trees and the creation of composite forest chronologies for the appropriate elements. If this was successful, it would indicate that tree-ring compositions faithfully record environmental conditions in some cases and for some elements. A possible correlation was found between the Ag and Au concentration in tree-rings and the intensity and frequency of dust storms. However, the promising results were only found for one tree out of four sampled in the Catacik forest. A future study could be dedicated to verifying the presence of the Ag and Au signals in other trees in the same forest. Future studies could also analyze the ground water near sample sites to mon

  2. Effect of Antioxidants on DC Tree and Grounded DC Tree in XLPE

    NASA Astrophysics Data System (ADS)

    Kawanami, Hiroshi; Komatsu, Isao; Sekii, Yasuo; Saito, Mitsugu; Sugi, Kazuyuki

    To study the effects of antioxidants on the initiation of the DC tree and the grounded DC tree, experiments were conducted using XLPE specimens containing phenolic and sulfur type antioxidants. Experimental results showed that sulfur type antioxidants in XLPE have the effect of increasing inception voltages of both the DC tree and the grounded DC tree. Based on results of those experiments, the mechanism of increase in the inception voltage of the DC tree and the grounded DC tree by antioxidants was examined along with the mechanism of polarity effects on those trees. Results showed a promotional effect of charge injection from a needle electrode by antioxidants, which are responsible for the increased inception voltages of the DC tree. Charge trapping by antioxidants explains the increase of inception voltages of the grounded DC tree.

  3. 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. PMID:26236888

  4. MixtureTree Annotator: A Program for Automatic Colorization and Visual Annotation of MixtureTree

    PubMed Central

    Chen, Shu-Chuan; Ogata, Aaron

    2015-01-01

    The MixtureTree Annotator, written in JAVA, allows the user to automatically color any phylogenetic tree in Newick format generated from any phylogeny reconstruction program and output the Nexus file. By providing the ability to automatically color the tree by sequence name, the MixtureTree Annotator provides a unique advantage over any other programs which perform a similar function. In addition, the MixtureTree Annotator is the only package that can efficiently annotate the output produced by MixtureTree with mutation information and coalescent time information. In order to visualize the resulting output file, a modified version of FigTree is used. Certain popular methods, which lack good built-in visualization tools, for example, MEGA, Mesquite, PHY-FI, TreeView, treeGraph and Geneious, may give results with human errors due to either manually adding colors to each node or with other limitations, for example only using color based on a number, such as branch length, or by taxonomy. In addition to allowing the user to automatically color any given Newick tree by sequence name, the MixtureTree Annotator is the only method that allows the user to automatically annotate the resulting tree created by the MixtureTree program. The MixtureTree Annotator is fast and easy-to-use, while still allowing the user full control over the coloring and annotating process. PMID:25826378

  5. Urushiol Induces Apoptosis via a p53-dependent Pathway in Human Gastric Cancer Cells

    PubMed Central

    Kim, Seaho; Kim, Dong Hwan; Lee, Sun Hwa; Kim, Min Jeong; Yoon, Jeong-Hyun; Chung, Hae Young; Na, Chun Soo; Kim, Nam Deuk

    2013-01-01

    Background: Urushiols are mixtures of olefinic catechols which is isolated from the sap of Korean lacquer tree (Rhus vernicifera Stokes). The aim of this study was to determine the anticancer effects of urushiol in human gastric adenocarcinoma cell lines. Methods: The cytotoxicity of urushiols was assessed by MTT assays on the two gastric adenocarcinoma cell lines, MKN-45 (wild type of p53) and MKN-28 (mutant type of p53). We also examined the action mechanisms of urushiol by analyzing its effects on cell cycle progression and apoptosis induction. Results: The cytotoxic results from MTT assays indicated that urushiol inhibited human gastric cancer cell growth in a dose-dependent manner, with IC50 values of approximately 15 and 20 ?g/ml on MKN-45 and MKN-28 cells, respectively. Urushiol mediated cell death on these two cancer cell lines through different pathways. Urushiol induced apoptosis on MKN-45 cells, concomitant with apoptotic nuclear change, DNA fragmentation, poly (ADP-ribose) polymerase cleavage and apoptotic body formation via extrinsic pathway of apoptosis. However, no apoptotic features were induced by urushiol treatment on MKN-28 cells. Urushiol induced cytostatic cell growth inhibition via upregulation of the cyclin-dependent kinase inhibitors, p21WAF1/CIP1 and p27KIP1 proteins and down-regulation of cyclin-dependent kinase 2 and 4 proteins in a p53-independent manner. Conclusions: These data provide evidence that urushiol has the potential to be used as a chemotherapeutic agent in human gastric cancer. PMID:25337543

  6. Laccase versus Laccase-Like Multi-Copper Oxidase: A Comparative Study of Similar Enzymes with Diverse Substrate Spectra

    PubMed Central

    Reiss, Renate; Ihssen, Julian; Richter, Michael; Eichhorn, Eric; Schilling, Boris; Thny-Meyer, Linda

    2013-01-01

    Laccases (EC 1.10.3.2) are multi-copper oxidases that catalyse the one-electron oxidation of a broad range of compounds including substituted phenols, arylamines and aromatic thiols to the corresponding radicals. Owing to their broad substrate range, copper-containing laccases are versatile biocatalysts, capable of oxidizing numerous natural and non-natural industry-relevant compounds, with water as the sole by-product. In the present study, 10 of the 11 multi-copper oxidases, hitherto considered to be laccases, from fungi, plant and bacterial origin were compared. A substrate screen of 91 natural and non-natural compounds was recorded and revealed a fairly broad but distinctive substrate spectrum amongst the enzymes. Even though the enzymes share conserved active site residues we found that the substrate ranges of the individual enzymes varied considerably. The EC classification is based on the type of chemical reaction performed and the actual name of the enzyme often refers to the physiological substrate. However, for the enzymes studied in this work such classification is not feasible, even more so as their prime substrates or natural functions are mainly unknown. The classification of multi-copper oxidases assigned as laccases remains a challenge. For the sake of simplicity we propose to introduce the term laccase-like multi-copper oxidase (LMCO) in addition to the term laccase that we use exclusively for the enzyme originally identified from the sap of the lacquer tree Rhus vernicifera. PMID:23755261

  7. Tree canopy radiance measurement system

    NASA Technical Reports Server (NTRS)

    Caldwell, William; Vanderbilt, V. C.

    1989-01-01

    A system is described for obtaining both an estimate of the spatial mean bidirectional reflectance factor (BRF) for a tree canopy (displaying a horizontally heterogeneous foliage distribution) and the statistical significance of that estimate. The system includes a manlift supporting a horizontal beam 7 m long on which are mounted four radiometers. These radiometers may be pointed, and radiance data acquired, in any of 11 view directions in the principal plane of the sun. A total of 80 data points, acquired in 3 min, were used to estimate the BRF of a walnut orchard 5 m tall and detect true differences of 12 percent of the mean approximately 90 percent of the time.

  8. Interception losses of rainfall from Cashew trees

    NASA Astrophysics Data System (ADS)

    Rao, A. Sambasiva

    1987-04-01

    The rainfall interception losses from Cashew trees were quantified, based on the records of 105 selected storms within the range ? 25.0 mm, occurring in a humid tropical region at Kottamparamba, India. The storage capacity of the Cashew trees was worked out as 0.8 mm and the throughfall coefficient as 0.391. The trees under observation were 15-20 years of age with a leaf area index of 1.0-1.25. About 31% of the storm rainfall for storms ? 25.0 mm was intercepted by the Cashew trees and lost to the atmosphere. The measured interception losses from the trees were compared with the estimated interception losses using the analytical model of Gash (1979). The predicted interception losses from the Cashew trees were within 10% for storms with total rainfall ? 10.0 mm and within 22% for storms with a rainfall of 10.1-25.0 mm.

  9. Hierarchical clustering in minimum spanning trees

    NASA Astrophysics Data System (ADS)

    Yu, Meichen; Hillebrand, Arjan; Tewarie, Prejaas; Meier, Jil; van Dijk, Bob; Van Mieghem, Piet; Stam, Cornelis Jan

    2015-02-01

    The identification of clusters or communities in complex networks is a reappearing problem. The minimum spanning tree (MST), the tree connecting all nodes with minimum total weight, is regarded as an important transport backbone of the original weighted graph. We hypothesize that the clustering of the MST reveals insight in the hierarchical structure of weighted graphs. However, existing theories and algorithms have difficulties to define and identify clusters in trees. Here, we first define clustering in trees and then propose a tree agglomerative hierarchical clustering (TAHC) method for the detection of clusters in MSTs. We then demonstrate that the TAHC method can detect clusters in artificial trees, and also in MSTs of weighted social networks, for which the clusters are in agreement with the previously reported clusters of the original weighted networks. Our results therefore not only indicate that clusters can be found in MSTs, but also that the MSTs contain information about the underlying clusters of the original weighted network.

  10. Phytoremediation of trichloroethene (TCE) using cottonwood trees

    USGS Publications Warehouse

    Jones, S.A.; Lee, R.W.; Kuniansky, E.L.

    1999-01-01

    The ability of cottonwood trees for phytoremediation was studied on aerobic shallow groundwater containing TCE. Cottonwood trees were planted over a 0.2-ha area at the Naval Air Station at Fort Worth, TX, in April 1996. Two years later, groundwater chemistry in the terrace alluvial aquifer was changing locally. Dissolved oxygen (DO) concentrations declined at the southern end of the whip plantings while total iron concentration increased. Groundwater chemistry near a mature cottonwood tree ~ 60 m from the caliper trees was different from that observed elsewhere. Anaerobic conditions near the mature cottonwood tree were evident. Reductive dechlorination of TCE occurred in the aquifer near the mature tree, as demonstrated by very small concentration of TCE in groundwater, a small median ratio of TCE to the degradation product cis-1,2-DCE and the presence of vinyl chloride.

  11. Pore tree structure of porous char

    SciTech Connect

    Simons, G.A.

    1982-01-01

    A theory is presented which describes the tree-like pore structure of carbon char. Each pore that reaches the exterior surface of a char particle is depicted as the trunk of a tree. A statistically derived and empirically verified pore distribution function specifies the size distribution of the tree trunks on the particle surface. A continuous branching description of the pore tree predicts the number and size of the pores as a function of the skewed distance into the pore tree. The pore structure is completely specified through measured values of the porosity theta, internal surface area s/sub p/, and the particle radius a. The oxidation rate of carbon char is shown to be sensitive to the structure of the pore tree and the present theory is shown to accurately model the oxidation data base.

  12. Tutorial: Advanced fault tree applications using HARP

    NASA Technical Reports Server (NTRS)

    Dugan, Joanne Bechta; Bavuso, Salvatore J.; Boyd, Mark A.

    1993-01-01

    Reliability analysis of fault tolerant computer systems for critical applications is complicated by several factors. These modeling difficulties are discussed and dynamic fault tree modeling techniques for handling them are described and demonstrated. Several advanced fault tolerant computer systems are described, and fault tree models for their analysis are presented. HARP (Hybrid Automated Reliability Predictor) is a software package developed at Duke University and NASA Langley Research Center that is capable of solving the fault tree models presented.

  13. Phillips goes subsea trees in Ivory Coast

    SciTech Connect

    Bryngelson, R.H.

    1982-11-15

    Describes installation of 3 wet, diver-assist trees, in the Espoir field offshore Ivory Coast, as part of Phillips Petroleum's plans to use 5 satellite wells with downhole completion equipment and subsea production trees. Simplicity in design and attention to training has resulted in an installation time of about 3 weeks for one of the largest subsea trees in the industry. Presents diagram showing the converted jackup, Dan Duke drilling unit, which supports equipment to handle production from subsea wells.

  14. Multispectral sensing of citrus young tree decline

    NASA Technical Reports Server (NTRS)

    Edwards, G. J.; Ducharme, E. P.; Schehl, T.

    1975-01-01

    Computer processing of MSS data to identify and map citrus trees affected by young tree decline is analyzed. The data were obtained at 1500-feet altitude in six discrete spectral bands covering regions from 0.53 to 1.3 millimicrons as well as from instrumental ground truths of tree crowns. Measurable spectral reflectance intensity differences are observed in the leaves of healthy and diseased trees, especially at wavelengths of 500 to 600 nm and 700 to 800 nm. The overall accuracy of the method is found to be 89%.

  15. Tree-Structured Infinite Sparse Factor Model

    PubMed Central

    Zhang, XianXing; Dunson, David B.; Carin, Lawrence

    2013-01-01

    A tree-structured multiplicative gamma process (TMGP) is developed, for inferring the depth of a tree-based factor-analysis model. This new model is coupled with the nested Chinese restaurant process, to nonparametrically infer the depth and width (structure) of the tree. In addition to developing the model, theoretical properties of the TMGP are addressed, and a novel MCMC sampler is developed. The structure of the inferred tree is used to learn relationships between high-dimensional data, and the model is also applied to compressive sensing and interpolation of incomplete images. PMID:25279389

  16. LISP-based fault tree development environment

    SciTech Connect

    Dixon, B.W.

    1986-01-01

    This paper describes an integrated graphical environment which can be used to build, modify, and analyze fault trees on a stand-alone work-station. The environment is written in LISP, utilizing graphics and menu features commonly found on LISP workstations. A unique fault tree solution algorithm is presented that efficiently utilizes a list-based tree structure and search space, and rule-based pruning to allow for rapid analysis of larger trees. Design and efficiency issues are discussed. 5 refs., 11 figs.

  17. Why are so many trees hollow?

    PubMed Central

    Ruxton, Graeme D.

    2014-01-01

    In many living trees, much of the interior of the trunk can be rotten or even hollowed out. Previously, this has been suggested to be adaptive, with microbial or animal consumption of interior wood producing a rain of nutrients to the soil beneath the tree that allows recycling of those nutrients into new growth via the trees roots. Here I propose an alternative (non-exclusive) explanation: such loss of wood comes at very little cost to the tree and so investment in costly chemical defence of this wood is not economic. I discuss how this theory can be tested empirically. PMID:25392312

  18. Creating ensembles of decision trees through sampling

    DOEpatents

    Kamath, Chandrika; Cantu-Paz, Erick

    2005-08-30

    A system for decision tree ensembles that includes a module to read the data, a module to sort the data, a module to evaluate a potential split of the data according to some criterion using a random sample of the data, a module to split the data, and a module to combine multiple decision trees in ensembles. The decision tree method is based on statistical sampling techniques and includes the steps of reading the data; sorting the data; evaluating a potential split according to some criterion using a random sample of the data, splitting the data, and combining multiple decision trees in ensembles.

  19. Combinatorics of distance-based tree inference

    PubMed Central

    Pardi, Fabio; Gascuel, Olivier

    2012-01-01

    Several popular methods for phylogenetic inference (or hierarchical clustering) are based on a matrix of pairwise distances between taxa (or any kind of objects): The objective is to construct a tree with branch lengths so that the distances between the leaves in that tree are as close as possible to the input distances. If we hold the structure (topology) of the tree fixed, in some relevant cases (e.g., ordinary least squares) the optimal values for the branch lengths can be expressed using simple combinatorial formulae. Here we define a general form for these formulae and show that they all have two desirable properties: First, the common tree reconstruction approaches (least squares, minimum evolution), when used in combination with these formulae, are guaranteed to infer the correct tree when given enough data (consistency); second, the branch lengths of all the simple (nearest neighbor interchange) rearrangements of a tree can be calculated, optimally, in quadratic time in the size of the tree, thus allowing the efficient application of hill climbing heuristics. The study presented here is a continuation of that by Mihaescu and Pachter on branch length estimation [Mihaescu R, Pachter L (2008) Proc Natl Acad Sci USA 105:13206–13211]. The focus here is on the inference of the tree itself and on providing a basis for novel algorithms to reconstruct trees from distances. PMID:23012403

  20. Combinatorics of distance-based tree inference.

    PubMed

    Pardi, Fabio; Gascuel, Olivier

    2012-10-01

    Several popular methods for phylogenetic inference (or hierarchical clustering) are based on a matrix of pairwise distances between taxa (or any kind of objects): The objective is to construct a tree with branch lengths so that the distances between the leaves in that tree are as close as possible to the input distances. If we hold the structure (topology) of the tree fixed, in some relevant cases (e.g., ordinary least squares) the optimal values for the branch lengths can be expressed using simple combinatorial formulae. Here we define a general form for these formulae and show that they all have two desirable properties: First, the common tree reconstruction approaches (least squares, minimum evolution), when used in combination with these formulae, are guaranteed to infer the correct tree when given enough data (consistency); second, the branch lengths of all the simple (nearest neighbor interchange) rearrangements of a tree can be calculated, optimally, in quadratic time in the size of the tree, thus allowing the efficient application of hill climbing heuristics. The study presented here is a continuation of that by Mihaescu and Pachter on branch length estimation [Mihaescu R, Pachter L (2008) Proc Natl Acad Sci USA 105:13206-13211]. The focus here is on the inference of the tree itself and on providing a basis for novel algorithms to reconstruct trees from distances. PMID:23012403

  1. Fruit load governs transpiration of olive trees.

    PubMed

    Bustan, Amnon; Dag, Arnon; Yermiyahu, Uri; Erel, Ran; Presnov, Eugene; Agam, Nurit; Kool, Dilia; Iwema, Joost; Zipori, Isaac; Ben-Gal, Alon

    2016-03-01

    We tested the hypothesis that whole-tree water consumption of olives (Olea europaea L.) is fruit load-dependent and investigated the driving physiological mechanisms. Fruit load was manipulated in mature olives grown in weighing-drainage lysimeters. Fruit was thinned or entirely removed from trees at three separate stages of growth: early, mid and late in the season. Tree-scale transpiration, calculated from lysimeter water balance, was found to be a function of fruit load, canopy size and weather conditions. Fruit removal caused an immediate decline in water consumption, measured as whole-plant transpiration normalized to tree size, which persisted until the end of the season. The later the execution of fruit removal, the greater was the response. The amount of water transpired by a fruit-loaded tree was found to be roughly 30% greater than that of an equivalent low- or nonyielding tree. The tree-scale response to fruit was reflected in stem water potential but was not mirrored in leaf-scale physiological measurements of stomatal conductance or photosynthesis. Trees with low or no fruit load had higher vegetative growth rates. However, no significant difference was observed in the overall aboveground dry biomass among groups, when fruit was included. This case, where carbon sources and sinks were both not limiting, suggests that the role of fruit on water consumption involves signaling and alterations in hydraulic properties of vascular tissues and tree organs. PMID:26802540

  2. Sulfur nutrition of deciduous trees

    NASA Astrophysics Data System (ADS)

    Herschbach, Cornelia; Rennenberg, Heinz

    2001-01-01

    Sulfur in its reduced form (-II) is an essential nutrient for growth and development, but is mainly available to plants in its oxidised form as sulfate. Deciduous trees take up sulfate by the roots from the soil solution and reduce sulfate to sulfide via assimilatory sulfate reduction in both roots and leaves. For reduction in the leaves, sulfate is loaded into the xylem and transported to the shoot. The surplus of sulfate not reduced in the chloroplast or stored in the vacuole and the surplus of reduced S not used for protein synthesis in the leaves is loaded into the phloem and transported back to the roots. Along the transport path, sulfate and glutathione (GSH) is unloaded from the phloem for storage in xylem and phloem parenchyma as well as in pit and ray cells. Re-mobilised S from storage tissues is loaded into the xylem during spring, but a phloem to xylem exchange does not appear to exist later in the season. As a consequence, a cycling pool of S was only found during the change of the seasons. The sulfate:glutathione ratio in the phloem seems to be involved in the regulation of S nutrition. This picture of S nutrition is discussed in relation to the different growth patterns of deciduous trees from the temperate climate zone, i.e. (1) terminated, (2) periodic and (3) indeterminate growth patterns, and in relation to environmental changes.

  3. Understory plant communities and the functional distinction between savanna trees, forest trees, and pines.

    SciTech Connect

    Veldman, Joseph, W., Mattingly, Brett, W., Brudvig, Lars, A.

    2013-04-01

    Abstract. 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 fire 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.

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

    ERIC Educational Resources Information Center

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

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

  5. 36 CFR 223.4 - Exchange of trees or portions of trees.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

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

  6. Species Tree Inference Using a Mixture Model.

    PubMed

    Ullah, Ikram; Parviainen, Pekka; Lagergren, Jens

    2015-09-01

    Species tree reconstruction has been a subject of substantial research due to its central role across biology and medicine. A species tree is often reconstructed using a set of gene trees or by directly using sequence data. In either of these cases, one of the main confounding phenomena is the discordance between a species tree and a gene tree due to evolutionary events such as duplications and losses. Probabilistic methods can resolve the discordance by coestimating gene trees and the species tree but this approach poses a scalability problem for larger data sets. We present MixTreEM-DLRS: A two-phase approach for reconstructing a species tree in the presence of gene duplications and losses. In the first phase, MixTreEM, a novel structural expectation maximization algorithm based on a mixture model is used to reconstruct a set of candidate species trees, given sequence data for monocopy gene families from the genomes under study. In the second phase, PrIME-DLRS, a method based on the DLRS model (kerborg O, Sennblad B, Arvestad L, Lagergren J. 2009. Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc Natl Acad Sci U S A. 106(14):5714-5719), is used for selecting the best species tree. PrIME-DLRS can handle multicopy gene families since DLRS, apart from modeling sequence evolution, models gene duplication and loss using a gene evolution model (Arvestad L, Lagergren J, Sennblad B. 2009. The gene evolution model and computing its associated probabilities. J ACM. 56(2):1-44). We evaluate MixTreEM-DLRS using synthetic and biological data, and compare its performance with a recent genome-scale species tree reconstruction method PHYLDOG (Boussau B, Szll?si GJ, Duret L, Gouy M, Tannier E, Daubin V. 2013. Genome-scale coestimation of species and gene trees. Genome Res. 23(2):323-330) as well as with a fast parsimony-based algorithm Duptree (Wehe A, Bansal MS, Burleigh JG, Eulenstein O. 2008. Duptree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics 24(13):1540-1541). Our method is competitive with PHYLDOG in terms of accuracy and runs significantly faster and our method outperforms Duptree in accuracy. The analysis constituted by MixTreEM without DLRS may also be used for selecting the target species tree, yielding a fast and yet accurate algorithm for larger data sets. MixTreEM is freely available at http://prime.scilifelab.se/mixtreem/. PMID:25963975

  7. The universal tree of life: an update.

    PubMed

    Forterre, Patrick

    2015-01-01

    Biologists used to draw schematic "universal" trees of life as metaphors illustrating the history of life. It is indeed a priori possible to construct an organismal tree connecting the three major domains of ribosome encoding organisms: Archaea, Bacteria and Eukarya, since they originated by cell division from LUCA. Several universal trees based on ribosomal RNA sequence comparisons proposed at the end of the last century are still widely used, although some of their main features have been challenged by subsequent analyses. Several authors have proposed to replace the traditional universal tree with a ring of life, whereas others have proposed more recently to include viruses as new domains. These proposals are misleading, suggesting that endosymbiosis can modify the shape of a tree or that viruses originated from the last universal common ancestor (LUCA). I propose here an updated version of Woese's universal tree that includes several rootings for each domain and internal branching within domains that are supported by recent phylogenomic analyses of domain specific proteins. The tree is rooted between Bacteria and Arkarya, a new name proposed for the clade grouping Archaea and Eukarya. A consensus version, in which each of the three domains is unrooted, and a version in which eukaryotes emerged within archaea are also presented. This last scenario assumes the transformation of a modern domain into another, a controversial evolutionary pathway. Viruses are not indicated in these trees but are intrinsically present because they infect the tree from its roots to its leaves. Finally, I present a detailed tree of the domain Archaea, proposing the sub-phylum neo-Euryarchaeota for the monophyletic group of euryarchaeota containing DNA gyrase. These trees, that will be easily updated as new data become available, could be useful to discuss controversial scenarios regarding early life evolution. PMID:26257711

  8. The universal tree of life: an update

    PubMed Central

    Forterre, Patrick

    2015-01-01

    Biologists used to draw schematic “universal” trees of life as metaphors illustrating the history of life. It is indeed a priori possible to construct an organismal tree connecting the three major domains of ribosome encoding organisms: Archaea, Bacteria and Eukarya, since they originated by cell division from LUCA. Several universal trees based on ribosomal RNA sequence comparisons proposed at the end of the last century are still widely used, although some of their main features have been challenged by subsequent analyses. Several authors have proposed to replace the traditional universal tree with a ring of life, whereas others have proposed more recently to include viruses as new domains. These proposals are misleading, suggesting that endosymbiosis can modify the shape of a tree or that viruses originated from the last universal common ancestor (LUCA). I propose here an updated version of Woese’s universal tree that includes several rootings for each domain and internal branching within domains that are supported by recent phylogenomic analyses of domain specific proteins. The tree is rooted between Bacteria and Arkarya, a new name proposed for the clade grouping Archaea and Eukarya. A consensus version, in which each of the three domains is unrooted, and a version in which eukaryotes emerged within archaea are also presented. This last scenario assumes the transformation of a modern domain into another, a controversial evolutionary pathway. Viruses are not indicated in these trees but are intrinsically present because they infect the tree from its roots to its leaves. Finally, I present a detailed tree of the domain Archaea, proposing the sub-phylum neo-Euryarchaeota for the monophyletic group of euryarchaeota containing DNA gyrase. These trees, that will be easily updated as new data become available, could be useful to discuss controversial scenarios regarding early life evolution. PMID:26257711

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

    SciTech Connect

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

    2009-07-31

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

  10. CRITIQUE OF CARBON BASED TREE GROWTH MODELS

    EPA Science Inventory

    Simulation models of the processes that control carbohydrate balance in coniferous trees are reviewed, and their appropriateness for assessing pollution effects is considered. Currently such models are at the forefront of attempts to simulate the growth process of trees, but they...

  11. Alcohol co-production from tree crops

    SciTech Connect

    Seibert, M.; Folger, G.; Milne, T.

    1982-06-01

    A concept for the sustainable production of alcohol from fermentable substrates produced on an annual basis by the reproductive organs (pods, fruits, nuts, berries, etc.) of tree crops is presented. The advantages of tree-crop systems include suitability for use on marginal land, potential productivity equivalent to row crops, minimal maintenance and energy-input requirements, environmental compatibility, and the possibility of co-product production. Honeylocust, mesquite, and persimmon are examined as potential US tree-crop species. Other species not previously considered, including osage orange and breadfruit, are suggested as tree-crop candidates for North America and the tropical developing world, respectively. Fermentation of tree-crop organs and the economics of tree-crop systems are also discussed. Currently the greatest area of uncertainty lies in actual pod or fruit yields one can expect from large tree farms under real life conditions. However, ballpark ethanol yield estimates of from 880 to 3470 l hectare/sup -1/ (94 to 400 gal acre/sup -1/) justify further consideration of tree crop systems.

  12. The Tree Man: Robert Mazibuko's Story.

    ERIC Educational Resources Information Center

    Bloch, Joanne, Ed.

    This book for beginning readers highlights Robert Mazibuko, the "Tree Man," who spent his life teaching people how to enrich the soil and plant vegetables and trees. Born in South Africa in 1904, he lived on a farm, learning to work with livestock, raise crops, and share with the community. In college, his professor of agriculture provided a…

  13. The "Ride for Russia" Tree Lichen Survey

    ERIC Educational Resources Information Center

    Young, Simon

    2013-01-01

    The prevalence of nine indicator lichens found on trees in Northern Europe and Western Russia was used for monitoring air quality. The 4200 mile route of the survey went through eight countries. Surveys were carried out in cities, towns, countryside and forests, and along motorways. The author has conducted tree lichen surveys with pupils from

  14. How Trees Help the Power Company!

    ERIC Educational Resources Information Center

    King, Rik

    1992-01-01

    Proposes the utilization of graph theory to solve optimization problems. Defines the notion of spanning trees and presents two algorithms to determine optimization of a spanning tree. Discusses an example to connect towns by power transmission lines at minimum cost. (MDH)

  15. Sewing String Tree Vertices with Ghosts

    NASA Astrophysics Data System (ADS)

    Sandoval Junior, Leonidas

    2002-03-01

    It is shown how to sew string vertices with ghosts at tree level in order to produce new tree vertices using the Group Theoretic approach to String Theory. It is then verified the BRST invariance of the sewn vertex and shown that it has the correct ghost number.

  16. The Tree Man: Robert Mazibuko's Story.

    ERIC Educational Resources Information Center

    Bloch, Joanne, Ed.

    This book for beginning readers highlights Robert Mazibuko, the "Tree Man," who spent his life teaching people how to enrich the soil and plant vegetables and trees. Born in South Africa in 1904, he lived on a farm, learning to work with livestock, raise crops, and share with the community. In college, his professor of agriculture provided a

  17. Algorithmic height compression of unordered trees.

    PubMed

    Ben-Naoum, Farah; Godin, Christophe

    2016-01-21

    By nature, tree structures frequently present similarities between their sub-parts. Making use of this redundancy, different types of tree compression techniques have been designed in the literature to reduce the complexity of tree structures. A popular and efficient way to compress a tree consists of merging its isomorphic subtrees, which produces a directed acyclic graph (DAG) equivalent to the original tree. An important property of this method is that the compressed structure (i.e. the DAG) has the same height as the original tree, thus limiting partially the possibility of compression. In this paper we address the problem of further compressing this DAG in height. The difficulty is that compression must be carried out on substructures that are not exactly isomorphic as they are strictly nested within each-other. We thus introduced a notion of quasi-isomorphism between subtrees that makes it possible to define similar patterns along any given path in a tree. We then proposed an algorithm to detect these patterns and to merge them, thus leading to compressed structures corresponding to DAGs augmented with return edges. In this way, redundant information is removed from the original tree in both width and height, thus achieving minimal structural compression. The complete compression algorithm is then illustrated on the compression of various plant-like structures. PMID:26551155

  18. Genetic interactions underlying tree branch orientation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Expanding our understanding of the molecular and genetic mechanisms behind branch orientation in trees both addresses a fundamental developmental phenomenon and can lead to significant impacts on tree crop agriculture and forestry. Using the p-nome (pooled genome) sequencing-based mapping approac...

  19. 'Christmas tree' created by Skylab 4 crewmembers

    NASA Technical Reports Server (NTRS)

    1973-01-01

    This 'Christmas tree' was created by the three crewmen of the third manned Skylab mission aboard the space station in Earth orbit. Food cans were used to fashion the tree. This photograph was made from a television transmission made from a video tape recording on December 24, 1973.

  20. Water tree retardant XLPE cable using VLDPE

    SciTech Connect

    Asano, Akihiro ); Takahashi, Tohru; Maeda, Kazunori; Niwa, Toshio )

    1994-01-01

    Investigations were carried out on water tree retardant XLPE (XLVLDPE) cable using very low density polyethylene (VLDPE) which is a very recent new grade of polyethylene. To begin with, when the water tree retardant effects of various types of VLDPE being sold on the market were evaluated by using sheet specimens, extremely good water tree retardant effects were exhibited when the type of VLDPE was selected appropriately. Next, the above selected varieties of VLDPE were tested regarding the extruding into cables. The extrusion of VLDPE was found to be more difficult compared to conventional XLPE, and consequently required the modification of extrusion conditions and a crosslinking agent. The result of the water tree acceleration test of XLVLDPE cables indicated that the generation of bow-tie trees was suppressed to a larger extent than conventional XLPE cables. Although the AC initial breakdown voltage of XLVLDPE cables was lower than that of the conventional XLPE cables, there was almost no decrease in the breakdown voltage due to the water tree test and the breakdown voltage became higher than that of the conventional XLPE cables after the water tree tests. The superior water tree retardation characteristics of XLVLDPE described above was deduced to be due to the combined effect of the low crystallinity of the base polyethylene and the presence of the additive material (neutralizing agent and antioxidant).

  1. Molecular basis of angiosperm tree architecture

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The shoot architecture of trees greatly impacts orchard and forest management methods. Amassing greater knowledge of the molecular genetics behind tree form can benefit these industries as well as contribute to basic knowledge of plant developmental biology. This review covers basic components of ...

  2. Electrical signals in avocado trees

    PubMed Central

    Oyarce, Patricio

    2010-01-01

    Plant responses to environmental changes are associated with electrical excitability and signaling; automatic and continuous measurements of electrical potential differences (ΔEP) between plant tissues can be effectively used to study information transport mechanisms and physiological responses that result from external stimuli on plants. The generation and conduction of electrochemical impulses within plant different tissues and organs, resulting from abiotic and biotic changes in environmental conditions is reported. In this work, electrical potential differences are monitored continuously using Ag/AgCl microelectrodes, inserted 5 mm deep into sapwood at two positions in the trunks of several Avocado trees. Electrodes are referenced to a non polarisable Ag/AgCl microelectrode installed 20 cm deep in the soil. Systematic patterns of ΔEP during absolute darkness, day-night cycles and different conditions of soil water availability are discussed as alternative tools to assess early plant stress conditions. PMID:20592805

  3. Robins gather in a tree

    NASA Technical Reports Server (NTRS)

    2000-01-01

    In a wooded area of Kennedy Space Center, robins gather on a tree branch just beginning to show new Spring growth. A member of the thrush family, robins inhabit towns, gardens, open woodlands and agricultural lands. They range through most of North America, spending winters in large roosts mostly in the United States but also Newfoundland, southern Ontario and British Columbia. The Center shares a boundary with the Merritt Island National Wildlife Refuge, a haven and habitat for more than 331 species of birds. The Refuge encompasses 92,000 acres that are also a habitat for 31 mammals, 117 fishes, and 65 amphibians and reptiles. The marshes and open water of the refuge provide wintering areas for 23 species of migratory waterfowl, as well as a year-round home for great blue herons, great egrets, wood storks, cormorants, brown pelicans and other species of marsh and shore birds, as well as a variety of insects.

  4. Genealogical Trees of Scientific Papers

    PubMed Central

    Waumans, Michaël Charles; Bersini, Hugues

    2016-01-01

    Many results have been obtained when studying scientific papers citations databases in a network perspective. Articles can be ranked according to their current in-degree and their future popularity or citation counts can even be predicted. The dynamical properties of such networks and the observation of the time evolution of their nodes started more recently. This work adopts an evolutionary perspective and proposes an original algorithm for the construction of genealogical trees of scientific papers on the basis of their citation count evolution in time. The fitness of a paper now amounts to its in-degree growing trend and a “dying” paper will suddenly see this trend declining in time. It will give birth and be taken over by some of its most prevalent citing “offspring”. Practically, this might be used to trace the successive published milestones of a research field. PMID:26954677

  5. A-3 First Tree Cutting

    NASA Technical Reports Server (NTRS)

    2007-01-01

    Tree clearing for the site of the new A-3 Test Stand at Stennis Space center began June 13. NASA's first new large rocket engine test stand to be built since the site's inception, A-3 construction begins a historic era for America's largest rocket engine test complex. The 300-foot-tall structure is scheduled for completion in August 2010. A-3 will perform altitude tests on the Constellation's J-2X engine that will power the upper stage of the Ares I crew launch vehicle and earth departure stage of the Ares V cargo launch vehicle. The Constellation Program, NASA's plan for carrying out the nation's Vision for Space Exploration, will return humans to the moon and eventually carry them to Mars and beyond.

  6. Language distance and tree reconstruction

    NASA Astrophysics Data System (ADS)

    Petroni, Filippo; Serva, Maurizio

    2008-08-01

    Languages evolve over time according to a process in which reproduction, mutation and extinction are all possible. This is very similar to haploid evolution for asexual organisms and for the mitochondrial DNA of complex ones. Exploiting this similarity, it is possible, in principle, to verify hypotheses concerning the relationship among languages and to reconstruct their family tree. The key point is the definition of the distances among pairs of languages in analogy with the genetic distances among pairs of organisms. Distances can be evaluated by comparing grammar and/or vocabulary, but while it is difficult, if not impossible, to quantify grammar distance, it is possible to measure a distance from vocabulary differences. The method used by glottochronology computes distances from the percentage of shared 'cognates', which are words with a common historical origin. The weak point of this method is that subjective judgment plays a significant role. Here we define the distance of two languages by considering a renormalized edit distance among words with the same meaning and averaging over the two hundred words contained in a Swadesh list. In our approach the vocabulary of a language is the analogue of DNA for organisms. The advantage is that we avoid subjectivity and, furthermore, reproducibility of results is guaranteed. We apply our method to the Indo-European and the Austronesian groups, considering, in both cases, fifty different languages. The two trees obtained are, in many respects, similar to those found by glottochronologists, with some important differences as regards the positions of a few languages. In order to support these different results we separately analyze the structure of the distances of these languages with respect to all the others.

  7. Node degree distribution in spanning trees

    NASA Astrophysics Data System (ADS)

    Pozrikidis, C.

    2016-03-01

    A method is presented for computing the number of spanning trees involving one link or a specified group of links, and excluding another link or a specified group of links, in a network described by a simple graph in terms of derivatives of the spanning-tree generating function defined with respect to the eigenvalues of the Kirchhoff (weighted Laplacian) matrix. The method is applied to deduce the node degree distribution in a complete or randomized set of spanning trees of an arbitrary network. An important feature of the proposed method is that the explicit construction of spanning trees is not required. It is shown that the node degree distribution in the spanning trees of the complete network is described by the binomial distribution. Numerical results are presented for the node degree distribution in square, triangular, and honeycomb lattices.

  8. Tree rings : timekeepers of the past

    USGS Publications Warehouse

    U.S. Geological Survey

    1973-01-01

    A casual look at the top of a tree stump reveals that it is composed of a series of concentric rings-tree rings -that become larger and larger in diameter outward from the center of the stump. Because a single tree ring is usually formed each year, the age of the tree at the time it was cut can be determined by simply counting the rings. If the year of cutting is known, the year during which each ring was formed can be determined by counting backwards from the outside ring. Such "dating" of rings may reveal that rings formed during certain extreme drought years are unusually narrow. This has led to speculation that tree ring characteristics may indicate a number of things about past water and climatic conditions.

  9. Fuzzy variable-branch decision tree

    NASA Astrophysics Data System (ADS)

    Yang, Shiueng-Bien

    2010-10-01

    Decision trees and their variants recently have been proposed. All trees used are fixed M-ary tree structured, such that the training samples in each node must be artificially divided into a fixed number of branches. This work proposes a fuzzy variable-branch decision tree (FVBDT) based on the fuzzy genetic algorithm (FGA). The FGA automatically searches for the proper number of branches of each node according to the classification error rate and the classification time of FVBDT. Therefore, FGA reduces both the classification error rate and classification time, and then optimizes the FVBDT. In our experiments, FVBDT outperforms the traditional C-fuzzy decision tree (CFDT) based on the fuzzy C-means (FCM) algorithm.

  10. Tree snubbing operation solves well control problem

    SciTech Connect

    Gebhardt, F.; Thompson, J.D.

    1987-09-01

    Wild Well Control, Inc. has used a unique method to remove a Christmas tree under high pressure and install BOPs without a rig. This allowed workover of a gas-condensate well with a shallow tubing break that could not be killed by surface pumping due to casing pressure limitations. The procedure eliminated the need for drilling a relief well. The tree-stripping procedure is applicable to wells with Christmas trees that are screwed to the tubing string and equipped with wrap-around tubing hangers. The method would not be required if the tree were provided with a mandrel hanger that could receive a back-pressure valve. The step-by-step procedure used to remove the tree under pressure is described.

  11. MTVis: tree exploration using a multitouch interface

    NASA Astrophysics Data System (ADS)

    Andrews, David; Teoh, Soon Tee

    2010-01-01

    We present MTVis, a multi-touch interactive tree visualization system. The multi-touch interface display hardware is built using the LED-LP technology, and the tree layout is based on RINGS, but enhanced with multitouch interactions. We describe the features of the system, and how the multi-touch interface enhances the user's experience in exploring the tree data structure. In particular, the multi-touch interface allows the user to simultaneously control two child nodes of the root, and rotate them so that some nodes are magnified, while preserving the layout of the tree. We also describe the other meaninful touch screen gestures the users can use to intuitively explore the tree.

  12. Practical application of fault tree analysis

    SciTech Connect

    Prugh, R.W.

    1980-01-01

    A detailed survey of standard and novel approaches to Fault Tree construction, based on recent developments at Du Pont, covers the effect-to-cause procedure for control systems as in process plants; the effect-to-cause procedure for processes; source-of-hazard analysis, as in pressure vessel rupture; use of the ''fire triangle'' in a Fault Tree; critical combinations of safeguard failures; action points for automatic or operator control of a process; situations involving hazardous reactant ratios; failure-initiating and failure-enabling events and intervention by the operator; ''daisy-chain'' hazards, e.g., in batch processes and ship accidents; combining batch and continuous operations in a Fault Tree; possible future structure-development procedures for fault-tree construction; and the use of quantitative results (calculated frequencies of Top-Event occurrence) to restructure the Fault Tree after improving the process to any acceptable risk level.

  13. Tapping tree rings for the environmental tales they tell

    SciTech Connect

    Amato, I.

    1988-10-01

    Elemental and chemical distributions in tree rings may be a record of the tree's chemical environment during its lifetime. This article examines spectroscopic techniques which are being used to analyze tree rings to obtain environmental clues.

  14. Benefits of tree mixes in carbon plantings

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

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

  15. Temperature histories from tree rings and corals

    NASA Astrophysics Data System (ADS)

    Cook, Edward R.

    1995-05-01

    Recent temperature trends in long tree-ring and coral proxy temperature histories are evaluated and compared in an effort to objectively determine how anomalous twentieth century temperature changes have been. These histories mostly reflect regional variations in summer warmth from the tree rings and annual warmth from the corals. In the Northern Hemisphere, the North American tree-ring temperature histories and those from the north Polar Urals, covering the past 1000 or more years, indicate that the twentieth century has been anomalously warm relative to the past. In contrast, the tree-ring history from northern Fennoscandia indicates that summer temperatures during the Medieval Warm Period were probably warmer on average than those than during this century. In the Southern Hemisphere, the tree-ring temperature histories from South America show no indication of recent warming, which is in accordance with local instrumental records. In contrast, the tree-ring records from Tasmania and New Zealand indicate that the twentieth century has been unusually warm particularly since 1960. The coral temperature histories from the Galapagos Islands and the Great Barrier Reef are in broad agreement with the tree-ring temperature histories in those sectors, with the former showing recent cooling and the latter showing recent warming that may be unprecedented. Overall, the regional temperature histories evaluated here broadly support the larger-scale evidence for anomalous twentieth century warming based on instrumental records. However, this warming cannot be confirmed as an unprecedented event in all regions.

  16. Comparison of tree-child phylogenetic networks.

    PubMed

    Cardona, Gabriel; Rossell, Francesc; Valiente, Gabriel

    2009-01-01

    Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of nontreelike evolutionary events, like recombination, hybridization, or lateral gene transfer. While much progress has been made to find practical algorithms for reconstructing a phylogenetic network from a set of sequences, all attempts to endorse a class of phylogenetic networks (strictly extending the class of phylogenetic trees) with a well-founded distance measure have, to the best of our knowledge and with the only exception of the bipartition distance on regular networks, failed so far. In this paper, we present and study a new meaningful class of phylogenetic networks, called tree-child phylogenetic networks, and we provide an injective representation of these networks as multisets of vectors of natural numbers, their path multiplicity vectors. We then use this representation to define a distance on this class that extends the well-known Robinson-Foulds distance for phylogenetic trees and to give an alignment method for pairs of networks in this class. Simple polynomial algorithms for reconstructing a tree-child phylogenetic network from its path multiplicity vectors, for computing the distance between two tree-child phylogenetic networks and for aligning a pair of tree-child phylogenetic networks, are provided. They have been implemented as a Perl package and a Java applet, which can be found at http://bioinfo.uib.es/~recerca/phylonetworks/mudistance/. PMID:19875855

  17. ASTRID: Accurate Species TRees from Internode Distances

    PubMed Central

    2015-01-01

    Background Incomplete lineage sorting (ILS), modelled by the multi-species coalescent (MSC), is known to create discordance between gene trees and species trees, and lead to inaccurate species tree estimations unless appropriate methods are used to estimate the species tree. While many statistically consistent methods have been developed to estimate the species tree in the presence of ILS, only ASTRAL-2 and NJst have been shown to have good accuracy on large datasets. Yet, NJst is generally slower and less accurate than ASTRAL-2, and cannot run on some datasets. Results We have redesigned NJst to enable it to run on all datasets, and we have expanded its design space so that it can be used with different distance-based tree estimation methods. The resultant method, ASTRID, is statistically consistent under the MSC model, and has accuracy that is competitive with ASTRAL-2. Furthermore, ASTRID is much faster than ASTRAL-2, completing in minutes on some datasets for which ASTRAL-2 used hours. Conclusions ASTRID is a new coalescent-based method for species tree estimation that is competitive with the best current method in terms of accuracy, while being much faster. ASTRID is available in open source form on github. PMID:26449326

  18. Urban Tree Effects on Soil Organic Carbon

    PubMed Central

    Edmondson, Jill L.; O'Sullivan, Odhran S.; Inger, Richard; Potter, Jonathan; McHugh, Nicola; Gaston, Kevin J.; Leake, Jonathan R.

    2014-01-01

    Urban trees sequester carbon into biomass and provide many ecosystem service benefits aboveground leading to worldwide tree planting schemes. Since soils hold ∼75% of ecosystem organic carbon, understanding the effect of urban trees on soil organic carbon (SOC) and soil properties that underpin belowground ecosystem services is vital. We use an observational study to investigate effects of three important tree genera and mixed-species woodlands on soil properties (to 1 m depth) compared to adjacent urban grasslands. Aboveground biomass and belowground ecosystem service provision by urban trees are found not to be directly coupled. Indeed, SOC enhancement relative to urban grasslands is genus-specific being highest under Fraxinus excelsior and Acer spp., but similar to grasslands under Quercus robur and mixed woodland. Tree cover type does not influence soil bulk density or C∶N ratio, properties which indicate the ability of soils to provide regulating ecosystem services such as nutrient cycling and flood mitigation. The trends observed in this study suggest that genus selection is important to maximise long-term SOC storage under urban trees, but emerging threats from genus-specific pathogens must also be considered. PMID:25003872

  19. Urban tree effects on soil organic carbon.

    PubMed

    Edmondson, Jill L; O'Sullivan, Odhran S; Inger, Richard; Potter, Jonathan; McHugh, Nicola; Gaston, Kevin J; Leake, Jonathan R

    2014-01-01

    Urban trees sequester carbon into biomass and provide many ecosystem service benefits aboveground leading to worldwide tree planting schemes. Since soils hold ?75% of ecosystem organic carbon, understanding the effect of urban trees on soil organic carbon (SOC) and soil properties that underpin belowground ecosystem services is vital. We use an observational study to investigate effects of three important tree genera and mixed-species woodlands on soil properties (to 1 m depth) compared to adjacent urban grasslands. Aboveground biomass and belowground ecosystem service provision by urban trees are found not to be directly coupled. Indeed, SOC enhancement relative to urban grasslands is genus-specific being highest under Fraxinus excelsior and Acer spp., but similar to grasslands under Quercus robur and mixed woodland. Tree cover type does not influence soil bulk density or C?N ratio, properties which indicate the ability of soils to provide regulating ecosystem services such as nutrient cycling and flood mitigation. The trends observed in this study suggest that genus selection is important to maximise long-term SOC storage under urban trees, but emerging threats from genus-specific pathogens must also be considered. PMID:25003872

  20. Detecting Coppice Legacies from Tree Growth

    PubMed Central

    Müllerová, Jana; Pejcha, Vít; Altman, Jan; Plener, Tomáš; Dörner, Petr; Doležal, Jiří

    2016-01-01

    In coppice-with-standards, once a common type of management in Central European lowland forests, selected trees (standards) were left to grow mature among the regularly harvested coppice stools to obtain construction wood. After the underwood was harvested, the forest canopy opened rapidly, giving standard trees an opportunity to benefit from reduced competition. Although this silvicultural system virtually disappeared after WWII, historical management cycles can still be traced in the tree-rings of remaining standards. Our research aims at answering the question whether tree-ring series of standard trees can be used to reconstruct past management practices. The study was carried out on 117 oak standard trees from five sites situated in formerly coppiced calcareous oak-hornbeam and acidophilous oak forests in the Bohemian Karst Protected Landscape Area, Czech Republic. The evaluation was based on the analysis of growth releases representing the response of the standards to coppicing events, and comparison to the archival records of coppice events. Our results showed that coppicing events can be successfully detected by tree-ring analysis, although there are some limitations. Altogether 241 releases were identified (49% of major releases). Large number of releases could be related to historical records, with the major ones giving better results. The overall probability of correct detection (positive predictive power) was 58%, ranging from 50 to 67%, probability for major releases was 78%, ranging from 63 to 100% for different sites. The ability of individual trees to mirror past coppice events was significantly affected by competition from neighboring trees (their number and the sum of distance-weighted basal areas). A dendro-ecological approach to the study of forest management history can serve as an input for current attempts of coppice reintroduction and for conservation purposes. PMID:26784583

  1. Detecting Coppice Legacies from Tree Growth.

    PubMed

    Müllerová, Jana; Pejcha, Vít; Altman, Jan; Plener, Tomáš; Dörner, Petr; Doležal, Jiří

    2016-01-01

    In coppice-with-standards, once a common type of management in Central European lowland forests, selected trees (standards) were left to grow mature among the regularly harvested coppice stools to obtain construction wood. After the underwood was harvested, the forest canopy opened rapidly, giving standard trees an opportunity to benefit from reduced competition. Although this silvicultural system virtually disappeared after WWII, historical management cycles can still be traced in the tree-rings of remaining standards. Our research aims at answering the question whether tree-ring series of standard trees can be used to reconstruct past management practices. The study was carried out on 117 oak standard trees from five sites situated in formerly coppiced calcareous oak-hornbeam and acidophilous oak forests in the Bohemian Karst Protected Landscape Area, Czech Republic. The evaluation was based on the analysis of growth releases representing the response of the standards to coppicing events, and comparison to the archival records of coppice events. Our results showed that coppicing events can be successfully detected by tree-ring analysis, although there are some limitations. Altogether 241 releases were identified (49% of major releases). Large number of releases could be related to historical records, with the major ones giving better results. The overall probability of correct detection (positive predictive power) was 58%, ranging from 50 to 67%, probability for major releases was 78%, ranging from 63 to 100% for different sites. The ability of individual trees to mirror past coppice events was significantly affected by competition from neighboring trees (their number and the sum of distance-weighted basal areas). A dendro-ecological approach to the study of forest management history can serve as an input for current attempts of coppice reintroduction and for conservation purposes. PMID:26784583

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

    PubMed

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

    2015-09-01

    Isolated trees in savannas worldwide are known to modify their local environment and interact directly with neighboring plants. Less is known about how related tree species differ in their impacts on surrounding communities, how the effects of trees vary between years, and how composition might change following loss of the tree. To address these knowledge gaps, we explored the following questions: How do savanna trees influence the surrounding composition of herbaceous plants? Is the influence of trees consistent across different species and years? How does this change following the death of the tree? We surveyed herbaceous species composition and environmental attributes surrounding living and dead evergreen and deciduous Quercus trees in California (USA) savannas across several years that differed in their total precipitation. Oak trees of all species created distinct, homogenous understory communities dominated by exotic grasses across several sites. The composition of the low-diversity understory communities showed less interannual variation than open grassland, despite a two-fold difference in precipitation between the driest and wettest year. Vegetation composition was correlated with variation in soil properties, which were strongly affected by trees. Oaks also influenced the communities beyond the edge of the crown, but this depended on site and oak species. Low-diversity understory communities persisted up to 43 years following the death of the tree. A gradual decline in the effect of trees on the physical, environment following death did not result in vegetation becoming more similar to open grassland over time. The presence of long-lasting legacies of past tree crowns highlights the difficulty of assigning control of the current distribution of herbaceous species in grassland to their contemporary environment. PMID:26594707

  3. Type I Error Control for Tree Classification

    PubMed Central

    Jung, Sin-Ho; Chen, Yong; Ahn, Hongshik

    2014-01-01

    Binary tree classification has been useful for classifying the whole population based on the levels of outcome variable that is associated with chosen predictors. Often we start a classification with a large number of candidate predictors, and each predictor takes a number of different cutoff values. Because of these types of multiplicity, binary tree classification method is subject to severe type I error probability. Nonetheless, there have not been many publications to address this issue. In this paper, we propose a binary tree classification method to control the probability to accept a predictor below certain level, say 5%. PMID:25452689

  4. Tree Death Study's Climate Change Connections

    ScienceCinema

    McDowell, Nate

    2014-06-25

    What are the exact physiological mechanisms that lead to tree death during prolonged drought and rising temperatures? These are the questions that scientists are trying to answer at a Los Alamos National Laboratory research project called SUMO. SUMO stands for SUrvival/MOrtality study; it's a plot of land on the Lab's southern border that features 18 climate controlled tree study chambers and a large drought structure that limits rain and snowfall. Scientists are taking a wide variety of measurements over a long period of time to determine what happens during drought and warming, and what the connections and feedback loops might be between tree death and climate change.

  5. Tree Death Study's Climate Change Connections

    SciTech Connect

    McDowell, Nate

    2012-09-10

    What are the exact physiological mechanisms that lead to tree death during prolonged drought and rising temperatures? These are the questions that scientists are trying to answer at a Los Alamos National Laboratory research project called SUMO. SUMO stands for SUrvival/MOrtality study; it's a plot of land on the Lab's southern border that features 18 climate controlled tree study chambers and a large drought structure that limits rain and snowfall. Scientists are taking a wide variety of measurements over a long period of time to determine what happens during drought and warming, and what the connections and feedback loops might be between tree death and climate change.

  6. IND - THE IND DECISION TREE PACKAGE

    NASA Technical Reports Server (NTRS)

    Buntine, W.

    1994-01-01

    A common approach to supervised classification and prediction in artificial intelligence and statistical pattern recognition is the use of decision trees. A tree is "grown" from data using a recursive partitioning algorithm to create a tree which has good prediction of classes on new data. Standard algorithms are CART (by Breiman Friedman, Olshen and Stone) and ID3 and its successor C4 (by Quinlan). As well as reimplementing parts of these algorithms and offering experimental control suites, IND also introduces Bayesian and MML methods and more sophisticated search in growing trees. These produce more accurate class probability estimates that are important in applications like diagnosis. IND is applicable to most data sets consisting of independent instances, each described by a fixed length vector of attribute values. An attribute value may be a number, one of a set of attribute specific symbols, or it may be omitted. One of the attributes is delegated the "target" and IND grows trees to predict the target. Prediction can then be done on new data or the decision tree printed out for inspection. IND provides a range of features and styles with convenience for the casual user as well as fine-tuning for the advanced user or those interested in research. IND can be operated in a CART-like mode (but without regression trees, surrogate splits or multivariate splits), and in a mode like the early version of C4. Advanced features allow more extensive search, interactive control and display of tree growing, and Bayesian and MML algorithms for tree pruning and smoothing. These often produce more accurate class probability estimates at the leaves. IND also comes with a comprehensive experimental control suite. IND consists of four basic kinds of routines: data manipulation routines, tree generation routines, tree testing routines, and tree display routines. The data manipulation routines are used to partition a single large data set into smaller training and test sets. The generation routines are used to build classifiers. The test routines are used to evaluate classifiers and to classify data using a classifier. And the display routines are used to display classifiers in various formats. IND is written in C-language for Sun4 series computers. It consists of several programs with controlling shell scripts. Extensive UNIX man entries are included. IND is designed to be used on any UNIX system, although it has only been thoroughly tested on SUN platforms. The standard distribution medium for IND is a .25 inch streaming magnetic tape cartridge in UNIX tar format. An electronic copy of the documentation in PostScript format is included on the distribution medium. IND was developed in 1992.

  7. Chlorinated ethenes from groundwater in tree trunks

    USGS Publications Warehouse

    Vroblesky, D.A.; Nietch, C.T.; Morris, J.T.

    1999-01-01

    The purpose of this investigation was to determine whether tree-core analysis could be used to delineate shallow groundwater contamination by chlorinated ethenes. Analysis of tree- Cores from bald cypress [Taxodium distichum (L.) Rich], tupelo (Nyssa aquatica L.), sweet gum (Liquidambar stryaciflua L.), oak (Quercus spp.), sycamore (Platanus occidentalis L.), and Ioblolly pine (Pinus taeda L.) growing over shallow groundwater contaminated with cis-1,2-dichloroethene (cDCE) and trichloroethene (TCE) showed that those compounds also were present in the trees. The cores were collected and analyzed by headspace gas chromatography. Bald cypress, tupelo, and loblolly pine contained the highest concentrations of TCE, with lesser amounts in nearby oak and sweet gum. The concentrations of cDCE and TCE in various trees appeared to reflect the configuration of the chlorinated-solvent groundwater contamination plume. Bald cypress cores collected along 18.6-m vertical transects of the same trunks showed that TCE concentrations decline by 30- 70% with trunk height. The ability of the tested trees to take up cDCE and TCE make tree coring a potentially cost-effective and simple approach to optimizing well placement at this site.The purpose of this investigation was to determine whether tree-core analysis could be used to delineate shallow groundwater contamination by chlorinated ethenes. Analysis of tree cores from bald cypress [Taxodium distichum (L.) Rich], tupelo (Nyssa aquatica L.), sweet gum (Liquidambar stryaciflua L.), oak (Quercus spp.), sycamore (Platanus occidentalis L.), and loblolly pine (Pinus taeda L.) growing over shallow groundwater contaminated with cis-1,2-dichloroethene (cDCE) and trichloroethene (TCE) showed that those compounds also were present in the trees. The cores were collected and analyzed by headspace gas chromatography. Bald cypress, tupelo, and loblolly pine contained the highest concentrations of TCE, with lesser amounts in nearby oak and sweet gum. The concentrations of cDCE and TCE in various trees appeared to reflect the configuration of the chlorinated-solvent groundwater contamination plume. Bald cypress cores collected along 18.6-m vertical transects of the same trunks showed that TCE concentrations decline by 30-70% with trunk height. The ability of the tested trees to take up cDCE and TCE make tree coring a potentially cost-effective and simple approach to optimizing well placement at this site.

  8. The decision tree approach to classification

    NASA Technical Reports Server (NTRS)

    Wu, C.; Landgrebe, D. A.; Swain, P. H.

    1975-01-01

    A class of multistage decision tree classifiers is proposed and studied relative to the classification of multispectral remotely sensed data. The decision tree classifiers are shown to have the potential for improving both the classification accuracy and the computation efficiency. Dimensionality in pattern recognition is discussed and two theorems on the lower bound of logic computation for multiclass classification are derived. The automatic or optimization approach is emphasized. Experimental results on real data are reported, which clearly demonstrate the usefulness of decision tree classifiers.

  9. Algorithms for optimal dyadic decision trees

    SciTech Connect

    Hush, Don; Porter, Reid

    2009-01-01

    A new algorithm for constructing optimal dyadic decision trees was recently introduced, analyzed, and shown to be very effective for low dimensional data sets. This paper enhances and extends this algorithm by: introducing an adaptive grid search for the regularization parameter that guarantees optimal solutions for all relevant trees sizes, revising the core tree-building algorithm so that its run time is substantially smaller for most regularization parameter values on the grid, and incorporating new data structures and data pre-processing steps that provide significant run time enhancement in practice.

  10. Behavior Trees for Evolutionary Robotics.

    PubMed

    Scheper, Kirk Y W; Tijmons, Sjoerd; de Visser, Cornelis C; de Croon, Guido C H E

    2016-01-01

    Evolutionary Robotics allows robots with limited sensors and processing to tackle complex tasks by means of sensory-motor coordination. In this article we show the first application of the Behavior Tree framework on a real robotic platform using the evolutionary robotics methodology. This framework is used to improve the intelligibility of the emergent robotic behavior over that of the traditional neural network formulation. As a result, the behavior is easier to comprehend and manually adapt when crossing the reality gap from simulation to reality. This functionality is shown by performing real-world flight tests with the 20-g DelFly Explorer flapping wing micro air vehicle equipped with a 4-g onboard stereo vision system. The experiments show that the DelFly can fully autonomously search for and fly through a window with only its onboard sensors and processing. The success rate of the optimized behavior in simulation is 88%, and the corresponding real-world performance is 54% after user adaptation. Although this leaves room for improvement, it is higher than the 46% success rate from a tuned user-defined controller. PMID:26606468

  11. Pendelluft in the bronchial tree

    PubMed Central

    Greenblatt, Elliot E.; Butler, James P.; Venegas, Jose G.

    2014-01-01

    Inhomogeneous inflation or deflation of the lungs can cause dynamic pressure differences between regions and lead to interregional airflows known as pendelluft. This work first uses analytical tools to clarify the theoretical limits of pendelluft at a single bifurcation. It then explores the global and regional pendelluft that may occur throughout the bronchial tree in a realistic example using an in silico model of bronchoconstriction. The theoretical limits of pendelluft volume exchanged at a local bifurcation driven by sinusoidal breathing range from 15.5% to 41.4% depending on the relative stiffness of the subtended regions. When nonsinusoidal flows are considered, pendelluft can be as high as 200% inlet tidal volume (Vin). At frequencies greater than 10 Hz, the inertia of the air in the airways becomes important, and the maximal local pendelluft is theoretically unbounded, even with sinusoidal breathing. In a single illustrative numerical simulation of bronchoconstriction with homogenous compliances, the overall magnitude of global pendelluft volume was <2% of the tidal volume. Despite the small overall magnitude, pendelluft volume exchange was concentrated in poorly ventilated regions of the lung, including local pendelluft at bifurcations of up to 13% Vin. This example suggests that pendelluft may be an important phenomena contributing to regional gas exchange, irreversible mixing, and aerosol deposition patterns inside poorly ventilated regions of the lung. The analytical results support the concept that pendelluft may be more prominent in diseases with significant heterogeneity in both resistance and compliance. PMID:25170072

  12. Distributed game-tree searching

    SciTech Connect

    Schaeffer, J. )

    1989-02-01

    Conventional parallelizations of the alpha-beta ({alpha}{beta}) algorithm have met with limited success. Implementations suffer primarily from the synchronization and search overheads of parallelization. This paper describes a parallel {alpha}{beta} searching program that achieves high performance through the use of four different types of processes: Controllers, Searchers, Table Managers, and Scouts. Synchronization is reduced by having Controller process reassigning idle processes to help out busy ones. Search overhead is reduced by having two types of parallel table management: global Table Managers and the periodic merging and redistribution of local tables. Experiments show that nine processors can achieve 5.67-fold speedups but beyond that, additional processors provide diminishing returns. Given that additional resources are of little benefit, speculative computing is introduced as a means of extending the effective number of processors that can be utilized. Scout processes speculatively search ahead in the tree looking for interesting features and communicate this information back to the {alpha}{beta} program. In this way, the effective search depth is extended. These ideas have been tested experimentally and empirically as part of the chess program ParaPhoenix.

  13. Tree Edit Distance Problems: Algorithms and Applications to Bioinformatics

    NASA Astrophysics Data System (ADS)

    Akutsu, Tatsuya

    Tree structured data often appear in bioinformatics. For example, glycans, RNA secondary structures and phylogenetic trees usually have tree structures. Comparison of trees is one of fundamental tasks in analysis of these data. Various distance measures have been proposed and utilized for comparison of trees, among which extensive studies have been done on tree edit distance. In this paper, we review key results and our recent results on the tree edit distance problem and related problems. In particular, we review polynomial time exact algorithms and more efficient approximation algorithms for the edit distance problem for ordered trees, and approximation algorithms for the largest common sub-tree problem for unordered trees. We also review applications of tree edit distance and its variants to bioinformatics with focusing on comparison of glycan structures.

  14. 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. PMID:26357320

  15. On some trees having partition dimension four

    NASA Astrophysics Data System (ADS)

    Ida Bagus Kade Puja Arimbawa, K.; Baskoro, Edy Tri

    2016-02-01

    In 1998, G. Chartrand, E. Salehi and P. Zhang introduced the notion of partition dimension of a graph. Since then, the study of this graph parameter has received much attention. A number of results have been obtained to know the values of partition dimensions of various classes of graphs. However, for some particular classes of graphs, finding of their partition dimensions is still not completely solved, for instances a class of general tree. In this paper, we study the properties of trees having partition dimension 4. In particular, we show that, for olive trees O(n), its partition dimension is equal to 4 if and only if 8 ≤ n ≤ 17. We also characterize all centipede trees having partition dimension 4.

  16. Worms and Trees: An Exciting Adventure.

    ERIC Educational Resources Information Center

    El Harim, Jean Love

    1997-01-01

    Outlines procedures for using silkworms in elementary science, mathematics, history, ecology, social studies, language arts, art, and physical education. Also focuses on the silkworm's use of the mulberry tree. (DDR)

  17. Constructing event trees for volcanic crises

    USGS Publications Warehouse

    Newhall, C.; Hoblitt, R.

    2002-01-01

    Event trees are useful frameworks for discussing probabilities of possible outcomes of volcanic unrest. Each branch of the tree leads from a necessary prior event to a more specific outcome, e.g., from an eruption to a pyroclastic flow. Where volcanic processes are poorly understood, probability estimates might be purely empirical - utilizing observations of past and current activity and an assumption that the future will mimic the past or follow a present trend. If processes are better understood, probabilities might be estimated from a theoritical model, either subjectively or by numerical simulations. Use of Bayes' theorem aids in the estimation of how fresh unrest raises (or lowers) the probabilities of eruptions. Use of event trees during volcanic crises can help volcanologists to critically review their analysis of hazard, and help officials and individuals to compare volcanic risks with more familiar risks. Trees also emphasize the inherently probabilistic nature of volcano forecasts, with multiple possible outcomes.

  18. Tree ring record chronicles major Mesoamerican droughts

    NASA Astrophysics Data System (ADS)

    Tretkoff, Ernie

    2011-05-01

    A new tree ring record chronicles major Mesoamerican droughts in the past millennium that may have contributed to the decline of some pre-Hispanic civilizations. Although there is other evidence of droughts during the past millennium, the paleoclimate record had gaps. Stahle et al. used core samples from Montezuma bald cypress trees found in Barranca de Amealco, Querétaro, Mexico, to develop a 1238-year tree ring chronology. They reconstructed the soil moisture record from the tree ring growth patterns. The new record provides the first dated, annually resolved climate record for Mexico and Central America spanning this time period.(Geophysical Research Letters, doi:10.1029/2010GL046472, 2011)

  19. Locating POPs Sources with Tree Bark.

    PubMed

    Peverly, Angela A; Salamova, Amina; Hites, Ronald A

    2015-12-01

    Locating sources of persistent organic pollutants (POPs) to the atmosphere can sometimes be difficult. We suggest that tree bark makes an excellent passive atmospheric sampler and that spatial analysis of tree bark POPs concentrations can often pinpoint their sources. This is an effective strategy because tree bark is lipophilic and readily adsorbs and collects POPs from the atmosphere. As such, tree bark is an ideal sampler to find POPs sources globally, regionally, or locally. This article summarizes some work on this subject with an emphasis on kriged maps and a simple power-law model, both of which have been used to locate sources. Three of the four examples led directly to the pollutant's manufacturing plant. PMID:25629888

  20. Decision tree helps select hydrotreating catalyst

    SciTech Connect

    Kellett, T.F.; Trevino, C.A.; Sartor, A.F.

    1980-01-01

    Decision tree helps select hydrotreating catalyst, as is shown by use of the decision tree to select between Shell 324, a second-generation nickel/molybdenum catalyst, and Shell 344, a second-generation cobalt/molybdenum catalyst, in a number of applications, including the desulfurization of a vacuum gas oil to 0.1% by wt product sulfur for a straight-run feedstock, desulfurization of a flashed distillate, denitrogenation, hydrotreating a gas oil for fluid catalytic cracker feed, and denitrogenation and H/sub 2/ uptake for cracked stocks. Operating data reported in the literature support the catalyst choices indicated by the decision tree. The decision tree does not indicate a preferred catalyst in cases involving desulfurization and denitrogenation of a straight run to given levels, and the hydrotreating for desulfurization of cracked stocks. Cracked stock processing difficulties, which sometimes require that a catalyst other than the preferred catalyst be used, are discussed.

  1. Systolic tree implementation of data structures

    SciTech Connect

    Chang, J.H.; Ibarra, O.H.; Chung, M.J.; Rao, K.K.

    1988-06-01

    The authors present systolic tree architectures for data structures such as stacks, queues, dequeues, priority queues, and dictionary machines. The stack, queue, and dequeue have a unit response time and a unit pipeline interval. The priority queue also has a unit response time, but the pipeline interval is 2. The response time and pipeline interval for the dictionary machine are O(log n) and O(1), respectively, where n is the number of data elements currently residing in the tree. In each node of the tree, the mechanism for controlling the transmission and distribution of data is finite state. This feature makes the designs presented here suitable for VLSI. If there are n data elements in the data structure, the depth of the tree is O(log n).

  2. Full modeling versus summarizing gene-tree uncertainty: method choice and species-tree accuracy.

    PubMed

    Knowles, L Lacey; Lanier, Hayley C; Klimov, Pavel B; He, Qixin

    2012-11-01

    With the proliferation of species-tree methods, empiricists now have to confront the daunting task of method choice. Such decisions might be made based on theoretical considerations alone. However, the messiness of real data means that theoretical ideals may not hold in practice (e.g., with convergence of complicated MCMC algorithms and computational times that limit analyses to small data sets). On the other hand, simplifying assumptions made by some approaches may compromise the accuracy of species-tree estimates. Here we examine the purported tradeoff between accuracy and computational simplicity for species-tree analysis, focusing on the different ways the approaches treat gene-tree uncertainty. By considering a diversity of species trees, as well as different sampling designs and total sampling efforts, we not only compare the accuracy of species-tree estimates across methods, but we also partition the variation in accuracy across factors to identify their relative importance. This analysis shows that although the method of analysis affects accuracy, other factors - namely, the history of species divergence and aspects of the sampling design - have a larger impact. Despite a full modeling of gene tree uncertainty (e.g., using a Bayesian framework), species-tree estimates may not be accurate, particularly for recent diversification histories. Nevertheless, we demonstrate how factors within the control of the empirical investigator (e.g., decisions about sampling) improve the accuracy of species tree estimates, and more so than the method of analysis. Lastly, with much of the attention on species-tree analyses focused on the discord among loci arising from the coalescent, this work also highlights a previously overlooked key determinant of species-tree accuracy for recent divergences - the level of genetic variation at a locus, which has important implications for improving species-tree estimates in practice. PMID:22835380

  3. Trees and networks before and after Darwin

    PubMed Central

    2009-01-01

    It is well-known that Charles Darwin sketched abstract trees of relationship in his 1837 notebook, and depicted a tree in the Origin of Species (1859). Here I attempt to place Darwin's trees in historical context. By the mid-Eighteenth century the Great Chain of Being was increasingly seen to be an inadequate description of order in nature, and by about 1780 it had been largely abandoned without a satisfactory alternative having been agreed upon. In 1750 Donati described aquatic and terrestrial organisms as forming a network, and a few years later Buffon depicted a network of genealogical relationships among breeds of dogs. In 1764 Bonnet asked whether the Chain might actually branch at certain points, and in 1766 Pallas proposed that the gradations among organisms resemble a tree with a compound trunk, perhaps not unlike the tree of animal life later depicted by Eichwald. Other trees were presented by Augier in 1801 and by Lamarck in 1809 and 1815, the latter two assuming a transmutation of species over time. Elaborate networks of affinities among plants and among animals were depicted in the late Eighteenth and very early Nineteenth centuries. In the two decades immediately prior to 1837, so-called affinities and/or analogies among organisms were represented by diverse geometric figures. Series of plant and animal fossils in successive geological strata were represented as trees in a popular textbook from 1840, while in 1858 Bronn presented a system of animals, as evidenced by the fossil record, in a form of a tree. Darwin's 1859 tree and its subsequent elaborations by Haeckel came to be accepted in many but not all areas of biological sciences, while network diagrams were used in others. Beginning in the early 1960s trees were inferred from protein and nucleic acid sequences, but networks were re-introduced in the mid-1990s to represent lateral genetic transfer, increasingly regarded as a fundamental mode of evolution at least for bacteria and archaea. In historical context, then, the Network of Life preceded the Tree of Life and might again supersede it. Reviewers This article was reviewed by Eric Bapteste, Patrick Forterre and Dan Graur. PMID:19917100

  4. Parallel object-oriented decision tree system

    DOEpatents

    Kamath; Chandrika , Cantu-Paz; Erick

    2006-02-28

    A data mining decision tree system that uncovers patterns, associations, anomalies, and other statistically significant structures in data by reading and displaying data files, extracting relevant features for each of the objects, and using a method of recognizing patterns among the objects based upon object features through a decision tree that reads the data, sorts the data if necessary, determines the best manner to split the data into subsets according to some criterion, and splits the data.

  5. GRFT - Genetic Records Family Tree Web Applet.

    PubMed

    Pimentel, Samuel; Walbot, Virginia; Fernandes, John

    2011-01-01

    Current software for storing and displaying records of genetic crosses does not provide an easy way to determine the lineage of an individual. The genetic records family tree (GRFT) applet processes records of genetic crosses and allows researchers to quickly visualize lineages using a family tree construct and to access other information from these records using any Internet browser. Users select from three display features: (1) a family tree view which displays a color-coded family tree for an individual, (2) a sequential list of crosses, and (3) a list of crosses matching user-defined search criteria. Each feature contains options to specify the number of records shown and the latter two contain an option to filter results by the owner of the cross. The family tree feature is interactive, displaying a popup box with genetic information when the user mouses over an individual and allowing the user to draw a new tree by clicking on any individual in the current tree. The applet is written in JavaScript and reads genetic records from a tab-delimited text file on the server, so it is cross-platform, can be accessed by anyone with an Internet connection, and supports almost instantaneous generation of new trees and table lists. Researchers can use the tool with their own genetic cross records for any sexually reproducing organism. No additional software is required and with only minor modifications to the script, researchers can add their own custom columns. GRFT's speed, versatility, and low overhead make it an effective and innovative visualization method for genetic records. A sample tool is available at http://stanford.edu/walbot/grft-sample.html. PMID:22303311

  6. Predicting Gene Function using Predictive Clustering Trees

    NASA Astrophysics Data System (ADS)

    Vens, Celine; Schietgat, Leander; Struyf, Jan; Blockeel, Hendrik; Kocev, Dragi; Deroski, Sao

    In this chapter, we show how the predictive clustering tree framework can be used to predict the functions of genes. The gene function prediction task is an example of a hierarchical multi-label classification (HMC) task: genes may have multiple functions and these functions are organized in a hierarchy. The hierarchy of functions can be such that each function has at most one parent (tree structure) or such that functions may have multiple parents (DAG structure).

  7. A Conceptual Tree of Laser Propulsion

    SciTech Connect

    Pakhomov, Andrew V.; Sinko, John E.

    2008-04-28

    An original attempt to develop a conceptual tree for laser propulsion is offered. The tree provides a systematic view for practically all possible laser propulsion concepts and all inter-conceptual links, based on propellant phases and phase transfers. It also helps to see which fields of laser propulsion have been already thoroughly explored, where the next effort must be applied, and which paths should be taken with proper care or avoided entirely.

  8. Fatal head trauma from tree related injuries.

    PubMed

    Escoffery, C T; Shirley, S E

    2001-10-01

    Two cases of death following tree related injuries are presented. Two females, an elderly woman and a child, suffered severe head trauma from falling objects from trees--a falling coconut and a falling branch respectively. Although this mode of injury has been previously documented, there have been no prior reports of in-hospital deaths in such patients. This uncommon cause of death is reviewed and recommendations made concerning its prevention. PMID:11693223

  9. TPM: Tree-Particle-Mesh code

    NASA Astrophysics Data System (ADS)

    Bode, Paul

    2013-05-01

    TPM carries out collisionless (dark matter) cosmological N-body simulations, evolving a system of N particles as they move under their mutual gravitational interaction. It combines aspects of both Tree and Particle-Mesh algorithms. After the global PM forces are calculated, spatially distinct regions above a given density contrast are located; the tree code calculates the gravitational interactions inside these denser objects at higher spatial and temporal resolution. The code is parallel and uses MPI for message passing.

  10. 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

  11. Microbes in tree swallow semen.

    PubMed

    Lombardo, M P; Thorpe, P A

    2000-07-01

    A frequently hypothesized but poorly studied cost of multiple mating in birds is that exposure to pathogenic sexually transmitted microbes (STM's) can lower reproductive success. Conversely, female birds may benefit from high frequencies of copulation and multiple copulation partners if they receive cloacal inoculations of beneficial STM's that can either protect them against future encounters with pathogens and/or serve as therapy against present infection. We examined the semen of 30 male tree swallows (Tachycineta bicolor) in 1998 to determine the presence and prevalence of potential pathogenic and beneficial STM's. Semen was collected directly from males after applying gentle pressure to the cloaca and we used standard microbiological techniques to identify microbes. We found that 19 of 30 samples contained one or more types of microbes. In these 19 positive samples, we isolated both pathogenic and beneficial microbes from 11, only pathogenic microbes from seven, and only beneficial microbes from one. This variation among males suggests that females would benefit from considering a particular male's potential as a donor of either pathogenic or beneficial STM's as a criterion for mate choice. There were few significant differences between males with pathogen-infected semen and those without pathogens in their semen in measures of size, morphology, and ectoparasite score and feather damage. Likewise, there were few significant differences between males with beneficial Lactobacilli spp. in their semen and those without Lactobacilli spp. in their semen in measures of size, morphology, and ectoparasite score and feather damage. We were unable to determine if there was a relationship between microbe presence and prevalence on reproductive performance. PMID:10941730

  12. Intraspecific scaling laws of vascular trees

    PubMed Central

    Huo, Yunlong; Kassab, Ghassan S.

    2012-01-01

    A fundamental physics-based derivation of intraspecific scaling laws of vascular trees has not been previously realized. Here, we provide such a theoretical derivation for the volumediameter and flowlength scaling laws of intraspecific vascular trees. In conjunction with the minimum energy hypothesis, this formulation also results in diameterlength, flowdiameter and flowvolume scaling laws. The intraspecific scaling predicts the volumediameter power relation with a theoretical exponent of 3, which is validated by the experimental measurements for the three major coronary arterial trees in swine (where a least-squares fit of these measurements has exponents of 2.96, 3 and 2.98 for the left anterior descending artery, left circumflex artery and right coronary artery trees, respectively). This scaling law as well as others agrees very well with the measured morphometric data of vascular trees in various other organs and species. This study is fundamental to the understanding of morphological and haemodynamic features in a biological vascular tree and has implications for vascular disease. PMID:21676970

  13. Chlorinated ethenes from groundwater in tree trunks

    SciTech Connect

    Vroblesky, D.A.; Nietch, C.T.; Morris, J.T.

    1999-02-01

    The purpose of this investigation was to determine whether tree-core analysis could be used to delineate shallow groundwater contamination by chlorinated ethenes. Analysis of tree cores from bald cypress [Taxodium distichum (L.) Rich], tupelo (Nyssa aquatica L.), sweet gum (Liquidambar stryaciflua L.), oak (Quercus spp.), sycamore (Platanus occidentalis L.), and loblolly pine (Pinus taeda L.) growing over shallow groundwater contaminated with cis-1,2-dichloroethene (cDCE) and trichloroethene (TCE) showed that those compounds also were present in the trees. The cores were collected and analyzed by headspace gas chromatography. Bald cypress, tupelo, and loblolly pine contained the highest concentrations of TCE, with lesser amounts in nearby oak and sweet gum. The concentrations of cDCE and TCE in various trees appeared to reflect the configuration of the chlorinated-solvent groundwater contamination plume. Bald cypress cores collected along 18.6-m vertical transects of the same trunks showed that TCE concentrations decline by 30--70% with trunk height. The ability of the tested trees to take up cDCE and TCE make tree coring a potentially cost-effective and simple approach to optimizing well placement at this site.

  14. ANTLR Tree Grammar Generator and Extensions

    NASA Technical Reports Server (NTRS)

    Craymer, Loring

    2005-01-01

    A computer program implements two extensions of ANTLR (Another Tool for Language Recognition), which is a set of software tools for translating source codes between different computing languages. ANTLR supports predicated- LL(k) lexer and parser grammars, a notation for annotating parser grammars to direct tree construction, and predicated tree grammars. [ LL(k) signifies left-right, leftmost derivation with k tokens of look-ahead, referring to certain characteristics of a grammar.] One of the extensions is a syntax for tree transformations. The other extension is the generation of tree grammars from annotated parser or input tree grammars. These extensions can simplify the process of generating source-to-source language translators and they make possible an approach, called "polyphase parsing," to translation between computing languages. The typical approach to translator development is to identify high-level semantic constructs such as "expressions," "declarations," and "definitions" as fundamental building blocks in the grammar specification used for language recognition. The polyphase approach is to lump ambiguous syntactic constructs during parsing and then disambiguate the alternatives in subsequent tree transformation passes. Polyphase parsing is believed to be useful for generating efficient recognizers for C++ and other languages that, like C++, have significant ambiguities.

  15. Growing Greener Cities: A Tree-Planting Handbook.

    ERIC Educational Resources Information Center

    Moll, Gary; Young, Stanley

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

  16. 7 CFR 1437.306 - Christmas tree crops.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 10 2011-01-01 2011-01-01 false Christmas tree crops. 1437.306 Section 1437.306... Determining Coverage Using Value 1437.306 Christmas tree crops. (a) A Christmas tree is a value loss crop and may generate a claim for benefits under this part only if the tree was grown exclusively...

  17. 7 CFR 1437.306 - Christmas tree crops.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 10 2013-01-01 2013-01-01 false Christmas tree crops. 1437.306 Section 1437.306... Determining Coverage Using Value 1437.306 Christmas tree crops. (a) A Christmas tree is a value loss crop and may generate a claim for benefits under this part only if the tree was grown exclusively...

  18. 7 CFR 1437.306 - Christmas tree crops.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 10 2014-01-01 2014-01-01 false Christmas tree crops. 1437.306 Section 1437.306... Determining Coverage Using Value 1437.306 Christmas tree crops. (a) A Christmas tree is a value loss crop and may generate a claim for benefits under this part only if the tree was grown exclusively...

  19. 7 CFR 1437.306 - Christmas tree crops.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 10 2012-01-01 2012-01-01 false Christmas tree crops. 1437.306 Section 1437.306... Determining Coverage Using Value 1437.306 Christmas tree crops. (a) A Christmas tree is a value loss crop and may generate a claim for benefits under this part only if the tree was grown exclusively...

  20. Growing Greener Cities: A Tree-Planting Handbook.

    ERIC Educational Resources Information Center

    Moll, Gary; Young, Stanley

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

  1. A Spring Playscape Project: Building a Tree Circle

    ERIC Educational Resources Information Center

    Keeler, Rusty

    2009-01-01

    The Tree Circle is a green gathering area for children made by planting trees in a circle. For children, the Tree Circle becomes a magical place for dramatic play, quiet retreat, or lively nature exploration. For teachers and parents it becomes a shady grove for snacks and stories. The trees create a sweet spot that changes during the seasons and

  2. A Spring Playscape Project: Building a Tree Circle

    ERIC Educational Resources Information Center

    Keeler, Rusty

    2009-01-01

    The Tree Circle is a green gathering area for children made by planting trees in a circle. For children, the Tree Circle becomes a magical place for dramatic play, quiet retreat, or lively nature exploration. For teachers and parents it becomes a shady grove for snacks and stories. The trees create a sweet spot that changes during the seasons and…

  3. Fault tree analysis for maintenance needs

    NASA Astrophysics Data System (ADS)

    Halme, Jari; Aikala, Antti

    2012-05-01

    One of the key issues in maintenance is to allocate focus and resources to those components and subsystems which are the most unreliable and prone to failures. In industrial systems, fault tree analysis technique can be used to study the reliability of the complex systems and their substructures. In this paper a fault tree application for analyzing online the current reliability and failure probability for maintenance purposes is presented. The analysis is utilizing data connected to the fault tree root causes and events. An indication of an anomaly case, service action, cumulative loading, etc., or just time passed or service hour counter level can trigger a new calculation of current probabilities of the fault tree events and subsystem interactions. In proposed approach real time, dynamic information from several available data sources and different measurement are interconnected to each fault tree event and root cause. There is also formulated an active, constantly updated link between the fault tree events and maintenance databases for the maintenance decision support, and to keep the analysis up to date. Typically top event probability is evaluated based on updated root cause probabilities and lower level events. At the industrial plant level an identification of a failure in a component event defined within a constructed and operatively existing fault tree explicitly means that the event's failure probability is one. By utilizing this indication, the most probable failure branches through the fault tree sub events to root causes can be identified and printed as a valid check list for maintenance purposes to focus service actions first to those fault tree branches most probable causing the failure. Respectively, during the checks, service actions, etc., components, especially those within the critical branches, detected as healthy can be a updated as having zero failure probability. This information can be used to further update the fault tree and produce online a new service order list. The added value of the proposed method with respect to developed software platform functions lies in its applicability to rationalize maintenance actions and in a case of a failure allocate resources where they are assumable mostly needed.

  4. 75 FR 51507 - WisdomTree Asset Management, Inc., and WisdomTree Trust; Notice of Application

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-20

    ... COMMISSION WisdomTree Asset Management, Inc., and WisdomTree Trust; Notice of Application August 13, 2010... materially amend subadvisory agreements without shareholder approval. Applicants: WisdomTree Asset Management, Inc (``WTAM'' or ``Adviser'') and WisdomTree Trust (``Trust''). Filing Dates: The application...

  5. Efficient Exploration of the Space of Reconciled Gene Trees

    PubMed Central

    Szll?si, 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 treespecies 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 treespecies 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 (Szll?si 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

  6. Radiocarbon in Tree STEM CO2 Efflux

    NASA Astrophysics Data System (ADS)

    Muhr, J.; Czimczik, C. I.; Angert, A.; Trumbore, S.

    2011-12-01

    Carbon dioxide efflux from tree stems can be a significant component of the stand-level carbon balance. Recent studies have demonstrated that tree stem CO2 efflux may reflect more than just in-situ respiration but also transport from other locations and it has been suggested that it may also include C originally respired in roots or even uptake of soil CO2. We report measurements of the radiocarbon signature of carbon emitted from a range of mature tree stems in tropical and temperate forest ecosystems. Comparison of the radiocarbon signature of respired CO2 with the observed rate of decline in atmsopheric 14C-CO2 provides a measure of the time elapsed between C fixation by the plant and its return to the atmosphere as stem CO2 efflux. In all investigated trees, we observed that stem CO2 efflux had higher radiocarbon signatures than the contemporary atmospheric 14C-CO2, and therefore was derived from C fixed one to several years earlier. In tropical forest trees, we found that the 14C signature of CO2 within the stem (~4-5 cm depth) had even higher radiocarbon signatures than the stem CO2 efflux. In one of the investigated tree species, the in-stem CO2 was derived from C sources fixed on average ~20 years previously. These results confirm observations of root-respired CO2 that also have shown contributions of C substrates older than recent photosynthetic products, and the presence of extracable C reserves in wood that reflect the presence of older C sources. Our results imply that stem CO2 efflux is not only derived from respiration of recent photosynthetic products but includes contributions from older, stored C pools. Ongoing investigations will enable us to compare CO2 efflux for trees subjected to experimental drought, and using different life strategies (deciduous versus evergreen oaks) to determine if the use of these older C stores varies with stress.

  7. Tree mineral nutrition is deteriorating in Europe.

    PubMed

    Jonard, Mathieu; Fürst, Alfred; Verstraeten, Arne; Thimonier, Anne; Timmermann, Volkmar; Potočić, Nenad; Waldner, Peter; Benham, Sue; Hansen, Karin; Merilä, Päivi; Ponette, Quentin; de la Cruz, Ana C; Roskams, Peter; Nicolas, Manuel; Croisé, Luc; Ingerslev, Morten; Matteucci, Giorgio; Decinti, Bruno; Bascietto, Marco; Rautio, Pasi

    2015-01-01

    The response of forest ecosystems to increased atmospheric CO2 is constrained by nutrient availability. It is thus crucial to account for nutrient limitation when studying the forest response to climate change. The objectives of this study were to describe the nutritional status of the main European tree species, to identify growth-limiting nutrients and to assess changes in tree nutrition during the past two decades. We analysed the foliar nutrition data collected during 1992-2009 on the intensive forest monitoring plots of the ICP Forests programme. Of the 22 significant temporal trends that were observed in foliar nutrient concentrations, 20 were decreasing and two were increasing. Some of these trends were alarming, among which the foliar P concentration in F. sylvatica, Q. Petraea and P. sylvestris that significantly deteriorated during 1992-2009. In Q. Petraea and P. sylvestris, the decrease in foliar P concentration was more pronounced on plots with low foliar P status, meaning that trees with latent P deficiency could become deficient in the near future. Increased tree productivity, possibly resulting from high N deposition and from the global increase in atmospheric CO2, has led to higher nutrient demand by trees. As the soil nutrient supply was not always sufficient to meet the demands of faster growing trees, this could partly explain the deterioration of tree mineral nutrition. The results suggest that when evaluating forest carbon storage capacity and when planning to reduce CO2 emissions by increasing use of wood biomass for bioenergy, it is crucial that nutrient limitations for forest growth are considered. PMID:24920268

  8. Temperature histories from tree rings and corals

    SciTech Connect

    Cook, E.R.

    1995-05-01

    Recent temperature trends in long tree-ring and coral proxy temperature histories are evaluated and compared in an effort to objectively determine how anomalous twentieth century temperature changes have been. These histories mostly reflect regional variations in summer warmth from the tree rings and annual warmth from the corals. In the Northern Hemisphere. the North American tree-ring temperature histories and those from the north Polar Urals, covering the past 1000 or more years, indicate that the twentieth century has been anomalously warm relative to the past. In contrast, the tree-ring history from northern Fennoscandia indicates that summer temperatures during the {open_quote}Medieval Warm Period{close_quote} were probably warmer on average than those than during this century. In the Southern Hemisphere, the tree-ring temperature histories from South America show no indication of recent warming, which is in accordance with local instrumental records. In contrast, the tree-ring, records from Tasmania and New Zealand indicate that the twentieth century has been unusually warm particularly since 1960. The coral temperature histories from the Galapagos Islands and the Great Barrier Reef are in broad agreement with the tree-ring temperature histories in those sectors, with the former showing recent cooling and the latter showing recent warming that may be unprecedented. Overall, the regional temperature histories evaluated here broadly support the larger-scale evidence for anomalous twentieth century warming based on instrumental records. However, this warming cannot be confirmed as an unprecedented event in all regions. 38 refs., 3 figs., 2 tabs.

  9. GM trees with increased resistance to herbivores: trait efficiency and their potential to promote tree growth.

    PubMed

    Hjältén, Joakim; Axelsson, E Petter

    2015-01-01

    Climate change, as well as a more intensive forestry, is expected to increase the risk of damage by pests and pathogens on trees, which can already be a severe problem in tree plantations. Recent development of biotechnology theoretically allows for resistance enhancement that could help reduce these risks but we still lack a comprehensive understanding of benefits and tradeoffs with pest resistant GM (genetically modified) trees. We synthesized the current knowledge on the effectiveness of GM forest trees with increased resistance to herbivores. There is ample evidence that induction of exogenous Bacillus thuringiensis genes reduce performance of target pests whereas upregulation of endogenous resistance traits e.g., phenolics, generates variable results. Our review identified very few studies estimating the realized benefits in tree growth of GM trees in the field. This is concerning as the realized benefit with insect resistant GM plants seems to be context-dependent and likely manifested only if herbivore pressure is sufficiently high. Future studies of secondary pest species and resistance evolution in pest to GM trees should be prioritized. But most importantly we need more long-term field tests to evaluate the benefits and risks with pest resistant GM trees. PMID:25983736

  10. Phylogenetic Tree Reconstruction Accuracy and Model Fit when Proportions of Variable Sites Change across the Tree

    PubMed Central

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

    2010-01-01

    Commonly used phylogenetic models assume a homogeneous process through time in all parts of the tree. However, it is known that these models can be too simplistic as they do not account for nonhomogeneous lineage-specific properties. In particular, it is now widely recognized that as constraints on sequences evolve, the proportion and positions of variable sites can vary between lineages causing heterotachy. The extent to which this model misspecification affects tree reconstruction is still unknown. Here, we evaluate the effect of changes in the proportions and positions of variable sites on model fit and tree estimation. We consider 5 current models of nucleotide sequence evolution in a Bayesian Markov chain Monte Carlo framework as well as maximum parsimony (MP). We show that for a tree with 4 lineages where 2 nonsister taxa undergo a change in the proportion of variable sites tree reconstruction under the best-fitting model, which is chosen using a relative test, often results in the wrong tree. In this case, we found that an absolute test of model fit is a better predictor of tree estimation accuracy. We also found further evidence that MP is not immune to heterotachy. In addition, we show that increased sampling of taxa that have undergone a change in proportion and positions of variable sites is critical for accurate tree reconstruction. PMID:20525636

  11. "Trees and Things That Live in Trees": Three Children with Special Needs Experience the Project Approach

    ERIC Educational Resources Information Center

    Griebling, Susan; Elgas, Peg; Konerman, Rachel

    2015-01-01

    The authors report on research conducted during a project investigation undertaken with preschool children, ages 3-5. The report focuses on three children with special needs and the positive outcomes for each child as they engaged in the project Trees and Things That Live in Trees. Two of the children were diagnosed with developmental delays, and…

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

    PubMed Central

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

    2013-01-01

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

  13. Growth cessation uncouples isotopic signals in leaves and tree rings of drought-exposed oak trees.

    PubMed

    Pflug, Ellen E; Siegwolf, R; Buchmann, N; Dobbertin, M; Kuster, T M; Günthardt-Goerg, M S; Arend, M

    2015-10-01

    An increase in temperature along with a decrease in summer precipitation in Central Europe will result in an increased frequency of drought events and gradually lead to a change in species composition in forest ecosystems. In the present study, young oaks (Quercus robur L. and Quercus petraea (Matt.) Liebl.) were transplanted into large mesocosms and exposed for 3 years to experimental warming and a drought treatment with yearly increasing intensities. Carbon and oxygen isotopic (δ(13)C and δ(18)O) patterns were analysed in leaf tissue and tree-ring cellulose and linked to leaf physiological measures and tree-ring growth. Warming had no effect on the isotopic patterns in leaves and tree rings, while drought increased δ(18)O and δ(13)C. Under severe drought, an unexpected isotopic pattern, with a decrease in δ(18)O, was observed in tree rings but not in leaves. This decrease in δ(18)O could not be explained by concurrent physiological analyses and is not supported by current physiological knowledge. Analysis of intra-annual tree-ring growth revealed a drought-induced growth cessation that interfered with the record of isotopic signals imprinted on recently formed leaf carbohydrates. This missing record indicates isotopic uncoupling of leaves and tree rings, which may have serious implications for the interpretation of tree-ring isotopes, particularly from trees that experienced growth-limiting stresses. PMID:26377873

  14. GM trees with increased resistance to herbivores: trait efficiency and their potential to promote tree growth

    PubMed Central

    Hjältén, Joakim; Axelsson, E. Petter

    2015-01-01

    Climate change, as well as a more intensive forestry, is expected to increase the risk of damage by pests and pathogens on trees, which can already be a severe problem in tree plantations. Recent development of biotechnology theoretically allows for resistance enhancement that could help reduce these risks but we still lack a comprehensive understanding of benefits and tradeoffs with pest resistant GM (genetically modified) trees. We synthesized the current knowledge on the effectiveness of GM forest trees with increased resistance to herbivores. There is ample evidence that induction of exogenous Bacillus thuringiensis genes reduce performance of target pests whereas upregulation of endogenous resistance traits e.g., phenolics, generates variable results. Our review identified very few studies estimating the realized benefits in tree growth of GM trees in the field. This is concerning as the realized benefit with insect resistant GM plants seems to be context-dependent and likely manifested only if herbivore pressure is sufficiently high. Future studies of secondary pest species and resistance evolution in pest to GM trees should be prioritized. But most importantly we need more long-term field tests to evaluate the benefits and risks with pest resistant GM trees. PMID:25983736

  15. Feedback of trees on nitrogen mineralization to restrict the advance of trees in C4 savannahs.

    PubMed

    Higgins, Steven I; Keretetse, Moagi; February, Edmund C

    2015-08-01

    Remote sensing studies suggest that savannahs are transforming into more tree-dominated states; however, progressive nitrogen limitation could potentially retard this putatively CO2-driven invasion. We analysed controls on nitrogen mineralization rates in savannah by manipulating rainfall and the cover of grass and tree elements against the backdrop of the seasonal temperature and rainfall variation. We found that the seasonal pattern of nitrogen mineralization was strongly influenced by rainfall, and that manipulative increases in rainfall could boost mineralization rates. Additionally, mineralization rates were considerably higher on plots with grasses and lower on plots with trees. Our findings suggest that shifting a savannah from a grass to a tree-dominated state can substantially reduce nitrogen mineralization rates, thereby potentially creating a negative feedback on the CO2-induced invasion of savannahs by trees. PMID:26268994

  16. Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

    PubMed Central

    Bryant, David; Bouckaert, Remco; Felsenstein, Joseph; Rosenberg, Noah A.; RoyChoudhury, Arindam

    2012-01-01

    The multispecies coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. However, practical applications of the multispecies coalescent model are limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation effectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms, and we have implemented it in SNAPP, a Markov chain Monte Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 amplified fragment length polymorphism loci in 69 individuals sampled from six species of Ourisia (New Zealand native foxglove). PMID:22422763

  17. Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis.

    PubMed

    Bryant, David; Bouckaert, Remco; Felsenstein, Joseph; Rosenberg, Noah A; RoyChoudhury, Arindam

    2012-08-01

    The multispecies coalescent provides an elegant theoretical framework for estimating species trees and species demographics from genetic markers. However, practical applications of the multispecies coalescent model are limited by the need to integrate or sample over all gene trees possible for each genetic marker. Here we describe a polynomial-time algorithm that computes the likelihood of a species tree directly from the markers under a finite-sites model of mutation effectively integrating over all possible gene trees. The method applies to independent (unlinked) biallelic markers such as well-spaced single nucleotide polymorphisms, and we have implemented it in SNAPP, a Markov chain Monte Carlo sampler for inferring species trees, divergence dates, and population sizes. We report results from simulation experiments and from an analysis of 1997 amplified fragment length polymorphism loci in 69 individuals sampled from six species of Ourisia (New Zealand native foxglove). PMID:22422763

  18. UniTree Name Server internals

    SciTech Connect

    Mecozzi, D.; Minton, J.

    1996-01-01

    The UniTree Name Server (UNS) is one of several servers which make up the UniTree storage system. The Name Server is responsible for mapping names to capabilities Names are generally human readable ASCII strings of any length. Capabilities are unique 256-bit identifiers that point to files, directories, or symbolic links. The Name Server implements a UNIX style hierarchical directory structure to facilitate name-to-capability mapping. The principal task of the Name Server is to manage the directories which make up the UniTree directory structure. The principle clients of the Name Server are the FTP Daemon, NFS and a few UniTree utility routines. However, the Name Server is a generalized server and will accept messages from any client. The purpose of this paper is to describe the internal workings of the UniTree Name Server. In cases where it seems appropriate, the motivation for a particular choice of algorithm as description of the algorithm itself will be given.

  19. Fast Image Texture Classification Using Decision Trees

    NASA Technical Reports Server (NTRS)

    Thompson, David R.

    2011-01-01

    Texture analysis would permit improved autonomous, onboard science data interpretation for adaptive navigation, sampling, and downlink decisions. These analyses would assist with terrain analysis and instrument placement in both macroscopic and microscopic image data products. Unfortunately, most state-of-the-art texture analysis demands computationally expensive convolutions of filters involving many floating-point operations. This makes them infeasible for radiation- hardened computers and spaceflight hardware. A new method approximates traditional texture classification of each image pixel with a fast decision-tree classifier. The classifier uses image features derived from simple filtering operations involving integer arithmetic. The texture analysis method is therefore amenable to implementation on FPGA (field-programmable gate array) hardware. Image features based on the "integral image" transform produce descriptive and efficient texture descriptors. Training the decision tree on a set of training data yields a classification scheme that produces reasonable approximations of optimal "texton" analysis at a fraction of the computational cost. A decision-tree learning algorithm employing the traditional k-means criterion of inter-cluster variance is used to learn tree structure from training data. The result is an efficient and accurate summary of surface morphology in images. This work is an evolutionary advance that unites several previous algorithms (k-means clustering, integral images, decision trees) and applies them to a new problem domain (morphology analysis for autonomous science during remote exploration). Advantages include order-of-magnitude improvements in runtime, feasibility for FPGA hardware, and significant improvements in texture classification accuracy.

  20. Towards optimizing wood development in bioenergy trees.

    PubMed

    Nieminen, Kaisa; Robischon, Marcel; Immanen, Juha; Helariutta, Yk

    2012-04-01

    To secure a sustainable energy source for the future, we need to develop an alternative to fossil fuels. Cellulose-based biofuel production has great potential for development into a sustainable and renewable energy source. The thick secondary walls of xylem cells provide a natural source of cellulose. As a result of the extensive production of wood through cambial activity, massive amounts of xylem cells can be harvested from trees. How can we obtain a maximal cellulose biomass yield from these trees? Thus far, tree breeding has been very challenging because of the long generation time. Currently, new breeding possibilities are emerging through the development of high-throughput technologies in molecular genetics. What potential does our current knowledge on the regulation of cambial activity provide for the domestication of optimal bioenergy trees? We examine the hormonal and molecular regulation of wood development with the aim of identifying the key regulatory aspects. We describe traits, including stem morphology and xylem cell dimensions, that could be modified to enhance wood production. Finally, we discuss the potential of novel marker-assisted tree breeding technologies. PMID:22474686

  1. Twistor-strings and gravity tree amplitudes

    NASA Astrophysics Data System (ADS)

    Adamo, Tim; Mason, Lionel

    2013-04-01

    Recently we discussed how Einstein supergravity tree amplitudes might be obtained from the original Witten and Berkovits twistor-string theory when external conformal gravitons are restricted to be Einstein gravitons. Here we obtain a more systematic understanding of the relationship between conformal and Einstein gravity amplitudes in that twistor-string theory. We show that although it does not in general yield Einstein amplitudes, we can nevertheless obtain some partial twistor-string interpretation of the remarkable formulae recently been found by Hodges and generalized to all tree amplitudes by Cachazo and Skinner. The Hodges matrix and its higher degree generalizations encode the world sheet correlators of the twistor string. These matrices control both Einstein amplitudes and those of the conformal gravity arising from the Witten and Berkovits twistor-string. Amplitudes in the latter case arise from products of the diagonal elements of the generalized Hodges matrices and reduced determinants give the former. The reduced determinants arise if the contractions in the worldsheet correlator are restricted to form connected trees at MHV. The (generalized) Hodges matrices arise as weighted Laplacian matrices for the graph of possible contractions in the correlators and the reduced determinants of these weighted Laplacian matrices give the sum of the connected tree contributions by an extension of the matrix-tree theorem.

  2. How tree roots respond to drought

    PubMed Central

    Brunner, Ivano; Herzog, Claude; Dawes, Melissa A.; Arend, Matthias; Sperisen, Christoph

    2015-01-01

    The ongoing climate change is characterized by increased temperatures and altered precipitation patterns. In addition, there has been an increase in both the frequency and intensity of extreme climatic events such as drought. Episodes of drought induce a series of interconnected effects, all of which have the potential to alter the carbon balance of forest ecosystems profoundly at different scales of plant organization and ecosystem functioning. During recent years, considerable progress has been made in the understanding of how aboveground parts of trees respond to drought and how these responses affect carbon assimilation. In contrast, processes of belowground parts are relatively underrepresented in research on climate change. In this review, we describe current knowledge about responses of tree roots to drought. Tree roots are capable of responding to drought through a variety of strategies that enable them to avoid and tolerate stress. Responses include root biomass adjustments, anatomical alterations, and physiological acclimations. The molecular mechanisms underlying these responses are characterized to some extent, and involve stress signaling and the induction of numerous genes, leading to the activation of tolerance pathways. In addition, mycorrhizas seem to play important protective roles. The current knowledge compiled in this review supports the view that tree roots are well equipped to withstand drought situations and maintain morphological and physiological functions as long as possible. Further, the reviewed literature demonstrates the important role of tree roots in the functioning of forest ecosystems and highlights the need for more research in this emerging field. PMID:26284083

  3. LocTree3 prediction of localization

    PubMed Central

    Goldberg, Tatyana; Hecht, Maximilian; Hamp, Tobias; Karl, Timothy; Yachdav, Guy; Ahmed, Nadeem; Altermann, Uwe; Angerer, Philipp; Ansorge, Sonja; Balasz, Kinga; Bernhofer, Michael; Betz, Alexander; Cizmadija, Laura; Do, Kieu Trinh; Gerke, Julia; Greil, Robert; Joerdens, Vadim; Hastreiter, Maximilian; Hembach, Katharina; Herzog, Max; Kalemanov, Maria; Kluge, Michael; Meier, Alice; Nasir, Hassan; Neumaier, Ulrich; Prade, Verena; Reeb, Jonas; Sorokoumov, Aleksandr; Troshani, Ilira; Vorberg, Susann; Waldraff, Sonja; Zierer, Jonas; Nielsen, Henrik; Rost, Burkhard

    2014-01-01

    The prediction of protein sub-cellular localization is an important step toward elucidating protein function. For each query protein sequence, LocTree2 applies machine learning (profile kernel SVM) to predict the native sub-cellular localization in 18 classes for eukaryotes, in six for bacteria and in three for archaea. The method outputs a score that reflects the reliability of each prediction. LocTree2 has performed on par with or better than any other state-of-the-art method. Here, we report the availability of LocTree3 as a public web server. The server includes the machine learning-based LocTree2 and improves over it through the addition of homology-based inference. Assessed on sequence-unique data, LocTree3 reached an 18-state accuracy Q18 = 80 3% for eukaryotes and a six-state accuracy Q6 = 89 4% for bacteria. The server accepts submissions ranging from single protein sequences to entire proteomes. Response time of the unloaded server is about 90 s for a 300-residue eukaryotic protein and a few hours for an entire eukaryotic proteome not considering the generation of the alignments. For over 1000 entirely sequenced organisms, the predictions are directly available as downloads. The web server is available at http://www.rostlab.org/services/loctree3. PMID:24848019

  4. Phillips goes subsea trees in Ivory Coast

    SciTech Connect

    Bryngelson, R.H.

    1982-11-15

    Describes installation of 3 satellite subsea trees in 500 ft of water from a semisubmersible drilling rig. These wet, diver-assist trees are part of Phillips Petroleum's early development and production program (EDPP) for the Espoir field offshore Ivory Coast, with plans calling for 5 satellite wells with downhole completion equipment and subsea production trees. Diagram shows how a converted jackup, Dan Duke, supports equipment to handle production from subsea wells. Table gives time breakdown of subsea tree installation. Before mobilizing the subsea trees, control system, and tubulars to the rig, a study of deck layout, payloads, and traffic patterns was performed. Concludes that, based on experience in this project and the cost differences between purchase and installation costs, final success is 90% dependent on informed and trained field personnel after engineering, design, and manufacturing; attention to installation procedures and training of field and operational personnel are as critical or more critical than design changes to equipment; and selection of a supplier for high technology equipment, based on a low bid alone, may not translate into lower installation costs.

  5. Factors affecting the concordance between orthologous gene trees and species tree in bacteria

    PubMed Central

    2008-01-01

    Background As originally defined, orthologous genes implied a reflection of the history of the species. In recent years, many studies have examined the concordance between orthologous gene trees and species trees in bacteria. These studies have produced contradictory results that may have been influenced by orthologous gene misidentification and artefactual phylogenetic reconstructions. Here, using a method that allows the detection and exclusion of false positives during identification of orthologous genes, we address the question of whether putative orthologous genes within bacteria really reflect the history of the species. Results We identified a set of 370 orthologous genes from the bacterial order Rhizobiales. Although manifesting strong vertical signal, almost every orthologous gene had a distinct phylogeny, and the most common topology among the orthologous gene trees did not correspond with the best estimate of the species tree. However, each orthologous gene tree shared an average of 70% of its bipartitions with the best estimate of the species tree. Stochastic error related to gene size affected the concordance between the best estimated of the species tree and the orthologous gene trees, although this effect was weak and distributed unevenly among the functional categories. The nodes showing the greatest discordance were those defined by the shortest internal branches in the best estimated of the species tree. Moreover, a clear bias was evident with respect to the function of the orthologous genes, and the degree of divergence among the orthologous genes appeared to be related to their functional classification. Conclusion Orthologous genes do not reflect the history of the species when taken as individual markers, but they do when taken as a whole. Stochastic error affected the concordance of orthologous genes with the species tree, albeit weakly. We conclude that two important biological causes of discordance among orthologous genes are incomplete lineage sorting and functional restriction. PMID:18973688

  6. Global tree network for computing structures enabling global processing operations

    DOEpatents

    Blumrich; Matthias A.; Chen, Dong; Coteus, Paul W.; Gara, Alan G.; Giampapa, Mark E.; Heidelberger, Philip; Hoenicke, Dirk; Steinmacher-Burow, Burkhard D.; Takken, Todd E.; Vranas, Pavlos M.

    2010-01-19

    A system and method for enabling high-speed, low-latency global tree network communications among processing nodes interconnected according to a tree network structure. The global tree network enables collective reduction operations to be performed during parallel algorithm operations executing in a computer structure having a plurality of the interconnected processing nodes. Router devices are included that interconnect the nodes of the tree via links to facilitate performance of low-latency global processing operations at nodes of the virtual tree and sub-tree structures. The global operations performed include one or more of: broadcast operations downstream from a root node to leaf nodes of a virtual tree, reduction operations upstream from leaf nodes to the root node in the virtual tree, and point-to-point message passing from any node to the root node. The global tree network is configurable to provide global barrier and interrupt functionality in asynchronous or synchronized manner, and, is physically and logically partitionable.

  7. Wind training in some prairie trees

    USGS Publications Warehouse

    Bogan, M.A.; Mollhagen, T.R.

    1969-01-01

    Asymmetry in tree crowns has been established for some time. Lawrence (Ecol. Monogr. 9:217-257, 1939) studied wind training, one cause of asymmetry, in the Columbia River Gorge. He and Boyce (Ecol. Monogr. 24: 29-67, 1954) cite the intensity and direction of wind during the growing season as the causative agents. In their study of trunk asymmetry, Potter and Green (Cology 45: 10-23, 1964) mention crown deformity in the open stands of trees. Prairie trees are typically found in open stands, and to our knowledge no quantitative studies have been done on their crown asymmetry. The present study on the nature of this asymmetry, is an attempt to fill the void.

  8. Forward estimation for game-tree search

    SciTech Connect

    Zhang, Weixiong

    1996-12-31

    It is known that bounds on the minimax values of nodes in a game tree can be used to reduce the computational complexity of minimax search for two-player games. We describe a very simple method to estimate bounds on the minimax values of interior nodes of a game tree, and use the bounds to improve minimax search. The new algorithm, called forward estimation, does not require additional domain knowledge other than a static node evaluation function, and has small constant overhead per node expansion. We also propose a variation of forward estimation, which provides a tradeoff between computational complexity and decision quality. Our experimental results show that forward estimation outperforms alpha-beta pruning on random game trees and the game of Othello.

  9. Tree attenuation at 20 GHz: Foliage effects

    NASA Technical Reports Server (NTRS)

    Vogel, Wolfhard J.; Goldhirsh, Julius

    1993-01-01

    Static tree attenuation measurements at 20 GHz (K-Band) on a 30 deg slant path through a mature Pecan tree with and without leaves showed median fades exceeding approximately 23 dB and 7 dB, respectively. The corresponding 1% probability fades were 43 dB and 25 dB. Previous 1.6 GHz (L-Band) measurements for the bare tree case showed fades larger than those at K-Band by 3.4 dB for the median and smaller by approximately 7 dB at the 1% probability. While the presence of foliage had only a small effect on fading at L-Band (approximately 1 dB additional for the median to 1% probability range), the attenuation increase was significant at K-Band, where it increased by about 17 dB over the same probability range.

  10. Tree attenuation at 20 GHz: Foliage effects

    NASA Astrophysics Data System (ADS)

    Vogel, Wolfhard J.; Goldhirsh, Julius

    1993-08-01

    Static tree attenuation measurements at 20 GHz (K-Band) on a 30 deg slant path through a mature Pecan tree with and without leaves showed median fades exceeding approximately 23 dB and 7 dB, respectively. The corresponding 1% probability fades were 43 dB and 25 dB. Previous 1.6 GHz (L-Band) measurements for the bare tree case showed fades larger than those at K-Band by 3.4 dB for the median and smaller by approximately 7 dB at the 1% probability. While the presence of foliage had only a small effect on fading at L-Band (approximately 1 dB additional for the median to 1% probability range), the attenuation increase was significant at K-Band, where it increased by about 17 dB over the same probability range.

  11. Optimal Branching Asymmetry of Hydrodynamic Pulsatile Trees

    NASA Astrophysics Data System (ADS)

    Florens, Magali; Sapoval, Bernard; Filoche, Marcel

    2011-04-01

    Most of the studies on optimal transport are done for steady state regime conditions. Yet, there exists numerous examples in living systems where supply tree networks have to deliver products in a limited time due to the pulsatile character of the flow, as it is the case for mammalian respiration. We report here that introducing a systematic branching asymmetry allows the tree to reduce the average delivery time of the products. It simultaneously increases its robustness against the inevitable variability of sizes related to morphogenesis. We then apply this approach to the human tracheobronchial tree. We show that in this case all extremities are supplied with fresh air, provided that the asymmetry is smaller than a critical threshold which happens to match the asymmetry measured in the human lung. This could indicate that the structure is tuned at the maximum asymmetry level that allows the lung to feed all terminal units with fresh air.

  12. Scattering measurements on natural and model trees

    NASA Technical Reports Server (NTRS)

    Rogers, James C.; Lee, Sung M.

    1990-01-01

    The acoustical back scattering from a simple scale model of a tree has been experimentally measured. The model consisted of a trunk and six limbs, each with 4 branches; no foliage or twigs were included. The data from the anechoic chamber measurements were then mathematically combined to construct the effective back scattering from groups of trees. Also, initial measurements have been conducted out-of-doors on a single tree in an open field in order to characterize its acoustic scattering as a function of azimuth angle. These measurements were performed in the spring, prior to leaf development. The data support a statistical model of forest scattering; the scattered signal spectrum is highly irregular but with a remarkable general resemblance to the incident signal spectrum. Also, the scattered signal's spectra showed little dependence upon scattering angle.

  13. Rooting Gene Trees without Outgroups: EP Rooting

    PubMed Central

    Sinsheimer, Janet S.; Little, Roderick J. A.; Lake, James A.

    2012-01-01

    Gene sequences are routinely used to determine the topologies of unrooted phylogenetic trees, but many of the most important questions in evolution require knowing both the topologies and the roots of trees. However, general algorithms for calculating rooted trees from gene and genomic sequences in the absence of gene paralogs are few. Using the principles of evolutionary parsimony (EP) (Lake JA. 1987a. A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Mol Biol Evol. 4:167–181) and its extensions (Cavender, J. 1989. Mechanized derivation of linear invariants. Mol Biol Evol. 6:301–316; Nguyen T, Speed TP. 1992. A derivation of all linear invariants for a nonbalanced transversion model. J Mol Evol. 35:60–76), we explicitly enumerate all linear invariants that solely contain rooting information and derive algorithms for rooting gene trees directly from gene and genomic sequences. These new EP linear rooting invariants allow one to determine rooted trees, even in the complete absence of outgroups and gene paralogs. EP rooting invariants are explicitly derived for three taxon trees, and rules for their extension to four or more taxa are provided. The method is demonstrated using 18S ribosomal DNA to illustrate how the new animal phylogeny (Aguinaldo AMA et al. 1997. Evidence for a clade of nematodes, arthropods, and other moulting animals. Nature 387:489–493; Lake JA. 1990. Origin of the metazoa. Proc Natl Acad Sci USA 87:763–766) may be rooted directly from sequences, even when they are short and paralogs are unavailable. These results are consistent with the current root (Philippe H et al. 2011. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature 470:255–260). PMID:22593551

  14. How do trees know it is autumn?

    NASA Astrophysics Data System (ADS)

    Jansson, Stefan

    2014-05-01

    To predict how forests will respond to climate change, it is necessary to understand how trees actually interpret environmental signals that the winter is approaching and use them to induce growth arrest, cold hardiness development, autumn leaf senescence and abscission. Autumn phenology traits and also under strong genetic control, and there exist within most tree species large variation in most phenology traits. Our model system is aspen (Populus tremula); one of the most widespread and abundant deciduous trees on earth. Growth arrest/bud set and cold hardiness in aspen is triggered by the gradual shortening of the photoperiod is the late season, and the molecular details behind have to some extent been deciphered. The molecular machinery triggering autumn leaf senescence - a trait developed to minimise nutrient loss - is in contrast, very poorly understood but bud set/growth arrest is a prerequisite for aspens to develop a competence to respond to the environmental signals triggering senescence. Once competence is developed, initiation of senescence seems to be triggered not by the daylength but some other daylight cue, and once senescence has been initiated the progression is influenced by temperature. The nitrogen, as well as carbohydrate, status interact can modify the senescence program of the tree. We are also identifying the precise genetic polymorphisms that are responsible for natural variation in autumn phenology traits in aspen, and study how different populations have different genetic makeups that provide local adaptation. Taken together, other environmental factors are more important than temperature is setting the timetable for aspens in the autumn. Although much less is know how autumn phenology traits are regulated in other tree species, the effect that increasing temperatures may have on future tree populations will also be discussed.

  15. Phenology of temperate trees in tropical climates

    NASA Astrophysics Data System (ADS)

    Borchert, Rolf; Robertson, Kevin; Schwartz, Mark D.; Williams-Linera, Guadalupe

    2005-09-01

    Several North American broad-leaved tree species range from the northern United States at ˜47°N to moist tropical montane forests in Mexico and Central America at 15-20°N. Along this gradient the average minimum temperatures of the coldest month (T Jan), which characterize annual variation in temperature, increase from -10 to 12°C and tree phenology changes from deciduous to leaf-exchanging or evergreen in the southern range with a year-long growing season. Between 30 and 45°N, the time of bud break is highly correlated with T Jan and bud break can be reliably predicted for the week in which mean minimum temperature rises to 7°C. Temperature-dependent deciduous phenology—and hence the validity of temperature-driven phenology models—terminates in southern North America near 30°N, where T Jan>7°C enables growth of tropical trees and cultivation of frost-sensitive citrus fruits. In tropical climates most temperate broad-leaved species exchange old for new leaves within a few weeks in January-February, i.e., their phenology becomes similar to that of tropical leaf-exchanging species. Leaf buds of the southern ecotypes of these temperate species are therefore not winter-dormant and have no chilling requirement. As in many tropical trees, bud break of Celtis, Quercus and Fagus growing in warm climates is induced in early spring by increasing daylength. In tropical climates vegetative phenology is determined mainly by leaf longevity, seasonal variation in water stress and day length. As water stress during the dry season varies widely with soil water storage, climate-driven models cannot predict tree phenology in the tropics and tropical tree phenology does not constitute a useful indicator of global warming.

  16. Low Power Gated Clock Tree Driven Placement

    NASA Astrophysics Data System (ADS)

    Shen, Weixiang; Cai, Yici; Hong, Xianlong; Hu, Jiang

    As power consumption of the clock tree dominates over 40% of the total power in modem high performance VLSI designs, measures must be taken to keep it under control. One of the most effective methods is based on clock gating to shut off the clock when the modules are idle. However, previous works on gated clock tree power minimization are mostly focused on clock routing and the improvements are often limited by the given registers placement. The purpose of this work is to navigate the registers during placement to further reduce the clock tree power based on clock gating. Our method performs activity-aware register clustering that reduces the clock tree power not only by clumping the registers into a smaller area, but also by pulling the registers with the similar activity patterns closely to shut off the clock more time for the resultant subtrees. In order to reduce the impact of signal nets wirelength and power due to register clustering, we apply the timing and activity based net weighting in [14], which reduces the nets switching power by assigning a combination of activity and timing weights to the nets with higher switching rates or more critical timing. To tradeoff the power dissipated by the clock tree and the control signal, we extend the idea of local ungating in [6] and propose an algorithm of gate control signal optimization, which still sets the gate enable signal high if a register is active for a number of consecutive clock cycles. Experimental results on a set of MCNC benchmarks show that our approach is able to reduce the power and total wirelength of clock tree greatly with minimal overheads.

  17. Monitoring trees outside forests: a review.

    PubMed

    Schnell, Sebastian; Kleinn, Christoph; Ståhl, Göran

    2015-09-01

    Trees outside forests (TOFs) are an important natural resource that contributes substantially to national biomass and carbon stocks and to the livelihood of people in many regions. Over the last decades, decision makers have become increasingly aware of the importance of TOF, and as a consequence, this tree resource is nowadays often considered in forest monitoring systems. Our review shows that in many cases, TOF are included in national forest inventories, applying traditional methodologies with relatively sparse networks of field sample plots. Only in some countries, such as India, the design of the inventories has considered the special features of how TOFs occur in the landscape. Several research studies utilising remote sensing for monitoring TOF have been conducted lately, but very few studies include comparative studies to optimise sampling strategies for TOF. Our review indicates that methods combining remote sensing and field surveys appear to be very promising, especially when remote sensing techniques that assess both the horizontal and vertical structures of tree resources are applied. For example, two-phase sampling strategies with laser scanning in the first phase and a field survey in the second phase appear to be effective for assessing TOF resources. However, TOFs often exhibit different characteristics than forest trees. Thus, to improve TOF monitoring, there is often a need to develop models, e.g. for biomass assessment, that are specifically adapted to this tree resource. Alternatively, field-based remote sensing methods that provide structural information about individual trees, notably terrestrial laser scanning, could be further developed for TOF monitoring applications. This also would have a potential to reduce the problem of accessing TOF during field surveys, which is a problem, for example, in countries where TOF are present on intensively utilised private grounds like gardens and agricultural fields. PMID:26318320

  18. Bayesian estimation of concordance among gene trees.

    PubMed

    An, Ccile; Larget, Bret; Baum, David A; Smith, Stacey D; Rokas, Antonis

    2007-02-01

    Multigene sequence data have great potential for elucidating important and interesting evolutionary processes, but statistical methods for extracting information from such data remain limited. Although various biological processes may cause different genes to have different genealogical histories (and hence different tree topologies), we also may expect that the number of distinct topologies among a set of genes is relatively small compared with the number of possible topologies. Therefore evidence about the tree topology for one gene should influence our inferences of the tree topology on a different gene, but to what extent? In this paper, we present a new approach for modeling and estimating concordance among a set of gene trees given aligned molecular sequence data. Our approach introduces a one-parameter probability distribution to describe the prior distribution of concordance among gene trees. We describe a novel 2-stage Markov chain Monte Carlo (MCMC) method that first obtains independent Bayesian posterior probability distributions for individual genes using standard methods. These posterior distributions are then used as input for a second MCMC procedure that estimates a posterior distribution of gene-to-tree maps (GTMs). The posterior distribution of GTMs can then be summarized to provide revised posterior probability distributions for each gene (taking account of concordance) and to allow estimation of the proportion of the sampled genes for which any given clade is true (the sample-wide concordance factor). Further, under the assumption that the sampled genes are drawn randomly from a genome of known size, we show how one can obtain an estimate, with credibility intervals, on the proportion of the entire genome for which a clade is true (the genome-wide concordance factor). We demonstrate the method on a set of 106 genes from 8 yeast species. PMID:17095535

  19. Rooting gene trees without outgroups: EP rooting.

    PubMed

    Sinsheimer, Janet S; Little, Roderick J A; Lake, James A

    2012-01-01

    Gene sequences are routinely used to determine the topologies of unrooted phylogenetic trees, but many of the most important questions in evolution require knowing both the topologies and the roots of trees. However, general algorithms for calculating rooted trees from gene and genomic sequences in the absence of gene paralogs are few. Using the principles of evolutionary parsimony (EP) (Lake JA. 1987a. A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Mol Biol Evol. 4:167-181) and its extensions (Cavender, J. 1989. Mechanized derivation of linear invariants. Mol Biol Evol. 6:301-316; Nguyen T, Speed TP. 1992. A derivation of all linear invariants for a nonbalanced transversion model. J Mol Evol. 35:60-76), we explicitly enumerate all linear invariants that solely contain rooting information and derive algorithms for rooting gene trees directly from gene and genomic sequences. These new EP linear rooting invariants allow one to determine rooted trees, even in the complete absence of outgroups and gene paralogs. EP rooting invariants are explicitly derived for three taxon trees, and rules for their extension to four or more taxa are provided. The method is demonstrated using 18S ribosomal DNA to illustrate how the new animal phylogeny (Aguinaldo AMA et al. 1997. Evidence for a clade of nematodes, arthropods, and other moulting animals. Nature 387:489-493; Lake JA. 1990. Origin of the metazoa. Proc Natl Acad Sci USA 87:763-766) may be rooted directly from sequences, even when they are short and paralogs are unavailable. These results are consistent with the current root (Philippe H et al. 2011. Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature 470:255-260). PMID:22593551

  20. Haplotype trees and modern human origins.

    PubMed

    Templeton, Alan R

    2005-01-01

    A haplotype is a multisite haploid genotype at two or more polymorphic sites on the same chromosome in a defined DNA region. An evolutionary tree of the haplotypes can be estimated if the DNA region had little to no recombination. Haplotype trees can be used to reconstruct past human gene-flow patterns and historical events, but any single tree captures only a small portion of evolutionary history, and is subject to error. A fuller view of human evolution requires multiple DNA regions, and errors can be minimized by cross-validating inferences across loci. An analysis of 25 DNA regions reveals an out-of-Africa expansion event at 1.9 million years ago. Gene flow with isolation by distance was established between African and Eurasian populations by about 1.5 million years ago, with no detectable interruptions since. A second out-of-Africa expansion occurred about 700,000 years ago, and involved interbreeding with at least some Eurasian populations. A third out-of-Africa event occurred around 100,000 years ago, and was also characterized by interbreeding, with the hypothesis of a total Eurasian replacement strongly rejected (P < 10(-17)). This does not preclude the possibility that some Eurasian populations could have been replaced, and the status of Neanderthals is indecisive. Demographic inferences from haplotype trees have been inconsistent, so few definitive conclusions can be made at this time. Haplotype trees from human parasites offer additional insights into human evolution and raise the possibility of an Asian isolate of humanity, but once again not in a definitive fashion. Haplotype trees can also indicate which genes were subject to positive selection in the lineage leading to modern humans. Genetics provides many insights into human evolution, but those insights need to be integrated with fossil and archaeological data to yield a fuller picture of the origin of modern humans. PMID:16369961

  1. Efficient exploration of the space of reconciled gene trees.

    PubMed

    Szllsi, Gergely J; Rosikiewicz, Wojciech; Boussau, Bastien; Tannier, Eric; Daubin, Vincent

    2013-11-01

    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 (Szll?si 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. PMID:23925510

  2. Decision Tree Approach for Soil Liquefaction Assessment

    PubMed Central

    Gandomi, Amir H.; Fridline, Mark M.; Roke, David A.

    2013-01-01

    In the current study, the performances of some decision tree (DT) techniques are evaluated for postearthquake soil liquefaction assessment. A database containing 620 records of seismic parameters and soil properties is used in this study. Three decision tree techniques are used here in two different ways, considering statistical and engineering points of view, to develop decision rules. The DT results are compared to the logistic regression (LR) model. The results of this study indicate that the DTs not only successfully predict liquefaction but they can also outperform the LR model. The best DT models are interpreted and evaluated based on an engineering point of view. PMID:24489498

  3. Surgical anatomy of the tracheobronchial tree

    PubMed Central

    Drevet, Gabrielle; Conti, Massimo

    2016-01-01

    Airway surgery is often indicated in the management of benign or malignant pathological processes of the tracheobronchial tree. The surgeon undertaking this type of work has, however, the responsibility of understanding the particular anatomy applicable to these structures and procedures as well as be able to correlate imaging, intraoperative findings and anatomy. These are important considerations if one wants to reduce operative morbidity and improve potential for better long-term results. This paper reviews the most important anatomic features of the tracheobronchial tree putting emphasis on those features that are important to surgeons performing surgical procedures on those organs. PMID:26981262

  4. Photoperiodic growth control in perennial trees.

    PubMed

    Azeez, Abdul; Sane, Aniruddha P

    2015-12-01

    Plants have to cope with changing seasons and adverse environmental conditions. Being sessile, plants have developed elaborate mechanisms for their survival that allow them to sense and adapt to the environment and reproduce successfully. A major adaptive trait for the survival of trees of temperate and boreal forests is the induction of growth cessation in anticipation of winters. In the last few years enormous progress has been made to elucidate the molecular mechanisms underlying SDs induced growth cessation in model perennial tree hybrid aspen (Populus tremula × P. tremuloides). In this review we discuss the molecular mechanism underlying photoperiodic control of growth cessation and adaptive responses. PMID:26340077

  5. Probability distribution on the parse trees.

    PubMed

    Tepes, Bozidar; Hunjet, Dubravko; Elezović, Slobodan

    2005-12-01

    Paper describes probability distribution on the parse trees of natural language by using Bayesian networks. First parts of the paper describes probabilistic context-free grammar and parse trees. In the second part of the paper, Bayesian network was modelled and joint probability distribution on their vertex. On these theoretical ideas, in the third part, we describe our model tested on Database of grammatical sentences of Croatian language (http:/ /infoz.ffzg.hr / tepes /). At the end was presented a backward procedure and evaluation of our results. PMID:16417191

  6. Investigating how students communicate tree-thinking

    NASA Astrophysics Data System (ADS)

    Boyce, Carrie Jo

    Learning is often an active endeavor that requires students work at building conceptual understandings of complex topics. Personal experiences, ideas, and communication all play large roles in developing knowledge of and understanding complex topics. Sometimes these experiences can promote formation of scientifically inaccurate or incomplete ideas. Representations are tools used to help individuals understand complex topics. In biology, one way that educators help people understand evolutionary histories of organisms is by using representations called phylogenetic trees. In order to understand phylogenetics trees, individuals need to understand the conventions associated with phylogenies. My dissertation, supported by the Tree-Thinking Representational Competence and Word Association frameworks, is a mixed-methods study investigating the changes in students' tree-reading, representational competence and mental association of phylogenetic terminology after participation in varied instruction. Participants included 128 introductory biology majors from a mid-sized southern research university. Participants were enrolled in either Introductory Biology I, where they were not taught phylogenetics, or Introductory Biology II, where they were explicitly taught phylogenetics. I collected data using a pre- and post-assessment consisting of a word association task and tree-thinking diagnostic (n=128). Additionally, I recruited a subset of students from both courses (n=37) to complete a computer simulation designed to teach students about phylogenetic trees. I then conducted semi-structured interviews consisting of a word association exercise with card sort task, a retrospective pre-assessment discussion, a post-assessment discussion, and interview questions. I found that students who received explicit lecture instruction had a significantly higher increase in scores on a tree-thinking diagnostic than students who did not receive lecture instruction. Students who received both explicit lecture instruction and the computer simulation had a higher level of representational competence and were better able to understand abstract-style phylogenetic trees than students who only completed the simulation. Students who received explicit lecture instruction had a slightly more scientific association of phylogenetic terms than students who received did not receive lecture instruction. My findings suggest that technological instruction alone is not as beneficial as lecture instruction.

  7. A survey of decision tree classifier methodology

    NASA Technical Reports Server (NTRS)

    Safavian, S. R.; Landgrebe, David

    1991-01-01

    Decision tree classifiers (DTCs) are used successfully in many diverse areas such as radar signal classification, character recognition, remote sensing, medical diagnosis, expert systems, and speech recognition. Perhaps the most important feature of DTCs is their capability to break down a complex decision-making process into a collection of simpler decisions, thus providing a solution which is often easier to interpret. A survey of current methods is presented for DTC designs and the various existing issues. After considering potential advantages of DTCs over single-state classifiers, subjects of tree structure design, feature selection at each internal node, and decision and search strategies are discussed.

  8. A survey of decision tree classifier methodology

    NASA Technical Reports Server (NTRS)

    Safavian, S. Rasoul; Landgrebe, David

    1990-01-01

    Decision Tree Classifiers (DTC's) are used successfully in many diverse areas such as radar signal classification, character recognition, remote sensing, medical diagnosis, expert systems, and speech recognition. Perhaps, the most important feature of DTC's is their capability to break down a complex decision-making process into a collection of simpler decisions, thus providing a solution which is often easier to interpret. A survey of current methods is presented for DTC designs and the various existing issue. After considering potential advantages of DTC's over single stage classifiers, subjects of tree structure design, feature selection at each internal node, and decision and search strategies are discussed.

  9. Maximum likelihood clustering with dependent feature trees

    NASA Technical Reports Server (NTRS)

    Chittineni, C. B. (Principal Investigator)

    1981-01-01

    The decomposition of mixture density of the data into its normal component densities is considered. The densities are approximated with first order dependent feature trees using criteria of mutual information and distance measures. Expressions are presented for the criteria when the densities are Gaussian. By defining different typs of nodes in a general dependent feature tree, maximum likelihood equations are developed for the estimation of parameters using fixed point iterations. The field structure of the data is also taken into account in developing maximum likelihood equations. Experimental results from the processing of remotely sensed multispectral scanner imagery data are included.

  10. WASTE MINIMIZATION ASSESSMENT FOR A MANUFACTURER OF PAINTS AND LACQUERS

    EPA Science Inventory

    The U. S. Environmental Protection Agency (EPA) has funded a pilot project to assist small and medium-size manufacturers who want to minimize their generation of waste but who lack the expertise to do so. In an effort to assist these manufacturers Waste Minimization Assessment Ce...

  11. Genome-Scale Phylogenetics: Inferring the Plant Tree of Life from 18,896 Gene Trees

    PubMed Central

    Burleigh, J. Gordon; Bansal, Mukul S.; Eulenstein, Oliver; Hartmann, Stefanie; Wehe, Andr; Vision, Todd J.

    2011-01-01

    Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life. PMID:21186249

  12. Molecular and physiological responses to abiotic stress in forest trees and their relevance to tree improvement.

    PubMed

    Harfouche, Antoine; Meilan, Richard; Altman, Arie

    2014-11-01

    Abiotic stresses, such as drought, salinity and cold, are the major environmental stresses that adversely affect tree growth and, thus, forest productivity, and play a major role in determining the geographic distribution of tree species. Tree responses and tolerance to abiotic stress are complex biological processes that are best analyzed at a systems level using genetic, genomic, metabolomic and phenomic approaches. This will expedite the dissection of stress-sensing and signaling networks to further support efficient genetic improvement programs. Enormous genetic diversity for stress tolerance exists within some forest-tree species, and due to advances in sequencing technologies the molecular genetic basis for this diversity has been rapidly unfolding in recent years. In addition, the use of emerging phenotyping technologies extends the suite of traits that can be measured and will provide us with a better understanding of stress tolerance. The elucidation of abiotic stress-tolerance mechanisms will allow for effective pyramiding of multiple tolerances in a single tree through genetic engineering. Here we review recent progress in the dissection of the molecular basis of abiotic stress tolerance in forest trees, with special emphasis on Populus, Pinus, Picea, Eucalyptus and Quercus spp. We also outline practices that will enable the deployment of trees engineered for abiotic stress tolerance to land owners. Finally, recommendations for future work are discussed. PMID:24695726

  13. Confirmatory Tree Sampling for Tritium in Trees at the Salmon Site, Mississippi

    SciTech Connect

    2010-06-01

    The sampling was conducted on April 20, 21, and 22, 2010. DOE acquired 36 samples for analysis, approximately 10 percent of the total number of samples the Mississippi Forestry Commission acquired. The plan was to sample trees that the Mississippi Forestry Commission also sampled, so that a tree-by-tree comparison of analysis results could be made. The Mississippi Forestry Commission provided DOE with latitude and longitude coordinates, determined by a global positioning system (GPS), for each sampled tree. The Mississippi Forestry Commission also placed a blaze-orange number on each sampled tree. DOE used a GPS unit to assist in locating trees for sampling. DOE acquired one sample from an off-site location to have a reference for comparison to on-site results if necessary. The other 35 samples were acquired on site, for a total of 36 samples. Figure 1 shows the sampling locations, the sample identifiers DOE assigned, and the corresponding tree numbers the Mississippi Forestry Commission assigned

  14. 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

  15. A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree

    PubMed Central

    2012-01-01

    Background The ancestries of genes form gene trees which do not necessarily have the same topology as the species tree due to incomplete lineage sorting. Available algorithms determining the probability of a gene tree given a species tree require exponential computational runtime. Results In this paper, we provide a polynomial time algorithm to calculate the probability of a ranked gene tree topology for a given species tree, where a ranked tree topology is a tree topology with the internal vertices being ordered. The probability of a gene tree topology can thus be calculated in polynomial time if the number of orderings of the internal vertices is a polynomial number. However, the complexity of calculating the probability of a gene tree topology with an exponential number of rankings for a given species tree remains unknown. Conclusions Polynomial algorithms for calculating ranked gene tree probabilities may become useful in developing methodology to infer species trees based on a collection of gene trees, leading to a more accurate reconstruction of ancestral species relationships. PMID:22546066

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

    PubMed

    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

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

    PubMed

    Franklin, Oskar; Palmroth, Sari; Näsholm, Torgny

    2014-11-01

    Tree breeding and biotechnology can enhance forest productivity and help alleviate the rising pressure on forests from climate change and human exploitation. While many physiological processes and genes are targeted in search of genetically improved tree productivity, an overarching principle to guide this search is missing. Here, we propose a method to identify the traits that can be modified to enhance productivity, based on the differences between trees shaped by natural selection and 'improved' trees with traits optimized for productivity. We developed a tractable model of plant growth and survival to explore such potential modifications under a range of environmental conditions, from non-water limited to severely drought-limited sites. We show how key traits are controlled by a trade-off between productivity and survival, and that productivity can be increased at the expense of long-term survival by reducing isohydric behavior (stomatal regulation of leaf water potential) and allocation to defense against pests compared with native trees. In contrast, at dry sites occupied by naturally drought-resistant trees, the model suggests a better strategy may be to select trees with slightly lower wood density than the native trees and to augment isohydric behavior and allocation to defense. Thus, which traits to modify, and in which direction, depend on the original tree species or genotype, the growth environment and wood-quality versus volume production preferences. In contrast to this need for customization of drought and pest resistances, consistent large gains in productivity for all genotypes can be obtained if root traits can be altered to reduce competition for water and nutrients. Our approach illustrates the potential of using eco-evolutionary theory and modeling to guide plant breeding and genetic technology in selecting target traits in the quest for higher forest productivity. PMID:25542897

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

    SciTech Connect

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

    2007-05-07

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

  19. Surveying Dead Trees and CO2-Induced Stressed Trees Using AVIRIS in the Long Valley Caldera

    NASA Technical Reports Server (NTRS)

    deJong, Steven M.

    1996-01-01

    Since 1980 the Long Valley Caldera in the eastern Sierra Nevada (California) has shown signs of renewed volcanic activity. Frequent earthquakes, a re-inflation of the caldera, hydrothermal activity and gas emissions are the outer symptoms of this renewed activity. In 1990 and 1991 several areas of dying trees were found around Mammoth Mountain. The cause of the die off of the trees was first sought in the persistent drought in the preceding years. However, the trees died regardless of age and species. Farrar et al. (1995) started a soil-gas survey in 1994 in the dead-tree areas and found carbon dioxide concentrations ranging from 30 to 96% at soil depths between 30 and 60 cm. CO2 concentrations in the atmosphere are usually around 0.03% and in the soil profile CO2 levels do commonly not exceed 4 to 5%. Although not much is known about the effect of high levels of carbon dioxide in the soil profile on roots, it is most likely that the trees are dying due to oxygen deprivation: the CO2 drives the oxygen out of the soil. So far, four sites of dead trees have been mapped around Mammoth Mountain. The two largest dying trees sites are located near Horseshoe Lake and near Mammoth Mountain Main Lodge covering approximately an area of 10 and 8 ha respectively. Analysis of the gas composition regarding the He-3/He-4 ratio and the percentage biogenic carbon reveals the source of the gas: the magma body beneath the Long Valley Caldera. Until recently it was not known that volcanoes release abundant carbon dioxide from their flanks as diffuse soil emanations. As a result of the magma gas emission around Mammoth Mountain there is an excellent sequence of dead trees, stressed trees, healthy trees and bare soil surfaces. This research site provides excellent opportunities to: (1) Study the capabilities of imaging spectrometry to map stressed (and dead) pine and fir species; (2) Study methods to separate the vivid vegetation, stressed vegetation and dead vegetation from the soil background of glacial deposits and crystalline rocks. The dead tree areas are located on the flanks of Mammoth Mountain (N:37 deg 37' 45" and W:119 deg 02' 05") at an elevation between 2600 and 3000 meters. The area is covered by an open type of Montane Forest. The dominant tree species are Lodgepole Pine (Pinus contorta), the Red Fir (Abies magnifica) and the Jeffrey Pine (Pinus jeffreyi). The soil surface near Horseshoe Lake is generally fairly bright. The surface is covered by glacial deposits (till) consisting mainly of weathered granitic rocks.

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  1. 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. PMID:15996961

  2. Effects of open-top chambers on 'Valencia' orange trees

    SciTech Connect

    Olszyk, D.M.; Takemoto, B.K.; Kats, G.; Dawson, P.J.; Morrison, C.L.

    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 chamber 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.

  3. Evaluation Theory Tree Re-Examined

    ERIC Educational Resources Information Center

    Christie, Christina A.; Alkin, Marvin C.

    2008-01-01

    When examining various evaluation prescriptive theories comparatively, we find it helpful to have a framework showing how they are related that highlights features that distinguish theoretical perspectives, thus a "theory" about theories. The evaluation theory tree that we presented in Alkin's recent book, "Evaluation Roots" [Eisner, E. (2004).…

  4. Understanding search trees via statistical physics

    NASA Astrophysics Data System (ADS)

    Majumdar, Satya N.; Dean, David S.; Krapivsky, P. L.

    2005-06-01

    We study the random m-ary search tree model (where m stands for the number of branches of the search tree), an important problem for data storage in computer science, using a variety of statistical physics techniques that allow us to obtain exact asymptotic results. In particular, we show that the probability distributions of extreme observables associated with a random search tree such as the height and the balanced height of a tree have a travelling front structure. In addition, the variance of the number of nodes needed to store a data string of a given size N is shown to undergo a striking phase transition at a critical value of the branching ratio m_{c}=26. We identified the mechanism of this phase transition and showed that it is generic and occurs in various other problems as well. New results are obtained when each element of the data string is a D-dimensional vector. We show that this problem also has a phase transition at a critical dimension, D_{c}= pi/sin^{-1}left(1/sqrt{8}right)=8.69363ldots.

  5. Joshua Trees at Pierce Ferry, AZ

    USGS Multimedia Gallery

    This image, from April 2004, shows mortality of some adult Joshua trees resulting from years of hot-dry climate. During the prior year, this area received only 17 percent of its average precipitation and was 4 degrees F warmer than average -- conditions that are projected to become even more frequen...

  6. Saliency tree: a novel saliency detection framework.

    PubMed

    Liu, Zhi; Zou, Wenbin; Le Meur, Olivier

    2014-05-01

    This paper proposes a novel saliency detection framework termed as saliency tree. For effective saliency measurement, the original image is first simplified using adaptive color quantization and region segmentation to partition the image into a set of primitive regions. Then, three measures, i.e., global contrast, spatial sparsity, and object prior are integrated with regional similarities to generate the initial regional saliency for each primitive region. Next, a saliency-directed region merging approach with dynamic scale control scheme is proposed to generate the saliency tree, in which each leaf node represents a primitive region and each non-leaf node represents a non-primitive region generated during the region merging process. Finally, by exploiting a regional center-surround scheme based node selection criterion, a systematic saliency tree analysis including salient node selection, regional saliency adjustment and selection is performed to obtain final regional saliency measures and to derive the high-quality pixel-wise saliency map. Extensive experimental results on five datasets with pixel-wise ground truths demonstrate that the proposed saliency tree model consistently outperforms the state-of-the-art saliency models. PMID:24710397

  7. Evaluation Theory Tree Re-Examined

    ERIC Educational Resources Information Center

    Christie, Christina A.; Alkin, Marvin C.

    2008-01-01

    When examining various evaluation prescriptive theories comparatively, we find it helpful to have a framework showing how they are related that highlights features that distinguish theoretical perspectives, thus a "theory" about theories. The evaluation theory tree that we presented in Alkin's recent book, "Evaluation Roots" [Eisner, E. (2004).

  8. Modeling huanglongbing transmission within a citrus tree

    PubMed Central

    Chiyaka, Christinah; Singer, Burton H.; Halbert, Susan E.; Morris, J. Glenn; van Bruggen, Ariena H. C.

    2012-01-01

    The citrus disease huanglongbing (HLB), associated with an uncultured bacterial pathogen, is threatening the citrus industry worldwide. A mathematical model of the transmission of HLB between its psyllid vector and citrus host has been developed to characterize the dynamics of the vector and disease development, focusing on the spread of the pathogen from flush to flush (a newly developing cluster of very young leaves on the expanding terminal end of a shoot) within a tree. This approach differs from that of prior models for vector-transmitted plant diseases where the entire plant is the unit of analysis. Dynamics of vector and host populations are simulated realistically as the flush population approaches complete infection. Model analysis indicates that vector activity is essential for initial infection but is not necessary for continued infection because infection can occur from flush to flush through internal movement in the tree. Flush production, within-tree spread, and latent period are the most important parameters influencing HLB development. The model shows that the effect of spraying of psyllids depends on time of initial spraying, frequency, and efficacy of the insecticides. Similarly, effects of removal of symptomatic flush depend on the frequency of removal and the time of initiation of this practice since the start of the epidemic. Within-tree resistance to spread, possibly affected by inherent or induced resistance, is a major factor affecting epidemic development, supporting the notion that alternate routes of transmission besides that by the vector can be important for epidemic development. PMID:22783015

  9. Acoustic Detection of Insects in Palm Trees

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Commercial-crop and ornamental palm trees serve important functions in tropical and subtropical regions of the world, and considerable precautions are taken each year to identify and control infestations of a variety of different insect pests. Large weevils, including the red palm weevil and the co...

  10. Teaching K. A. Porter's "That Tree."

    ERIC Educational Resources Information Center

    Monton, Elena Ortells

    2003-01-01

    Susan Lanser's poetics of point of view provides sound basis for the unveiling of the deeper layers of significance embedded behind the formal properties of a literary text. By applying her theory to the analysis of Porter's "That Tree," this article aims to yield a practical example of its enlightening use in the classroom. (Contains 18…

  11. Why trees and shrubs but rarely trubs?

    PubMed

    Scheffer, Marten; Vergnon, Remi; Cornelissen, J Hans C; Hantson, Stijn; Holmgren, Milena; van Nes, Egbert H; Xu, Chi

    2014-08-01

    An analysis of the maximum height of woody plant species across the globe reveals that an intermediate size is remarkably rare. We speculate that this may be due to intrinsic suboptimality or to ecosystem bistability with open landscapes favouring shrubs, and closed canopies propelling trees to excessive tallness. PMID:24951396

  12. Investigating Tree Thinking & Ancestry with Cladograms

    ERIC Educational Resources Information Center

    Davenport, K. D.; Milks, Kirstin Jane; Van Tassell, Rebecca

    2015-01-01

    Interpreting cladograms is a key skill for biological literacy. In this lesson, students interpret cladograms based on familial relationships and language relationships to build their understanding of tree thinking and to construct a definition of "common ancestor." These skills can then be applied to a true biological cladogram.

  13. POW Plus TREE Equals Powerful Opinion Essays.

    ERIC Educational Resources Information Center

    Harris, Karen R.; Graham, Steve; Mason, Linda

    2002-01-01

    The benefits of a self-regulated strategy development approach for teaching elementary school students with learning disabilities how to write opinion essays are discussed, and the steps of the POW plus TREE strategy of instruction are outlined: develop background knowledge, discuss, model, memorize, support it, and perform independently.

  14. DYNAMIC STANDARDIZATION OF TREE-RING SERIES

    EPA Science Inventory

    The compound growth function of Warren (W.G. Warren, 1980. ree-Ring Bull. 40:35-44) represented an attempt to develop a model-based approach that standardized tree ring width sequences and was more flexible than the monotonic functions that were then commonly used. hile the idea ...

  15. The value of our public trees

    EPA Science Inventory

    An assessment of the value and annual benefits of public trees in the Corvallis Urban Growth Boundary (UGB) was recently conducted by Don Phillips (Research Biologist at the U.S. Environmental Protection Agency [EPA] research lab in Corvallis), along with Connie Burdick (EPA geog...

  16. Disease and spray coverage in pecan trees

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pecan scab (Fusicladium effusum) is a destructive disease of pecan in the southeastern US. This study was conducted to investigate the vertical distribution of scab in tall pecan trees (14-16 m tall) in three experiments in 2010 and 2011. Although 2010 had average rainfall, a factor that drives scab...

  17. Pushing the pace of tree species migration.

    PubMed

    Lazarus, Eli D; McGill, Brian J

    2014-01-01

    Plants and animals have responded to past climate changes by migrating with habitable environments, sometimes shifting the boundaries of their geographic ranges by tens of kilometers per year or more. Species migrating in response to present climate conditions, however, must contend with landscapes fragmented by anthropogenic disturbance. We consider this problem in the context of wind-dispersed tree species. Mechanisms of long-distance seed dispersal make these species capable of rapid migration rates. Models of species-front migration suggest that even tree species with the capacity for long-distance dispersal will be unable to keep pace with future spatial changes in temperature gradients, exclusive of habitat fragmentation effects. Here we present a numerical model that captures the salient dynamics of migration by long-distance dispersal for a generic tree species. We then use the model to explore the possible effects of assisted colonization within a fragmented landscape under a simulated tree-planting scheme. Our results suggest that an assisted-colonization program could accelerate species-front migration rates enough to match the speed of climate change, but such a program would involve an environmental-sustainability intervention at a massive scale. PMID:25162663

  18. Vacuum treatments for California tree nuts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    California walnuts, almonds and pistachios must be free of insect infestation to meet consumer demands and export requirements. Fumigants such as methyl bromide have long been used to disinfest tree nuts of field pests such as codling moth and navel orangeworm, and storage pests such as Indianmeal ...

  19. TREAT (TREe-based Association Test)

    Cancer.gov

    TREAT is an R package for detecting complex joint effects in case-control studies. The test statistic is derived from a tree-structure model by recursive partitioning the data. Ultra-fast algorithm is designed to evaluate the significance of association between candidate gene and disease outcome

  20. Disease and spray coverage in pecan trees

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pecan scab (Fusicladium effusum G. Winter) is the major disease of pecan in the southeastern U.S., and severe epidemics on susceptible cultivars can result in complete yield loss. Anecdotal evidence indicates adequate scab control in the tops of tall trees in mature orchards is difficult, but no dat...