Variability of antioxidant and biological activities of Rhus tripartitum related to phenolic compounds

PubMed Central

Ben Miled, Hanène; Saada, Mariem; Jallali, Ines; Ben Barka, Zaineb; Tlili, Mounira; Alimi, Hichem; Sakly, Mohsen; Ben Rhouma, Khémais; Abderrabba, Manef; Abdelmelek, Hafedh; Tebourbi, Olfa; Ksouri, Riadh

2017-01-01

Rhus species are known in traditional medicine for their therapeutic virtue and their extracts showed numerous important properties including antimalarial, antimicrobial, antiviral, and hypoglycemic and anticonvulsant activities. Rhus tripartitum (Ucria) is a medicinal plant widely used in Tunisia folk medicine against chronic diarrhea and gastric ulcer. This study was designed to examine in vitro and ex vivo antioxidant, anti-inflammatory and anticancer activities of four extracts of Rhus tripartitum root cortex with increasing solvent polarity (hexane, dichloromethane, methanol and water). HPLC was used to identify and quantify phenolic compounds in Rhus extract. Water extract showed the highest antioxidant activity using oxygen radical absorbance capacity (ORAC method) with 8.95 ± 0.47 µmol Trolox/mg and a cell based-assay with 0.28 ± 0.12 µmol Trolox/mg as compared to the other fractions. Moreover, methanol extract displayed the strongest anti-cancer activity against human lung carcinoma (A-549) and colon adenocarcinoma cell lines (DLD-1) with an IC50 value of 60.69 ± 2.58 and 39.83 ± 4.56 µg/ml (resazurin test) and 44.52 ± 5.96 and 55.65 ± 6.00 µg/ml (hoechst test), respectively. Besides, the highest anti-inflammatory activity, inhibiting nitric oxide (NO) release, was exhibited by dichloromethane extract with 31.5 % at 160 µg/ml in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages. The HPLC analysis showed that catechol and kaempferol were the major phenolics. These data suggest the richness of all fractions of Ucria root on interesting bioactive molecules with different polarity and confirm the known traditional therapeutics virtues of this species for the treatment of dysentery, diarrhea and gastric ulcer. PMID:28694749

Variability of antioxidant and biological activities of Rhus tripartitum related to phenolic compounds.

PubMed

Ben Miled, Hanène; Saada, Mariem; Jallali, Ines; Ben Barka, Zaineb; Tlili, Mounira; Alimi, Hichem; Sakly, Mohsen; Ben Rhouma, Khémais; Abderrabba, Manef; Abdelmelek, Hafedh; Tebourbi, Olfa; Ksouri, Riadh

2017-01-01

Rhus species are known in traditional medicine for their therapeutic virtue and their extracts showed numerous important properties including antimalarial, antimicrobial, antiviral, and hypoglycemic and anticonvulsant activities. Rhus tripartitum (Ucria) is a medicinal plant widely used in Tunisia folk medicine against chronic diarrhea and gastric ulcer. This study was designed to examine in vitro and ex vivo antioxidant, anti-inflammatory and anticancer activities of four extracts of Rhus tripartitum root cortex with increasing solvent polarity (hexane, dichloromethane, methanol and water). HPLC was used to identify and quantify phenolic compounds in Rhus extract. Water extract showed the highest antioxidant activity using oxygen radical absorbance capacity (ORAC method) with 8.95 ± 0.47 µmol Trolox/mg and a cell based-assay with 0.28 ± 0.12 µmol Trolox/mg as compared to the other fractions. Moreover, methanol extract displayed the strongest anti-cancer activity against human lung carcinoma (A-549) and colon adenocarcinoma cell lines (DLD-1) with an IC 50 value of 60.69 ± 2.58 and 39.83 ± 4.56 µg/ml (resazurin test) and 44.52 ± 5.96 and 55.65 ± 6.00 µg/ml (hoechst test), respectively. Besides, the highest anti-inflammatory activity, inhibiting nitric oxide (NO) release, was exhibited by dichloromethane extract with 31.5 % at 160 µg/ml in lipopolysaccharide (LPS)-stimulated RAW 264.7 macrophages. The HPLC analysis showed that catechol and kaempferol were the major phenolics. These data suggest the richness of all fractions of Ucria root on interesting bioactive molecules with different polarity and confirm the known traditional therapeutics virtues of this species for the treatment of dysentery, diarrhea and gastric ulcer.

Elucidation of non-intentionally added substances migrating from polyester-polyurethane lacquers using automated LC-HRMS data processing.

PubMed

Omer, Elsa; Cariou, Ronan; Remaud, Gérald; Guitton, Yann; Germon, Hélène; Hill, Paul; Dervilly-Pinel, Gaud; Le Bizec, Bruno

2018-03-08

An untargeted strategy aiming at identifying non-intentionally added substances (NIAS) migrating from coatings was developed. This innovative approach was applied to two polyester-polyurethane lacquers, for which suppliers previously provided the identity of the monomers involved. Lacquers were extracted with acetonitrile and analyzed by liquid chromatography-high resolution mass spectrometry (LC-HRMS). Data, acquired in the full scan mode, were processed using an open-source R-environment (xcms and CAMERA packages) to list the detected features and deconvolute them in groups related to individual compounds. The most intense groups, accounting for more than 85% of cumulated feature intensities, were then investigated. A homemade database, populated with predicted polyester oligomer combinations from a relevant selection of diols and diacids, enabled highlighting the presence of 14 and 17 cyclic predicted polyester oligomers in the two lacquers, including three mutual combinations explained by common known monomers. Combination hypotheses were strengthened by chromatographic considerations and by the investigation of fragmentation patterns. Regarding unpredicted migrating substances, four monomers were hypothesised to explain several polyester or caprolactam oligomer series. Finally, considering both predicted and tentatively elucidated unpredicted oligomers, it was possible to assign hypotheses to features representing up to 82% and 90% of the cumulated intensities in the two lacquers, plus 9% and 3% (respectively) originating from the procedural blank. Graphical abstract Elucidation of non-intentionally added substances.

Efficacy of topical resin lacquer, amorolfine and oral terbinafine for treating toenail onychomycosis: a prospective, randomized, controlled, investigator-blinded, parallel-group clinical trial.

PubMed

Auvinen, T; Tiihonen, R; Soini, M; Wangel, M; Sipponen, A; Jokinen, J J

2015-10-01

Norway spruce (Picea abies) produces resin to protect against decomposition by microbial pathogens. In vitro tests have shown that spruce resin has antifungal properties against dermatophytes known to cause nearly 90% of onychomycosis in humans. To confirm previous in vivo observations that a topical resin lacquer provides mycological and clinical efficacy, and to compare this lacquer with topical amorolfine hydrochloride lacquer and systemic terbinafine for treating dermatophyte toenail onychomycosis. In this prospective, randomized, controlled, investigator-blinded study, 73 patients with onychomycosis were randomized to receive topical 30% resin lacquer once daily for 9 months, topical 5% amorolfine lacquer once weekly for 9 months, or 250 mg oral terbinafine once daily for 3 months. The primary outcome measure was complete mycological cure at 10 months. Secondary outcomes were clinical efficacy, cost-effectiveness and patient compliance. At 10 months, complete mycological cure rates with the resin, amorolfine and terbinafine treatments were 13% [95% confidence interval (CI) 0-28], 8% (95% CI 0-19) and 56% (95% CI 35-77), respectively (P ≤ 0·002). At 10 months, clinical responses were complete in four patients (16%) treated with terbinafine, and partial in seven (30%), seven (28%) and nine (36%) patients treated with resin, amorolfine and terbinafine, respectively (P < 0·05). Resin, amorolfine and terbinafine treatments cost €41·6, €56·3 and €52·1, respectively, per patient (P < 0·001). Topical 30% resin lacquer and topical 5% amorolfine lacquer provided similar efficacy for treating dermatophyte toenail onychomycosis. However, orally administered terbinafine was significantly more effective in terms of mycological cure and clinical outcome than either topical therapy at the 10-month follow-up. © 2015 British Association of Dermatologists.

Historical biogeography of Eastern Asian-Eastern North American disjunct Melaphidina aphids (Hemiptera: Aphididae: Eriosomatinae) on Rhus hosts (Anacardiaceae).

PubMed

Ren, Zhumei; Zhong, Yang; Kurosu, Utako; Aoki, Shigeyuki; Ma, Enbo; von Dohlen, Carol D; Wen, Jun

2013-12-01

Intercontinental biotic disjunctions have been documented and analyzed in numerous Holarctic taxa. Patterns previously synthesized for animals compared to plants suggest that the timing of animal disjunctions are mostly Early Tertiary and were generated by migration and vicariance events occurring in the North Atlantic, while plant disjunctions are mostly Mid-Late Tertiary and imply migration and vicariance over Beringia. Melaphidina aphids (Hemiptera: Aphididae: Fordini) exhibit host-alternating life cycles comprising an obligate seasonal shift between Rhus subgenus Rhus species (Anacardiaceae) and mosses (Bryophyta). Similar to their Rhus hosts, melaphidines are distributed disjunctly between Eastern Asia and Eastern North America. We examined evolutionary relationships within Melaphidina to determine the position of the North American lineage, date its divergence from Asian relatives, and compare these results to a previous historical biogeographic study of Rhus. We sampled nine species and three subspecies representing all six genera of Melaphidina. Data included sequences of mitochondrial cytochrome c oxidase subunits I and II+leucine tRNA, cytochrome b, and nuclear elongation factor 1α genes. Phylogenetic analyses (Bayesian, maximum-likelihood, parsimony) of the combined data (3282 bp) supported the monophyly of all genera except Nurudea and Schlechtendalia, due to the position of N. ibofushi. While the exact position of the North American Melaphis was not well resolved, there was high support for a derived position within Asian taxa. The divergence of Melaphis from Asian relatives centered on the Eocene-Oligocene boundary (~33-35Ma), which coincides with closure of Beringian Land Bridge I. This also corresponded to the Asian-North American disjunction previously estimated for subgenus Rhus spp. We suggest the late-Eocene Bering Land Bridge as the most likely migration route for Melaphis ancestors, as was also hypothesized for North American Rhus ancestors

Inter-species comparative antioxidant assay and HPTLC analysis of sakuranetin in the chloroform and ethanol extracts of aerial parts of Rhus retinorrhoea and Rhus tripartita.

PubMed

Alam, Perwez; Parvez, Mohammad Khalid; Arbab, Ahmed Hassan; Siddiqui, Nasir Ali; Al-Dosary, Mohammed Salem; Al-Rehaily, Adnan Jathlan; Ahmed, Sarfaraz; Kalam, Mohd Abul; Ahmad, Mohammad Shamim

2017-12-01

Extensive research on Rhus (Anacardiaceae) shows their antioxidant potential, which warrants further evaluation of its other species. To perform a comparative antioxidant assay on extracts of R. retinorrhoea and R. tripartita, including sakuranetin quantification by a validated HPTLC method. In vitro antioxidant assay was performed on chloroform and ethanol extracts of R. retinorrhoea Steud. ex Oliv. (RRCE and RREE) and R. tripartita (Ucria) Grande (RTCE and RTEE) by DPPH radical scavenging (at 31.25, 62.5, 125, 250 and 500 μg/mL concentrations) and β-carotene-linoleic acid bleaching methods at 500 μg/mL concentration. Densitometric HPTLC method was developed and validated using toluene: ethyl acetate: methanol (8:2:0.2; v/v/v) as mobile phase, executed on glass-backed silica gel F 254 plate and scanned at 292 nm. Antioxidant activity of Rhus extracts tested by the two methods (DPPH/BCB) was found in order of RTEE > RREE > RTCE > RRCE with IC 50 118.67/256.26, 315.75/82.35, 827.92/380.0 and 443.69/292.75, respectively. Scanning of the HPTLC plate provided an intense peak of sakuranetin at R f = 0.59. The estimated sakuranetin content in the dry weight of the extracts was highest in RREE (27.95 μg/mg) followed by RRCE (25.22 μg/mg), RTEE (0.487 μg/mg) and RTCE (0.0 μg/mg). Presence of sakuranetin in RREE, RRCE and RTEE supported the highest antioxidant property of the two Rhus species. Nonetheless, low sakuratenin in R. tripartita indicated the presence of other bioactive constituents responsible for synergistic antioxidant activity. The developed HPTLC method therefore guarantees its application in quality control of commercialized herbal drugs and formulations containing sakuranetin.

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

PHARMACOGNOSTIC EVALUATION OF THE LEAF OF Rhus succedanea VAR. HIMALAICA. J. D HOOKER.

PubMed Central

Khan, Shafqat Ali; Ibrar, Muhammad; Barkatullah

2016-01-01

Background: Rhus succedanea is generally traded, distributed and sold in the markets in its crude and raw form. This may have been mixed with adulterants, mismanaged by malpractices and substituted with other closely related drugs having different effect. This study is therefore carried out to authenticate the plant through pharmacogonostic evaluations. Material & Methods: The organoleptic studies were carried through sensory organs i.e size, shape, texrure, odour, etc. Histological studies were conducted by preparing hand slides, mounting the specimen in potato tuber; fluorescence characters were determined through UV and phytochemical screening was investigated using various standard and common methods from relevant literature. Results: Morphologically, the Rhus is a perennial small sized deciduous tree, 5–9 m tall with opposite imparipinnately compound leaves and small grayish yellow flowers born on paniculate inflorescence; locally, called as Rakhkal in Pashto and Kakarsingi in Urdu. The organoleptic evaluation showed leaf had pleasant, aromatic odour and astringent taste. Transverse section of leaf through midrib region was worked out. The anatomy of the midrib has shown to be surrounded by both upper and lower epidermis with multicellular non-glandular trichomes. The leaf was hypostomatic showing anomocytic stomata with average stomatal number 27.1 ± 7.2 and stomatal index 14 ± 3.63. The average vein islet, vein termination and palisade ratios were 13.6 ± 3.04, 10.21 ± 1.92 and 6 ± 2.01 respectively. Leaf powder showed the existance of anomocytic stomata, spirally thickened xylem vessels, non-glandular multicellular and stellate trichomes. Fluorescence study and percent extractive values was also carried out. The phytochemical screening showed the presence of carbohydrates, protein, alkaloids, phenols, flavonoids, terpenoids and anthraquenones, while tannins and fixed oil was not detected. Quantitatively highest amount of alkaloids 16% and flavonoids

Enhanced Ungual Permeation of Terbinafine HCl Delivered Through Liposome-Loaded Nail Lacquer Formulation Optimized by QbD Approach.

PubMed

Shah, Viral H; Jobanputra, Amee

2018-01-01

The present investigation focused on developing, optimizing, and evaluating a novel liposome-loaded nail lacquer formulation for increasing the transungual permeation flux of terbinafine HCl for efficient treatment of onychomycosis. A three-factor, three-level, Box-Behnken design was employed for optimizing process and formulation parameters of liposomal formulation. Liposomes were formulated by thin film hydration technique followed by sonication. Drug to lipid ratio, sonication amplitude, and sonication time were screened as independent variables while particle size, PDI, entrapment efficiency, and zeta potential were selected as quality attributes for liposomal formulation. Multiple regression analysis was employed to construct a second-order quadratic polynomial equation and contour plots. Design space (overlay plot) was generated to optimize a liposomal system, with software-suggested levels of independent variables that could be transformed to desired responses. The optimized liposome formulation was characterized and dispersed in nail lacquer which was further evaluated for different parameters. Results depicted that the optimized terbinafine HCl-loaded liposome formulation exhibited particle size of 182 nm, PDI of 0.175, zeta potential of -26.8 mV, and entrapment efficiency of 80%. Transungual permeability flux of terbinafine HCl through liposome-dispersed nail lacquer formulation was observed to be significantly higher in comparison to nail lacquer with a permeation enhancer. The developed formulation was also observed to be as efficient as pure drug dispersion in its antifungal activity. Thus, it was concluded that the developed formulation can serve as an efficient tool for enhancing the permeability of terbinafine HCl across human nail plate thereby improving its therapeutic efficiency.

Bioaccumulation and detoxification mechanisms for lead uptake identified in Rhus chinensis Mill. seedlings.

PubMed

Zhou, Chuifan; Huang, Meiying; Ren, Huijun; Yu, Jiaoda; Wu, Jiamei; Ma, Xiangqing

2017-08-01

A greenhouse experiment was conducted to assay the bioaccumulation and tolerance characteristics of Rhus chinensis Mill. to lead (Pb). The effects of exposing R. chinensis Mill seedlings to increasing Pb concentrations (0, 250, 500, 100mgkg-1) in the soil were assessed by measuring Pb accumulation, subcellular distribution, ultrastructure, photosynthetic characteristics, antioxidative enzyme activity, malondialdehyde content, and phytochelatin content. The majority of Pb taken up by R. chinensis Mill was associated with the cell wall fraction in the roots, where the absorption of Ca increased to maintain cell wall stability, and Pb deposits were found in the intercellular space or in the cell wall structures. In leaves, Pb was primarily stored in the cell wall, while it was compartmentalized into the vacuolar structures in the stem. Pb concentrations adversely affected the morphology of Rhus chinensis Mill cellular substructures. Furthermore, increased Peroxidase (POD) and catalase (CAT) activity was observed in plants grown in Pb-amended soil, and this may have led to reduced ROS to maintain the function of the membrane. Changes in phytochelatin levels (PCs) that were observed in Pb treated plants suggest that PCs formed complexes with Pb in the cytoplasm to reduce Pb 2+ toxicity in the metabolically active cellular compartment. This mechanism may allow for the plant to accumulate higher concentrations of toxic Pb and survive for a longer period of time. Our study provides a better understanding of how Rhus chinensis Mill detoxifies Pb. Copyright © 2017. Published by Elsevier Inc.

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…

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

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...

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

... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Plant extract derived from Opuntia...) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Exemptions From Tolerances § 180.1179 Plant extract derived from Opuntia lindheimeri, Quercus falcata, Rhus aromatica, and...

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

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Plant extract derived from Opuntia...) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Exemptions From Tolerances § 180.1179 Plant extract derived from Opuntia lindheimeri, Quercus falcata, Rhus aromatica, and...

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...) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Exemptions From Tolerances § 180.1179 Plant extract derived from Opuntia lindheimeri, Quercus falcata, Rhus aromatica, and...

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

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Plant extract derived from Opuntia...) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Exemptions From Tolerances § 180.1179 Plant extract derived from Opuntia lindheimeri, Quercus falcata, Rhus aromatica, and...

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

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Plant extract derived from Opuntia...) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Exemptions From Tolerances § 180.1179 Plant extract derived from Opuntia lindheimeri, Quercus falcata, Rhus aromatica, and...

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.

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.

Fire effects on germination of seeds from Rhus and Rubus: competitors to pine during natural regeneration

Treesearch

Michael D. Cain; Michael G. Shelton

2003-01-01

Throughout the southeastern United States, Rhus and Rubus species are common associates of the southern pines on a wide array of upland site and stand conditions. Because of their ability to overrun disturbed sites, these species are categorized as competitors to pine during stand regeneration. Since prescribed burning is often...

36 kDa glycoprotein isolated from Rhus verniciflua stokes inhibits G/GO-induced mitochondrial apoptotic signal pathways in BNL CL.2 cells.

PubMed

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

2005-12-01

Rhus verniciflua Stokes is one of the medicinal plants traditionally used to heal and treat hepatic and inflammatory diseases. We found that a glycoprotein isolated from the fruit has a molecular weight of 36 kDa and consists of a carbohydrate component (38.75%) and a protein (61.25%), and that the glycoprotein has a strong scavenging activity against hydroxyl radicals without any pro-oxidant activity in the cell-free system. In glucose/glucose oxidase (G/GO)-induced BNL CL.2 cells, the results showed that Rhus verniciflua Stokes glycoprotein has dose-dependent blocking activities against G/GO-induced cytotoxicity and apoptosis, increasing the glutathione (GSH) peroxidase activity. In the activity of the mitochondrial apoptotic mediators (cytochrome c, caspases and poly(ADP-ribose)polymerase (PARP)), the glycoprotein (100 microg/ml) showed an inhibitory effect on cytochrome c release, caspase-9/3 activation, and PARP cleavage. Moreover, Rhus verniciflua Stokes glycoprotein has a stimulating effect on the nitric oxide production. Here, we speculate that this glycoprotein is one of the natural antioxidants and of the modulators of apoptotic signal pathways in BNL CL.2 cells.

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. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Phylogeny of Rhus gall aphids (Hemiptera:Pemphigidae) based on combined molecular analysis of nuclear EF1α and mitochondrial COII genes

Treesearch

Zi-xiang Yang; Xiao-ming Chen; Nathan P. Havill; Ying Feng; Hang Chen

2010-01-01

Rhus gall aphids (Fordinae : Melaphidini) have a disjunct distribution in East Asia and North America and have specific host plant relationships. Some of them are of economic importance and all species form sealed galls which show great variation in shape, size, structure, and galling-site. We present a phylogeny incorporating ten species and four...

Flavonoids with DNA strand-scission activity from Rhus javanica var. roxburghiana.

PubMed

Lin, Chun-Nan; Chen, Hui-Ling; Yen, Ming-Hong

2008-01-01

The flavonoids isolated from the stems of Rhus javanica var. roxburghiana, taxifolin (1), fisetin (2), fustin (3), 3,7,4'-trihydroxyflavanone (4) and 3,7,4'-trihydroxyflavone (5) caused breakage of supercoiled plasmid pBR322 DNA in the presence of Cu(II). Cu(I) was shown to be an essential intermediate by using the Cu(I)-specific sequestering reagent neocuproine. The Cu(II)-mediated DNA scissions induced by 1, 2, 3 and 5 were inhibited by the addition of catalase and exhibited DNA strand break by the addition of KI and superoxide dimutase (SOD), while in the Cu(II)-mediated DNA scissions induced by 4 was inhibited by the addition of KI, SOD, and catalase. It is concluded that 1, 2, 3, and 5 can induce H2O2 and superoxide anion, while 4 can induce OH* and H2O2 and subsequent oxidative damage of DNA in the presence of Cu(II).

Rhus copallinum L.

Treesearch

K.F Connor

2004-01-01

Shining sumac is an upright, deciduous, clonal shrub or (rarely) small tree from 3 to 6 m tall. Bark ranges in color from light brown to gray to reddish-brown. Shoots and twigs are hairy and reddish in color. Twigs have conspicuous lenticels. The sparsely branched, flat crown is composed of alternate, pinnately compound leaves approximately 15 to 30 cm long, with wings...

Evaluation of the anti-diarrheal activity of the hydromethanolic root extract of Rhus tripartita (Ucria) (Anacardiacae).

PubMed

Ben Barka, Zaineb; Aouadhi, Chedia; Tlili, Mounira; Alimi, Hichem; Ben Miled, Hanene; Ben Rhouma, Khémais; Sakly, Mohsen; Ksouri, Riadh; Schneider, Yves Jacques; Maaroufi, Abderrazek; Tebourbi, Olfa

2016-10-01

Rhus tripartita (Anacardiacae) is a plant which is traditionally used for the treatment of ulcer and diarrhea in Tunisia. However, the scientific basis for this usage has not been well established. The core aim of the present study is to evaluate the antidiarrheal activity of Rhus tripartita root methanolic extract (RRE). The antidiarrheal activity of RRE oral doses (50, 100, 200 and 300mg/kg) was evaluated using the castor oil-induced diarrhea, the intestinal fluid emptying method and the normal intestinal transit test. The antibacterial activity was tested against four pathogenic bacteria using two methods. The RRE was also phytochemical studied. Diarrhea experiments showed a protective effect of the RRE which produced a significant (p<0.05) and dose-dependent reduction of all the diarrhea parameters. It delayed the onset of diarrhea, produced a significant decrease in the frequency of defecation and the diarrhea score severity and decreased the volume of intestinal fluid induced by castor oil as well as the propulsion intestinal transit. The effect of the extract at the highest dose (300mg/kg) was similar to that of loperamide, the standard anti-diarrheal drug (10mg/kg). The anti-bacterial activity test showed that RRE exhibited a great inhibition activity against four pathogenic bacteria strains (Esherichia coli, Salmonella typhimurium, Salmonella argenosa, Staphylococcus aureus). Oral administration of the extract up to 3g/kg did not produce any acute toxicity in rats. The preliminary phytochemical screening of the RRE revealed the presence of flavonoids, tannins, and polyphenols. Results showed that RRE at 300mg/kg possesses the highest anti-diarrheal activity possibly mediated by the inhibitory effects on gastrointestinal propulsion and intestinal fluid accumulation. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Air formaldehyde and solvent concentrations during surface coating with acid-curing lacquers and paints in the woodworking and furniture industry.

PubMed

Thorud, Syvert; Gjolstad, Merete; Ellingsen, Dag G; Molander, Paal

2005-06-01

An investigation of contemporary exposure to formaldehyde and organic solvents has been carried out during surface coating with acid-curing lacquers and paints in the Norwegian woodworking and furniture industry over a period of 3 years. The investigation covered 27 factories of different sizes and with different types of production, and totally 557 parallel formaldehyde and solvent samples were collected. The formaldehyde concentration (geometric mean) was 0.15 ppm (range 0.01-1.48 ppm) with about 10% of the samples exceeding the Norwegian occupational exposure limit of 0.5 ppm. The solvent concentration as additive effect (geometric mean) was 0.13 (range 0.0004-5.08) and about 5% of the samples exceeded the Norwegian occupational exposure limit. The most frequently occurring solvents from acid-curing lacquers were n-butyl acetate, ethanol, ethyl acetate and 1-butanol, which were found in 88-98% of the samples. Toluene, n-butyl acetate and 1-butanol were the only solvents with maximum concentrations exceeding their respective occupational exposure limits. Curtain painting machine operators were exposed to the highest concentrations of both formaldehyde (geometric mean 0.51 ppm, range 0.08-1.48 ppm) and organic solvents (additive effect, geometric mean 1.18, range 0.02-5.08). Other painting application work tasks such as automatic and manual spray-painting, manual painting and dip painting, showed on average considerably lower concentrations of both formaldehyde (geometric means 0.07-0.16 ppm) and organic solvents (additive effect, geometric mean 0.02-0.18). Non-painting work tasks also displayed moderate concentrations of formaldehyde (geometric means 0.11-0.17 ppm) and organic solvents (additive effect, geometric mean 0.04-0.07).

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

DTIC Science & Technology

2005-03-31

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

Agronomic and chemical evaluation of smooth sumac, Rhus glabra

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

Campbell, T.A.

Smooth sumac (Rhus glabra) is a potential whole-plant source of polyphenol and oil. In a 2-yr evaluation of progenies from 14 Maryland, 1 northern Virginia, and 2 Georgia populations, highly significant variation (1% level) in vigor, number of plants surviving the seeding year, dry matter yield the seeding year, and number of tillers produced the second year was observed. In 15 entries, highly significant variation (1% level) in polyphenol + oil and in gallotannins was observed. Dry matter yields, extrapolated to Mg ha/sup -1/, ranged from 0.02 to 1.4 (for a single harvest), % polyphenol + oil from 19.4-31.1, andmore » % gallotannins (a class of polyphenols) from 9.8 to 15.7. It is suggested that significantly improved lines could be developed through breeding. Based on estimated ratios of sigma/sup 2//sub Entries//sigma/sup 2//sub Entries/ + sigma/sup 2/, genetic variation for most agronomic traits could be estimated with fair precision whereas variation for chemical traits could be affected substantially by nongenetic factors. Factor analysis indicated plants that would perform reasonably well over a 2-yr period could be selected on the basis of early seeding-year vigor scores. Selection for high amount of polyphenol + oil and gallotannins would have to be done independently of agronomic selection. Cutting frequencies should not exceed 2 x yr/sup -1/ or serious stand loss would occur.« less

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; Thöny-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

Anti‑inflammatory and anti‑proliferative effects of Rhus verniciflua Stokes in RAW264.7 cells.

PubMed

Choi, Han-Seok; Seo, Hye Sook; Kim, Soon Re; Choi, Youn Kyung; Jang, Bo-Hyoung; Shin, Yong-Cheol; Ko, Seong-Gyu

2014-01-01

Inflammatory response is a major defense mechanism against pathogens and chemical or mechanical injury. Rhus verniciflua Stokes (RVS) has traditionally been used as an ingredient in East Asian medicine for the treatment of gastritis, stomach cancer and atherosclerosis. The aim of the current study was to analyze the effect of RVS on LPS‑induced inflammatory responses in the RAW264.7 mouse macrophage cell line. RAW264.7 cells were treated with various concentrations of RVS and LPS at specific time points. WST assay, trypan blue assay and quantification of activated cells revealed that RVS suppressed cell proliferation in a dose‑dependent manner. RVS induced G1 cell cycle arrest, suppressed iNOS and COX‑2 mRNA expression induced by LPS and decreased intracellular ROS levels induced by LPS. In addition, RVS induced PARP and caspase‑3 cleavage suggesting that RVS causes cell death. Results of the present study indicate that RVS may be advantageous in treating inflammatory disease.

In vitro antibacterial and antifungal activities of Rhus tripartitum used as antidiarrhoeal in Tunisian folk medicine.

PubMed

Abbassi, Feten; Hani, Khaled

2012-01-01

Rhus tripartitum (African sumac) is a plant commonly used in Tunisian traditional medicine to treat diarrhoea and dysentery. In this study, we have demonstrated that R. tripartitum extracts exhibited a significant broad spectrum activity against one or more of the test microorganisms with a zone size ranging from 8 to 28 mm in diameter. These diameters are much higher than those obtained with standard antibiotics. The chloroformic extracts were found to be effective against bacterial and fungal strains tested, with MIC values ranging between 0.07 and 0.62 mg mL(-1) against Staphylococcus aureus and Candida albicans. However, ethyl-acetate/methanol fractions showed a selective activity only against bacterial microorganisms with low MIC values between 0.07 and 0.15 mg mL(-1). The overall results suggested that the traditional use of R. tripartitum for the treatment of diarrhoea tract infections was attributed to the presence of antibacterial agents.

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 2008–2010. 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

Interaction of α-synuclein with Rhus typhina tannin - Implication for Parkinson's disease.

PubMed

Sekowski, Szymon; Ionov, Maksim; Abdulladjanova, Nodira; Makhmudov, Rustam; Mavlyanov, Saidmukhtar; Milowska, Katarzyna; Bryszewska, Maria; Zamaraeva, Maria

2017-07-01

The etiology of Parkinson's disease (PD) relates to α-synuclein, a small protein with the ability to aggregate and form Lewy bodies. One of its prevention strategies is inhibition of α-synuclein oligomerization. We have investigated the interaction of α-synuclein and human serum albumin with 3,6-bis-О-di-О-galloyl-1,2,4-tri-О-galloyl-β-d-glucose (a tannin isolated from the plant Rhus typhina). Using fluorescence spectroscopy method we found that this tannin interacts strongly with α-synuclein forming complexes. Circular dichroism analysis showed a time-dependent inhibition of α-synuclein aggregation in the presence of the tannin. On the other hand, 3,6-bis-О-di-О-galloyl-1,2,4-tri-О-galloyl-β-d-glucose had a much stronger interaction with human serum albumin than α-synuclein. The calculated binding constant for tannin-protein interaction was considerably higher for albumin than α-synuclein. This tannin interacted with albumin through a "sphere of action" mechanism. The results lead to the conclusion that 3,6-bis-О-di-О-galloyl-1,2,4-tri-О-galloyl-β-d-glucose is a potent preventive compound against Parkinson's disease. However, this tannin interacts very strongly with human serum albumin, significantly reducing the bioavailability of this compound. Copyright © 2017 Elsevier B.V. All rights reserved.

Extract of Rhus verniciflua Bark Suppresses 2,4-Dinitrofluorobenzene-Induced Allergic Contact Dermatitis

PubMed Central

Park, Dong Ki; Lee, Yang Gi; Park, Hye-Jin

2013-01-01

Rhus verniciflua Stokes (RV) has traditionally been used as a food supplement and a traditional herbal medicine for centuries in Korea. Recent studies suggest that RV has potent antioxidative, antitumor, and anti-inflammatory properties. In this study, the anti-inflammatory effects of RV from mice sensitized with 2,4-dinitrofluorobenzene (DNFB) and activated macrophages were investigated. The results showed that RV reduced ear swelling and hyperplasia of ear tissue as well as an increase in vascular permeability, which are characteristics of allergic contact dermatitis (ACD) with evident histomorphological changes in epidermis and dermis. Decreased numbers of infiltrated mast cells were seen in RV extract treated group, using toluidine blue staining. RV extract significantly regulates the expression of inducible nitric oxide synthase (iNOS) at the translational level in activated macrophages. Furthermore, RV extract and its active compound, fisetin, attenuated the level of tumor necrosis factor-α (TNF-α) and interleukin 6 (IL-6) mRNA in LPS-stimulated macrophages. Anti-ACD effect of RV extract may be due to the suppression of iNOS and proinflammatory cytokines which might be mediated via the NFκB signaling pathways. Collectively, RV extract has potential for alleviating ACD-like symptoms induced by DNFB in the mouse. PMID:23710240

Role of structural changes induced in biological membranes by hydrolysable tannins from sumac leaves (Rhus typhina L.) in their antihemolytic and antibacterial effects.

PubMed

Olchowik-Grabarek, Ewa; Swiecicka, Izabela; Andreeva-Kovaleskaya, Zhanna; Solonin, Alexander; Bonarska-Kujawa, Dorota; Kleszczyńska, Halina; Mavlyanov, Saidmukhtar; Zamaraeva, Maria

2014-06-01

In this study, we found that the sumac tannins (Rhus typhina L.) exert to a various extent antihemolytic effects and antibacterial activity against Bacillus cereus and Pseudomonas aeruginosa depending on structural specificity of bacteria and different mechanisms of their toxic action. The sumac tannins exert the most expressed activity against B. cereus. The antihemolytic effect of the sumac tannins seems to be connected to a greater extent with their modifying action on the erythrocyte membrane structure. It was found that the sumac tannins are incorporated into the erythrocyte membrane, causing transformation of discocytes into echinocytes and enhancing the rigidity of the hydrophilic region of the lipid bilayer. We suggest that the embedding of sumac tannins into the membrane of erythrocytes alters their physical properties and, as a consequence, can limit their interaction with bacterial toxins.

Evolution of Volatile Emission in Rhus coriaria Organs During Different Stages of Growth and Evaluation of the Essential Oil Composition.

PubMed

Reidel, Rose Vanessa Bandeira; Cioni, Pier Luigi; Majo, Luigi; Pistelli, Luisa

2017-11-01

Rhus coriaria, also known as Sumac, has been traditionally used in many countries as spice, condiment, dying agent, and medicinal herb. The chemical composition of essential oils (EOs) and the volatile emissions from different organs of this species collected in Sicily (Italy) were analyzed by gas chromatography-flame ionization detection and gas chromatography/mass spectrometry. Monoterpene and sesquiterpene hydrocarbons were the most abundant class in the volatile emissions with β-caryophyllene and α-pinene were the main constituents in the majority of the examined samples. The EO composition was characterized by high amount of monoterpene and sesquiterpene hydrocarbons together with diterpenes. The main compounds in the EO obtained from the leaves and both stages of fruit maturation were cembrene and β-caryophyllene, while α-pinene and tridecanoic acid were the key compounds in the flower EO. All the data were submitted to multivariate statistical analysis showing many differences among the different plant parts and their ontogenetic stages. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

Relationships between macular pigment optical density and lacquer cracks in high myopia.

PubMed

Benoudis, L; Ingrand, P; Jeau, J; Lichtwitz, O; Boissonnot, M; Leveziel, N

2016-09-01

A low concentration of macular carotenoid pigment (lutein and zeaxanthin) is a significant risk factor for macular degeneration. The goal of this paper is to investigate the relationship between macular pigment optical density (MPOD) and lacquer cracks (LC) in high myopia. This is a prospective comparative observational study (NCT02205632) including high myopic patients with or without LC. High myopia was defined as a refractive error greater than 6 diopters of myopia or axial length greater than 26mm. All patients underwent best-corrected visual acuity in logMAR, MPOD measurement, multicolor imaging, SD-OCT, autofluorescence and axial length measurement. MPOD was calculated using heterochromatic flicker photometry. Group 1 was defined as eyes without LC and group 2 as eyes with LC. Forty-five eyes of 32 patients with a mean age of 51.3 years were included in group 1, and 15 eyes of 13 patients aged 54.1 in group 2 (P=0.56). Mean spherical equivalent was -10.11 diopters in group 1 and -15.11 in group 2 (P=0.0004). Mean visual acuity was +0.08 logMAR (0.8 in decimal notation) in group 1 and +0.11 logMAR (0.8 in decimal notation) in group 2 (P=0.061). Axial length was 27.8mm in group 1 and 29.2 in group 2 (P=0.0052). Central macular thickness was lower in group 1 (295μm) than in group 2 (305μm) (P<0.0001), and macular choroidal thickness did not differ between the two groups (P=0.094). Mean MPOD in group 2 was 0.52 and 0.63 in group 1 (P=0.042). Differences in axial length were not related to MPOD measurements (P=0.74). A lower rate of MPOD was observed in cases of LC in high myopia. Further studies are needed to investigate if dietary carotenoids could have a protective effect in reducing the risk of LC. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Anticancer activity of botanical alkyl hydroquinones attributed to topoisomerase II poisoning

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

Huang, C.-P.; Fang, W.-H.; Lin, L.-I.

2008-03-15

Cytotoxic alkyl hydroquinone compounds have been isolated from many plants. We previously isolated 3 structurally similar cytotoxic alkyl hydroquinone compounds from the sap of the lacquer tree Rhus succedanea L. belonging to the sumac family, which have a long history of medicinal use in Asia. Each has an unsaturated alkyl chain attached to the 2-position of a hydroquinone ring. One of these isolates, 10'(Z),13'(E),15'(E)-heptadecatrienylhydroquinone [HQ17(3)], being the most cytotoxic, was chosen for studying the anticancer mechanism of these compounds. We found that HQ17(3) was a topoisomerase (Topo) II poison. It irreversibly inhibited Topo II{alpha} activity through the accumulation of Topomore » II-DNA cleavable complexes. A cell-based assay showed that HQ17(3) inhibited the growth of leukemia HL-60 cells with an EC{sub 50} of 0.9 {mu}M, inhibited the topoisomerase-II-deficient cells HL-60/MX2 with an EC{sub 50} of 9.6 {mu}M, and exerted no effect on peripheral blood mononuclear cells at concentrations up to 50 {mu}M. These results suggest that Topo II is the cellular drug target. In HL-60 cells, HQ17(3) promptly inhibited DNA synthesis, induced chromosomal breakage, and led to cell death with an EC{sub 50} about one-tenth that of hydroquinone. Pretreatment of the cells with N-acetylcysteine could not attenuate the cytotoxicity and DNA damage induced by HQ17(3). However, N-acetylcysteine did significantly reduce the cytotoxicity of hydroquinone. In F344 rats, intraperitoneal injection of HQ17(3) for 28 days induced no clinical signs of toxicity. These results indicated that HQ17(3) is a potential anticancer agent, and its structural features could be a model for anticancer drug design.« less

Photosynthesis and fluctuating asymmetry as indicators of plant response to soil disturbance in the Fall-Line Sandhills of Georgia: a case study using Rhus copallinum and Ipomoea pandurata

USGS Publications Warehouse

Freeman, D. Carl; Brown, Michelle L.; Duda, Jeffrey J.; Graham, John H.; Emlen, John M.; Krzysik, Anthony J.; Balbach, Harold E.; Kovacic, David A.; Zak, John C.

2004-01-01

We examined net photosynthesis, transpiration, stomatal conductance, and leaf fluctuating asymmetry on two species (Rhus copallinum and Ipomoea pandurata) as indicators of stress at nine sites across a gradient of soil disturbance at Fort Benning, Georgia. There were three sites for each of three disturbance levels. Physical habitat disturbance was caused by activities associated with infantry training, including mechanized elements (tanks and personnel carriers) and foot soldiers. In addition, we examined the influence of prescribed burns and microhabitat effects (within meter‐square quadrats centered about the plant) on these measures of plant stress. Net photosynthesis declined with increasing disturbance in the absence of burning for both species. However, when sites were burned the previous year, net photosynthesis increased with increasing disturbance. Developmental instability in Rhus, as measured by fluctuating asymmetry, also declined with increasing disturbance in the absence of burning but increased with disturbance if sites were burned the previous year. Developmental instability was much less sensitive to burning in Ipomoea and in general was lowest at intermediate disturbance sites. Microenvironmental and microhabitat effects were weakly correlated with measures of plant stress when all sites were combined. However, higher correlations were obtained within site categories, especially when the recent history of prescribed burning was used as a category. Finally, using all of the combined data in a discriminant function analysis allowed us to correctly predict the disturbance level of more than 80% of the plants. Plant stress is responsive to both large‐scale perturbations, such as burning, and microhabitat parameters. Because of this, it is important to include macro‐ and microhabitat parameters when assessing stress. Similarly, we found a combination of developmental and physiological indicators of stress was superior to using them

Neuroprotective and Anti-Inflammatory Effects of Rhus coriaria Extract in a Mouse Model of Ischemic Optic Neuropathy.

PubMed

Khalilpour, Saba; Behnammanesh, Ghazaleh; Suede, Fouad; Ezzat, Mohammed O; Muniandy, Jayadhisan; Tabana, Yasser; Ahamed, Mohamed Khadeer; Tamayol, Ali; Majid, Amin Malik Shah; Sangiovanni, Enrico; Dell'Agli, Mario; Majid, Aman Shah

2018-04-23

Modulating oxidative stresses and inflammation can potentially prevent or alleviate the pathological conditions of diseases associated with the nervous system, including ischemic optic neuropathy. In this study we evaluated the anti-neuroinflammatory and neuroprotective activities of Rhus coriaria ( R. coriaria) extract in vivo. The half maximal inhibitory concentration (IC 50 ) for DPPH, ABTS and β⁻carotene were 6.79 ± 0.009 µg/mL, 10.94 ± 0.09 µg/mL, and 6.25 ± 0.06 µg/mL, respectively. Retinal ischemia was induced by optic nerve crush injury in albino Balb/c mice. The anti-inflammatory activity of ethanolic extract of R. coriaria (ERC) and linoleic acid (LA) on ocular ischemia was monitored using Fluorescence Molecular Tomography (FMT). Following optic nerve crush injury, the mice treated with 400 mg/kg of ERC and LA exhibited an 84.87% and 86.71% reduction of fluorescent signal (cathepsin activity) respectively. The results of this study provide strong scientific evidence for the neuroprotective activity of the ERC, identifying LA as one of the main components responsible for the effect. ERC may be useful and worthy of further development for its adjunctive utilization in the treatment of optic neuropathy.

Leaf extract of Rhus verniciflua Stokes protects dopaminergic neuronal cells in a rotenone model of Parkinson's disease.

PubMed

Kim, Seung; Park, Se-Eun; Sapkota, Kumar; Kim, Myung-Kon; Kim, Sung-Jun

2011-10-01

The present study investigated the neuroprotective effects of Rhus verniciflua Stokes (RVS) leaf extract on rotenone-induced apoptosis in human dopaminergic cells, SH-SY5Y. Cells were pretreated with RVS extract for 1 h then treated with vehicle or rotenone for 24 h. Cell viability, cell cytotoxicity, cell morphology and nuclear morphology were examined by MTT assay, lactate dehydrogenase release assay, phase contrast microscopy and staining with Hoechast 33342, respectively. Reactive oxygen species were measured by 2'7'-dichlorofluorescein diacetate and fragmented DNA was observed by TUNEL assay. Mitochondrial membrane potential was determined by Rhodamine 123. Pro-apoptotic and anti-apoptotic proteins and tyrosine hydroxylase were analysed by Western blotting. Results showed that RVS suppressed rotenone-induced reactive oxygen species generation, cellular injury and apoptotic cell death. RVS also prevented rotenone-mediated changes in Bax/Bcl-2 levels, mitochondrial membrane potential dissipation and Caspase 3 activation. Moreover, RVS pretreatment increased the tyrosine hydroxylase levels in SH-SY5Y cells. These findings demonstrate that RVS protects SH-SY5Y cells against rotenone-induced injury and suggest that RVS may have potential therapeutic value for neurodegenerative disease associated with oxidative stress. © 2011 The Authors. JPP © 2011 Royal Pharmaceutical Society.

Selective antiproliferative and apoptotic effects of flavonoids purified from Rhus verniciflua Stokes on normal versus transformed hepatic cell lines.

PubMed

Son, Young-Ok; Lee, Kyung-Yeol; Lee, Jeong-Chae; Jang, Hyon-Seok; Kim, Jong-Ghee; Jeon, Young-Mi; Jang, Yong-Suk

2005-01-15

Considerable attention is being concentrated on dietary flavonoids in developing novel cancer-preventive approaches due to their potential ability to induce selective apoptosis of cancer cells. In this study, we prepared a flavonoid-containing fraction from a crude acetone extract of Rhus verniciflua Stokes (RVS), traditionally used as a food additive and as an herbal medicine, and named RVS chloroform-methanol fraction (RCMF). We evaluated the effects of RCMF on proliferation and apoptosis using mouse embryonic primary hepatic cells (MPHC), embryonic normal hepatic cell line (BNL CL.2), and its SV40-mediated transformed cell line (BNL SV A.8). We also investigated the effects of RCMF on the antioxidant defense system in those cells. This study demonstrated that RCMF exhibited a selective growth inhibition and apoptosis induction on transformed cells. BNL SV A.8 cells were more sensitive to RCMF-mediated cytotoxicity than were MPHC or BNL CL.2. RCMF-mediated reduction of MnSOD activity and glutathione (GSH) content in BNL SV A.8 cells is thought to be associated with RCMF-induced apoptosis. Our findings suggest that RCMF is an agent which may be capable of inducing growth inhibition and apoptosis of hepatic tumor cells.

Detoxified extract of Rhus verniciflua stokes inhibits rotenone-induced apoptosis in human dopaminergic cells, SH-SY5Y.

PubMed

Sapkota, Kumar; Kim, Seung; Park, Se-Eun; Kim, Sung-Jun

2011-03-01

Rhus verniciflua Stokes (RVS), traditionally used as a food supplement and in traditional herbal medicine for centuries in Korea, is known to possess various pharmacological properties. Environmental neurotoxins such as rotenone, a specific inhibitor of complex I provide models of Parkinson's disease (PD) both in vivo and in vitro. In this study, we investigated the neuroprotective effect of RVS against rotenone-induced toxicity in human dopaminergic cells, SH-SY5Y. Cells exposed to rotenone for 24 h-induced cellular injury and apoptotic cell death. Pretreatment of cells with RVS provided significant protection to SH-SY5Y cells. Further, RVS offered remarkable protection against rotenone-induced oxidative stress and markedly inhibited mitochondrial membrane potential (MMP) disruption. RVS also attenuated the up-regulation of Bax, Caspase-9 and Caspase-3 and down-regulation of Bcl-2. Moreover, pretreatment with RVS prevented the decrease in tyrosine hydroxylase (TH) levels in SH-SY5Y cells. Interestingly, RVS conferred profound protection to human dopaminergic cells by preventing the downregulation of brain-derived neurotrophic factor (BDNF) and glial cell line-derived neurotrophic factor (GDNF). These results suggest that RVS may protect dopaminergic neurons against rotenone-induced apoptosis by multiple functions and contribute to neuroprotection in neurodegenerative diseases, such as PD.

Rhus verniciflua Stokes Extract and Its Flavonoids Protect PC-12 Cells against H2O2-Induced Cytotoxicity.

PubMed

Nam, Tae Gyu; Lee, Bong Han; Choi, Hyo-Kyoung; Mansur, Ahmad Rois; Lee, Sang Gil; Kim, Dae-Ok

2017-06-28

Rhus verniciflua Stokes (RVS), an herbal medicine found in East Asia, was extracted and further fractionated to investigate its antioxidant capacity and neuroprotective effects. The RVS ethyl acetate (EtOAc) fraction had the highest level of total phenolics and antioxidant capacity among all solvent fractions tested. Pretreatment of PC-12 cells with the EtOAc fraction effectively attenuated H 2 O 2 -induced oxidative damage. Furthermore, the EtOAc fraction significantly attenuated caspase-3 activity, resulting in inhibition of H 2 O 2 -induced apoptosis. We identified and quantified fustin, sulfuretin, and butein in the EtOAc fraction using accurate mass quadrupole time-of-flight mass spectrometry and reversed-phase high-performance liquid chromatography. The intracellular antioxidant capacity and superoxide dismutase (SOD) activity were significantly increased in PC-12 cells treated with the EtOAc fraction and with individual flavonoids. When cells were pretreated with the EtOAc fraction or individual flavonoids and then co-incubated with diethyldithiocarbamic acid (an inhibitor of SOD activity), cell viability against H 2 O 2 -induced oxidative stress was attenuated. These results suggest that the RVS EtOAc fraction and its flavonoid constituents protect PC-12 cells against H 2 O 2 -induced neurotoxicity through their antioxidant properties.

Treatment with Ruta graveolens 5CH and Rhus toxicodendron 9CH may reduce joint pain and stiffness linked to aromatase inhibitors in women with early breast cancer: results of a pilot observational study.

PubMed

Karp, Jean-Claude; Sanchez, Carole; Guilbert, Philippe; Mina, William; Demonceaux, Antoine; Curé, Hervé

2016-11-01

To determine the possible effect of two homeopathic medicines, Ruta graveolens 5CH and Rhus toxicodendron 9CH, in the prevention of aromatase inhibitor (AI) associated joint pain and/or stiffness in women with early, hormone-receptor positive, breast cancer. This prospective, unrandomized observational study was carried out between April and October 2014. Women were recruited in two groups, according to which of the two study centres they attended: one receiving homeopathy in addition to standard treatment (group H) and a control group, receiving standard treatment (group C). All women were treated with an AI. In addition, women in group H also took Ruta graveolens 5CH and Rhus toxicodendron 9CH (5 granules, twice a day) up to 7 days before starting AI treatment. The homeopathic medicines were continued for 3 months. Demographic and clinical data were recorded using a self-assessment questionnaire at inclusion (T0) and 3 months (T3). Primary evaluation criteria were the evolution of scores for joint pain and stiffness, the impact of pain on sleep and analgesic consumption in the two groups after 3 months of treatment. Forty patients (mean age 64.9±8.1 years) were recruited, 20 in each group. Two-thirds of the patients had joint pain before starting AI treatment. There was a significant difference in the evolution of mean composite pain score between T0 and T3 in the two groups (-1.3 in group H vs. +3.4 in group C; p=0.0001). The individual components of the pain score (frequency, intensity and number of sites of pain) also decreased significantly in group H. Nine patients in group C (45%) vs. 1 (5%) in group H increased their analgesic consumption between T0 and T3 (p=0.0076). After 3 months of treatment, joint pain had a worse impact on sleep in patients in group C (35% vs. 0% of patients; p=0.0083). The differences observed in the evolution of morning and daytime stiffness between the two groups were smaller (p=0.053 and p=0.33, respectively), with the exception

Phytoremediation potential of transplanted bare-root seedlings of trees for lead/zinc and copper mine tailings.

PubMed

Shi, Xiang; Chen, Yi-Tai; Wang, Shu-Feng; Pan, Hong-Wei; Sun, Hai-Jing; Liu, Cai-Xia; Liu, Jian-Feng; Jiang, Ze-Ping

2016-11-01

Selecting plant species that can overcome unfavorable conditions and increase the recovery of degraded mined lands remains a challenge. A pot experiment was conducted to evaluate the feasibility of using transplanted tree seedlings for the phytoremediation of lead/zinc and copper mine tailings. One-year-old bare-root of woody species (Rhus chinensis Mill, Quercus acutissima Carruth, Liquidambar formosana Hance, Vitex trifolia Linn. var. simplicifolia Cham, Lespedeza cuneata and Amorpha fruticosa Linn) were transplanted into pots with mine tailings and tested as potential metal-tolerant plants. Seedling survival, plant growth, root trait, nutrient uptake, and metal accumulation and translocation were assessed. The six species grew in both tailings and showed different tolerance level. A. fruticosa was highly tolerant of Zn, Pb and Cu, and grew normally in both tailings. Metal concentrations were higher in the roots than in the shoots of the six species. All of the species had low bioconcentration and translocation factor values. However, R. chinensis and L. formosana had significantly higher translocation factor values for Pb (0.88) and Zn (1.78) than the other species. The nitrogen-fixing species, A. fruticosa, had the highest tolerance and biomass production, implying that it has great potential in the phytoremediation of tailing areas in southern China.

Shrub communities as inhibitors of plant succession in southern Quebec

NASA Astrophysics Data System (ADS)

Meilleur, Alain; Véronneau, Hélène; Bouchard, André

1994-11-01

The purpose of our research was to identify shrub species growing in southern Quebec that inhibit ecological succession in power-line corridors. Results are presented in three parts. First, clonal characteristics that allowed the establishment of stable communities were identified. Second, successional vector analysis identified those species that have the potential to inhibit succession. In poorly drained sites those species were Cornus stolonifera, C. obliqua, Salix petiolaris, and Spiraea alba. In well-drained sites, those species were Zanthoxylum americanum, Rubus idaeus, Spiraea alba, Rhus typhina, and Thuja occidentalis. Third, analysis of variance showed that there is a significantly larger number of tree seedlings found in adjacent herbaceous communities than found under the dense cover of Cornus stolonifera, C. obliqua, Salix petiolaris, Spiraea alba, Rhus typhina, Rubus idaeus, Thuya occidentalis, and Zanthoxylum americanum. These results indicate that the planting of selected shrub species could, through biological control, delay reforestation.

Antiplatelet effects of Rhus verniciflua stokes heartwood and its active constituents--fisetin, butein, and sulfuretin--in rats.

PubMed

Lee, Jun-Hyeong; Kim, Mikyung; Chang, Kyung-Hwa; Hong, Cheol Yi; Na, Chun-Soo; Dong, Mi-Sook; Lee, Dongho; Lee, Moo-Yeol

2015-01-01

Rhus verniciflua stokes (RVS) is known to promote blood circulation by preventing blood stasis, although the active ingredients and the underlying mechanism are unclear. Platelets are the primary cells that regulate circulation and contribute to the development of diverse cardiovascular diseases by aggregation and thrombosis. The study assessed the antiplatelet activity of RVS and sought to identify the active constituents. Pretreatment of washed platelets with RVS heartwood extract blunted the aggregatory response of platelets to collagen. In the subfractions, fisetin, butein, and sulfuretin were identified as effective inhibitors of platelet aggregation by collagen, thrombin, and adenosine-5'-diphosphate. Antiplatelet activities of all three compounds were concentration dependent, and fisetin had longer in vitro duration of action compared with butein or sulfuretin. Extracellular signal-regulated kinase (ERK) mitogen-activated protein kinase activation by collagen was prevented by fisetin, whereas butein and sulfuretin failed to inhibit ERK and p38 activation was not affected by any of the compounds. Rats orally administered 100 mg/(kg·day(-1)) fisetin for 7 days were resistant to arterial thrombosis, although total extract of RVS heartwood exhibited little effect at a dose of 1000 mg/(kg·day(-1)). RVS heartwood may have cardiovascular protective activity by inhibiting platelet aggregation. The active constituents are fisetin, butein, and sulfuretin, and fisetin is orally effective against thrombosis.

Pacific island landbird monitoring annual report, National Park of American Samoa, Ta‘u and Tutuila units, 2011

USGS Publications Warehouse

Judge, Seth W.; Camp, Richard J.; Vaivai, Visa; Hart, Patrick J.

2013-01-01

NPSA canopy and understory composition was predominantly native, and trees formed a dense closed canopy at nearly 90% of the stations sampled. More than half of the tree heights in both units were taller than 5 m and the majority of slopes were steeper than 20 degrees. There were no clear dominant tree species in the mixed native forests. The most common tree species documented included Syzygium spp., Dysoxylum spp., Ficus spp., Hibiscus tiliaceus and Rhus taitensis (among others). There were significant differences in the distribution of bird densities between legacy and random transects. Determining differences in detection probabilities cannot be definitively assessed from a single survey. We recommend both panels be sampled in the future until bias in density and abundance can be evaluated, or if sampling may be reduced.

Method for applying photographic resists to otherwise incompatible substrates

NASA Technical Reports Server (NTRS)

Fuhr, W. (Inventor)

1981-01-01

A method for applying photographic resists to otherwise incompatible substrates, such as a baking enamel paint surface, is described wherein the uncured enamel paint surface is coated with a non-curing lacquer which is, in turn, coated with a partially cured lacquer. The non-curing lacquer adheres to the enamel and a photo resist material satisfactorily adheres to the partially cured lacquer. Once normal photo etching techniques are employed the lacquer coats can be easily removed from the enamel leaving the photo etched image. In the case of edge lighted instrument panels, a coat of uncured enamel is placed over the cured enamel followed by the lacquer coats and the photo resists which is exposed and developed. Once the etched uncured enamel is cured, the lacquer coats are removed leaving an etched panel.

Cultural Resource Investigations in the L’Anguille River Basin, Lee, St. Francis, Cross and Poinsett Counties, Arkansas.

DTIC Science & Technology

1989-01-01

Paleovegetational Record, Hood Lake, Poinsett County, Arkansas Pollen Diagram: Trees, Shrubs , and Vines . 20 Figure 7. Terminal Pleistocene/Holocene Paleovegetational...herbs and shrubs , as well as low percentages of vines (lianas), ferns, and fern allies. Among the herbs, sedge pollen rose from 5% to a peak of 25%, and...Rhus copallinum). The nonwoody complement of plants contained moderate abundances of shrubs , vines , herbs, and ferns (Figure 7). The life-form group of

Microelement contents and fatty acid compositions of Rhus coriaria L. and Pistacia terebinthus L. fruits spread commonly in the south eastern Anatolia region of Turkey.

PubMed

Kizil, Suleyman; Turk, Murat

2010-01-01

Sumac (Rhus coriaria L.) and terebinth (Pistacia terebinthus L.) are two important spice plants of south eastern Anatolia, Turkey. Nutrients, physical properties including moisture, ash, dry matter, protein, fatty oil and essential oil content, along with Al, Ca, Cd, Cr, Cu, Fe, K, Mg, Na, Ni, Pb, Zn and characteristics of fruit sizes and fatty acid compositions of both plants were determined from ripe fruits. The free fatty acid content was determined in the fruit oil, and the main fatty acids of sumac and terebinth were identified by gas chromatography/mass spectrometry. They included oleic, linoleic, palmitic and stearic acids in a ratio of 37.7% and 34.8%, 27.4% and 17.3%, 21.1% and 21.7% and, 4.7% and 2.5%, respectively. The fruits of both plants were rich in oil, fatty acids and minerals, suggesting that they are valuable for using in food. The data may also be useful for the evaluation of nutritional information.

Stabilization of erythrocytes against oxidative and hypotonic stress by tannins isolated from sumac leaves (Rhus typhina L.) and grape seeds (Vitis vinifera L.).

PubMed

Olchowik, Ewa; Lotkowski, Karol; Mavlyanov, Saidmukhtar; Abdullajanova, Nodira; Ionov, Maksim; Bryszewska, Maria; Zamaraeva, Maria

2012-09-01

Erythrocytes are constantly exposed to ROS due to their function in the organism. High tension of oxygen, presence of hemoglobin iron and high concentration of polyunsaturated fatty acids in membrane make erythrocytes especially susceptible to oxidative stress. A comparison of the antioxidant activities of polyphenol-rich plant extracts containing hydrolysable tannins from sumac leaves (Rhus typhina L.) and condensed tannins from grape seeds (Vitis vinifera L.) showed that at the 5-50 μg/ml concentration range they reduced to the same extent hemolysis and glutathione, lipid and hemoglobin oxidation induced by erythrocyte treatment with 400 μM ONOO(-) or 1 mM HClO. However, extract (condensed tannins) from grape seeds in comparison with extract (hydrolysable tannins) from sumac leaves stabilized erythrocytes in hypotonic NaCl solutions weakly. Our data indicate that both hydrolysable and condensed tannins significantly decrease the fluidity of the surface of erythrocyte membranes but the effect of hydrolysable ones was more profound. In conclusion, our results indicate that extracts from sumac leaves (hydrolysable tannins) and grape seeds (condensed tannins) are very effective protectors against oxidative damage in erythrocytes.

Modification of lignin for the production of new compounded materials.

PubMed

Hüttermann, A; Mai, C; Kharazipour, A

2001-05-01

The cell walls of woody plants are compounded materials made by in situ polymerization of a polyphenolic matrix (lignin) into a web of fibers (cellulose), a process that is catalysed by polyphenoloxidases (laccases) or peroxidases. The first attempt to transform the basic strategy of this natural process for use in human craftsmanship was the ancient lacquer method. The sap of the lacquer tree (Rhus verniciflua) contains large amounts of a phenol (urushiol), a polysaccharide and the enzyme laccase. This oil-in-water emulsion solidifies in the presence of oxygen. The Chinese began using this phenomenon for the production of highly creative artwork more than 6,000 years ago. It was the first example of an isolated enzyme being used as a catalyst to create an artificial plastic compound. In order to apply this process to the production of products on an industrial scale, an inexpensive phenol must be used, which is transferred by an enzyme to active radicals that react with different components to form a compounded material. At present, the following approaches have been studied: (1) In situ polymerization of lignin for the production of particle boards. Adhesive cure is based on the oxidative polymerization of lignin using phenoloxidases (laccase) as radical donors. This lignin-based bio-adhesive can be applied under conventional pressing conditions. The resulting particle boards meet German performance standards. By this process, 80% of the petrochemical binders in the wood-composite industry can be replaced by materials from renewable resources. (2) Enzymatic copolymerization of lignin and alkenes. In the presence of organic hydroperoxides, laccase catalyses the reaction between lignin and olefins. Detailed studies on the reaction between lignin and acrylate monomers showed that chemo-enzymatic copolymerization offers the possibility to produce defined lignin-acrylate copolymers. The system allows control of the molecular weights of the products in a way that has

Analyte detection using an active assay

DOEpatents

Morozov, Victor; Bailey, Charles L.; Evanskey, Melissa R.

2010-11-02

Analytes using an active assay may be detected by introducing an analyte solution containing a plurality of analytes to a lacquered membrane. The lacquered membrane may be a membrane having at least one surface treated with a layer of polymers. The lacquered membrane may be semi-permeable to nonanalytes. The layer of polymers may include cross-linked polymers. A plurality of probe molecules may be arrayed and immobilized on the lacquered membrane. An external force may be applied to the analyte solution to move the analytes towards the lacquered membrane. Movement may cause some or all of the analytes to bind to the lacquered membrane. In cases where probe molecules are presented, some or all of the analytes may bind to probe molecules. The direction of the external force may be reversed to remove unbound or weakly bound analytes. Bound analytes may be detected using known detection types.

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

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.

A combination of NMR and liquid chromatography to characterize the protective effects of Rhus tripartita extracts on ethanol-induced toxicity and inflammation on intestinal cells.

PubMed

Ben Barka, Zaineb; Grintzalis, Konstantinos; Polet, Madeleine; Heude, Clement; Sommer, Ulf; Ben Miled, Hanène; Ben Rhouma, Khémais; Mohsen, Sakly; Tebourbi, Olfa; Schneider, Yves-Jacques

2018-02-20

Consumption of ethanol may have severe effects on human organs and tissues and lead to acute and chronic inflammation of internal organs. The present study aims at investigating the potential protective effects of three different extracts prepared from the leaves, root, and stem of the sumac, Rhus tripartita, against ethanol-induced toxicity and inflammation using intestinal cells as a cell culture system, in vitro model of the intestinal mucosa. The results showed an induction of cytotoxicity by ethanol, which was partially reversed by co-administration of the plant extracts. As part of investigating the cellular response and the mechanism of toxicity, the role of reduced thiols and glutathione-S-transferases were assessed. In addition, intestinal cells were artificially imposed to an inflammation state and the anti-inflammatory effect of the extracts was estimated by determination of interleukin-8. Finally, a detailed characterization of the contents of the three plant extracts by high resolution Nuclear Magnetic Resonance (NMR) spectroscopy and mass spectrometry revealed significant differences in their chemical compositions. Copyright © 2017 Elsevier B.V. All rights reserved.

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)

TreeCmp: Comparison of Trees in Polynomial Time

PubMed Central

Bogdanowicz, Damian; Giaro, Krzysztof; Wróbel, Borys

2012-01-01

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

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

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

ColorTree: a batch customization tool for phylogenic trees

PubMed Central

Chen, Wei-Hua; Lercher, Martin J

2009-01-01

Background Genome sequencing projects and comparative genomics studies typically aim to trace the evolutionary history of large gene sets, often requiring human inspection of hundreds of phylogenetic trees. If trees are checked for compatibility with an explicit null hypothesis (e.g., the monophyly of certain groups), this daunting task is greatly facilitated by an appropriate coloring scheme. Findings In this note, we introduce ColorTree, a simple yet powerful batch customization tool for phylogenic trees. Based on pattern matching rules, ColorTree applies a set of customizations to an input tree file, e.g., coloring labels or branches. The customized trees are saved to an output file, which can then be viewed and further edited by Dendroscope (a freely available tree viewer). ColorTree runs on any Perl installation as a stand-alone command line tool, and its application can thus be easily automated. This way, hundreds of phylogenic trees can be customized for easy visual inspection in a matter of minutes. Conclusion ColorTree allows efficient and flexible visual customization of large tree sets through the application of a user-supplied configuration file to multiple tree files. PMID:19646243

ColorTree: a batch customization tool for phylogenic trees.

PubMed

Chen, Wei-Hua; Lercher, Martin J

2009-07-31

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

Tree Colors: Color Schemes for Tree-Structured Data.

PubMed

Tennekes, Martijn; de Jonge, Edwin

2014-12-01

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

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

PubMed

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

2018-01-01

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

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.

CartograTree: connecting tree genomes, phenotypes and environment.

PubMed

Vasquez-Gross, Hans A; Yu, John J; Figueroa, Ben; Gessler, Damian D G; Neale, David B; Wegrzyn, Jill L

2013-05-01

Today, researchers spend a tremendous amount of time gathering, formatting, filtering and visualizing data collected from disparate sources. Under the umbrella of forest tree biology, we seek to provide a platform and leverage modern technologies to connect biotic and abiotic data. Our goal is to provide an integrated web-based workspace that connects environmental, genomic and phenotypic data via geo-referenced coordinates. Here, we connect the genomic query web-based workspace, DiversiTree and a novel geographical interface called CartograTree to data housed on the TreeGenes database. To accomplish this goal, we implemented Simple Semantic Web Architecture and Protocol to enable the primary genomics database, TreeGenes, to communicate with semantic web services regardless of platform or back-end technologies. The novelty of CartograTree lies in the interactive workspace that allows for geographical visualization and engagement of high performance computing (HPC) resources. The application provides a unique tool set to facilitate research on the ecology, physiology and evolution of forest tree species. CartograTree can be accessed at: http://dendrome.ucdavis.edu/cartogratree. © 2013 Blackwell Publishing Ltd.

Tree Nut Allergies

MedlinePlus

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

Big trees, old trees, and growth factor tables

Treesearch

Kevin T. Smith

2018-01-01

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

TreeNetViz: revealing patterns of networks over tree structures.

PubMed

Gou, Liang; Zhang, Xiaolong Luke

2011-12-01

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

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…

Spatial variability in oviposition damage by periodical cicadas in a fragmented landscape.

PubMed

Cook, William M; Holt, Robert D; Yao, Jin

2001-03-01

Effects of the periodical cicada (Magicicada spp.) on forest dynamics are poorly documented. A 1998 emergence of M. cassini in eastern Kansas led to colonization of a fragmented experimental landscape undergoing secondary succession. We hypothesized that per-tree rates of oviposition damage by cicadas would reflect: (1) distance from the source of the emergence, (2) patch size, and (3) local tree density. Ovipositing females displayed clear preferences for host species and damage incidence showed predictable spatial patterns. Two species (smooth sumac, Rhus glabra, and eastern red cedar, Juniperus virginiana) were rarely attacked, whereas others (rough-leaved dogwood, Cornus drummondii; slippery elm, Ulmus rubra; box elder, Acer negundo, and honey locust, Gleditsia triacanthos) were strongly attacked. The dominant early successional tree, dogwood, received on average the most attacks. As predicted, attacks per stem declined strongly with distance from the emergence source, and with local stem density (a "dilution" effect). Contrary to expectations, there were more attacks per stem on larger patches. Because ovipositing cicadas cut damaging slits in host tree branches, potentially affecting tree growth rate, competitive ability, and capacity to reproduce, cicada damage could potentially influence spatial variation in secondary succession.

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

Code of Federal Regulations, 2011 CFR

2011-07-01

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

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

Code of Federal Regulations, 2012 CFR

2012-07-01

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

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

Code of Federal Regulations, 2014 CFR

2014-07-01

... 36 Parks, Forests, and Public Property 2 2014-07-01 2014-07-01 false Exchange of trees or portions of trees. 223.4 Section 223.4 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF... PRODUCTS General Provisions § 223.4 Exchange of trees or portions of trees. Trees or portions of trees may...

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

Code of Federal Regulations, 2013 CFR

2013-07-01

... 36 Parks, Forests, and Public Property 2 2013-07-01 2013-07-01 false Exchange of trees or portions of trees. 223.4 Section 223.4 Parks, Forests, and Public Property FOREST SERVICE, DEPARTMENT OF... PRODUCTS General Provisions § 223.4 Exchange of trees or portions of trees. Trees or portions of trees may...

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

2014-03-06

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

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

2014-01-01

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

Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest.

PubMed

Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

2016-11-18

Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest.

Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest

PubMed Central

Purahong, Witoon; Durka, Walter; Fischer, Markus; Dommert, Sven; Schöps, Ricardo; Buscot, François; Wubet, Tesfaye

2016-01-01

Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest. PMID:27857198

Appraisal of phytochemical and in vitro biological attributes of an unexplored folklore: Rhus Punjabensis Stewart.

PubMed

Tabassum, Saira; Ahmed, Madiha; Mirza, Bushra; Naeem, Muhammad; Zia, Muhammad; Shanwari, Zabta Khan; Khan, Gul Majid

2017-03-09

The role of plants for discovery of therapeutic potential accentuates the need to know their biological attributes. The present study aims to comprehend the biological attributes of Rhus punjabensis, an unexplored traditional medicinal plant. Leaf and stem extracts of R. punjabensis prepared in 11 different organic solvents are evaluated for multimode antioxidant potential, total phenolic and flavonoid contents were determined through colorimetric assays, HPLC-DAD analysis was carried out for quantification of various polyphenols in extracts. Brine shrimp lethality, SRB and MTT assays were used to elucidate plant's cytotoxic and antileishmanial potentials. Disc diffusion assay was used to elucidate the protein kinase inhibitory, antibacterial and antifungal spectrum. Ethanol + ethyl acetate yielded maximum extract recovery from leaf (6.11 ± 1.09% w/w), total phenolic content (80.5 ± 2.18 μg GAE/mg extract) and reducing power potential (165.4 ± 2.29 μg AAE/mg extract). Maximum flavonoid content (30.50 ± 1.11 μg QE/mg extract) and highest DPPH based free radical scavenging activity (IC 50 11.4 ± 2.07) was exhibited by the methanol + chloroform leaf extract. The methanol extract showed maximum total antioxidant capacity (74.5 ± 2.25 μg AAE/mg DW), protein kinase inhibitory (12.5 ± 1.10 bald phenotype at 100 μg/disc) and antifungal (MIC = 25 μg/disc against Aspergillus flavus) potential. Reverse phase HPLC-DAD based quantification reveals presence of gallic acid, apigenin, rutin and catechin in various extracts. Brine shrimp lethality assay demonstrated most extracts as highly cytotoxic (LC 50  < 50 μg/mL) whereas chloroform extract of leaf demonstrated maximuminhibition against human leukemia cell line (IC 50 7.80 ± 0.01 μg/mL). A significant activity against leishmanial promastigotes was demonstrated by n-hexane leaf extract (IC 50  = 15.78 ± 0.15 μg/mL). A better antibacterial

TreeVector: scalable, interactive, phylogenetic trees for the web.

PubMed

Pethica, Ralph; Barker, Gary; Kovacs, Tim; Gough, Julian

2010-01-28

Phylogenetic trees are complex data forms that need to be graphically displayed to be human-readable. Traditional techniques of plotting phylogenetic trees focus on rendering a single static image, but increases in the production of biological data and large-scale analyses demand scalable, browsable, and interactive trees. We introduce TreeVector, a Scalable Vector Graphics-and Java-based method that allows trees to be integrated and viewed seamlessly in standard web browsers with no extra software required, and can be modified and linked using standard web technologies. There are now many bioinformatics servers and databases with a range of dynamic processes and updates to cope with the increasing volume of data. TreeVector is designed as a framework to integrate with these processes and produce user-customized phylogenies automatically. We also address the strengths of phylogenetic trees as part of a linked-in browsing process rather than an end graphic for print. TreeVector is fast and easy to use and is available to download precompiled, but is also open source. It can also be run from the web server listed below or the user's own web server. It has already been deployed on two recognized and widely used database Web sites.

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

PubMed Central

2017-01-01

Abstract Summary: IcyTree is an easy-to-use application which can be used to visualize a wide variety of phylogenetic trees and networks. While numerous phylogenetic tree viewers exist already, IcyTree distinguishes itself by being a purely online tool, having a responsive user interface, supporting phylogenetic networks (ancestral recombination graphs in particular), and efficiently drawing trees that include information such as ancestral locations or trait values. IcyTree also provides intuitive panning and zooming utilities that make exploring large phylogenetic trees of many thousands of taxa feasible. Availability and Implementation: IcyTree is a web application and can be accessed directly at http://tgvaughan.github.com/icytree. Currently supported web browsers include Mozilla Firefox and Google Chrome. IcyTree is written entirely in client-side JavaScript (no plugin required) and, once loaded, does not require network access to run. IcyTree is free software, and the source code is made available at http://github.com/tgvaughan/icytree under version 3 of the GNU General Public License. Contact: tgvaughan@gmail.com PMID:28407035

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

PubMed

Vaughan, Timothy G

2017-08-01

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

Exact solutions for species tree inference from discordant gene trees.

PubMed

Chang, Wen-Chieh; Górecki, Paweł; Eulenstein, Oliver

2013-10-01

Phylogenetic analysis has to overcome the grant challenge of inferring accurate species trees from evolutionary histories of gene families (gene trees) that are discordant with the species tree along whose branches they have evolved. Two well studied approaches to cope with this challenge are to solve either biologically informed gene tree parsimony (GTP) problems under gene duplication, gene loss, and deep coalescence, or the classic RF supertree problem that does not rely on any biological model. Despite the potential of these problems to infer credible species trees, they are NP-hard. Therefore, these problems are addressed by heuristics that typically lack any provable accuracy and precision. We describe fast dynamic programming algorithms that solve the GTP problems and the RF supertree problem exactly, and demonstrate that our algorithms can solve instances with data sets consisting of as many as 22 taxa. Extensions of our algorithms can also report the number of all optimal species trees, as well as the trees themselves. To better asses the quality of the resulting species trees that best fit the given gene trees, we also compute the worst case species trees, their numbers, and optimization score for each of the computational problems. Finally, we demonstrate the performance of our exact algorithms using empirical and simulated data sets, and analyze the quality of heuristic solutions for the studied problems by contrasting them with our exact solutions.

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

PubMed

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

2016-12-01

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

Tree Data (TD)

Treesearch

Robert E. Keane

2006-01-01

The Tree Data (TD) methods are used to sample individual live and dead trees on a fixed-area plot to estimate tree density, size, and age class distributions before and after fire in order to assess tree survival and mortality rates. This method can also be used to sample individual shrubs if they are over 4.5 ft tall. When trees are larger than the user-specified...

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

PubMed

Feragen, Aasa; Owen, Megan; Petersen, Jens; Wille, Mathilde M W; Thomsen, Laura H; Dirksen, Asger; de Bruijne, Marleen

2013-01-01

Statistical analysis of anatomical trees is hard to perform due to differences in the topological structure of the trees. In this paper we define statistical properties of leaf-labeled anatomical trees with geometric edge attributes by considering the anatomical trees as points in the geometric space of leaf-labeled trees. This tree-space is a geodesic metric space where any two trees are connected by a unique shortest path, which corresponds to a tree deformation. However, tree-space is not a manifold, and the usual strategy of performing statistical analysis in a tangent space and projecting onto tree-space is not available. Using tree-space and its shortest paths, a variety of statistical properties, such as mean, principal component, hypothesis testing and linear discriminant analysis can be defined. For some of these properties it is still an open problem how to compute them; others (like the mean) can be computed, but efficient alternatives are helpful in speeding up algorithms that use means iteratively, like hypothesis testing. In this paper, we take advantage of a very large dataset (N = 8016) to obtain computable approximations, under the assumption that the data trees parametrize the relevant parts of tree-space well. Using the developed approximate statistics, we illustrate how the structure and geometry of airway trees vary across a population and show that airway trees with Chronic Obstructive Pulmonary Disease come from a different distribution in tree-space than healthy ones. Software is available from http://image.diku.dk/aasa/software.php.

Juvenile Rhus glabra leaves have higher temperatures and lower gas exchange rates than mature leaves when compared in the field during periods of high irradiance.

PubMed

Snider, John L; Choinski, John S; Wise, Robert R

2009-05-01

We sought to test the hypothesis that stomatal development determines the timing of gas exchange competency, which then influences leaf temperature through transpirationally driven leaf cooling. To test this idea, daily patterns of gas exchange and leaflet temperature were obtained from leaves of two distinctively different developmental stages of smooth sumac (Rhus glabra) grown in its native habitat. Juvenile and mature leaves were also sampled for ultrastructural studies of stomatal development. When plants were sampled in May-June, the hypothesis was supported: juvenile leaflets were (for part of the day) from 1.4 to 6.0 degrees C warmer than mature leaflets and as much as 2.0 degrees C above ambient air temperature with lower stomatal conductance and photosynthetic rates than mature leaflets. When measurements were taken from July to October, no significant differences were observed, although mature leaflet gas exchange rates declined to the levels of the juvenile leaves. The gas exchange data were supported by the observations that juvenile leaves had approximately half the number of functional stomata on a leaf surface area basis as did mature leaves. It was concluded that leaf temperature and stage of leaf development in sumac are strongly linked with the higher surface temperatures observed in juvenile leaflets in the early spring possibly being involved in promoting photosynthesis and leaf expansion when air temperatures are cooler.

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;…

Relative Suffix Trees.

PubMed

Farruggia, Andrea; Gagie, Travis; Navarro, Gonzalo; Puglisi, Simon J; Sirén, Jouni

2018-05-01

Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into reducing the space usage, leading ultimately to compressed suffix trees. These compressed data structures can efficiently simulate the suffix tree, while using space proportional to a compressed representation of the sequence. In this work, we take a new approach to compressed suffix trees for repetitive sequence collections, such as collections of individual genomes. We compress the suffix trees of individual sequences relative to the suffix tree of a reference sequence. These relative data structures provide competitive time/space trade-offs, being almost as small as the smallest compressed suffix trees for repetitive collections, and competitive in time with the largest and fastest compressed suffix trees.

Relative Suffix Trees

PubMed Central

Farruggia, Andrea; Gagie, Travis; Navarro, Gonzalo; Puglisi, Simon J; Sirén, Jouni

2018-01-01

Abstract Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into reducing the space usage, leading ultimately to compressed suffix trees. These compressed data structures can efficiently simulate the suffix tree, while using space proportional to a compressed representation of the sequence. In this work, we take a new approach to compressed suffix trees for repetitive sequence collections, such as collections of individual genomes. We compress the suffix trees of individual sequences relative to the suffix tree of a reference sequence. These relative data structures provide competitive time/space trade-offs, being almost as small as the smallest compressed suffix trees for repetitive collections, and competitive in time with the largest and fastest compressed suffix trees. PMID:29795706

Steiner trees and spanning trees in six-pin soap films

NASA Astrophysics Data System (ADS)

Dutta, Prasun; Khastgir, S. Pratik; Roy, Anushree

2010-02-01

The problem of finding minimum (local as well as absolute) path lengths joining given points (or terminals) on a plane is known as the Steiner problem. The Steiner problem arises in finding the minimum total road length joining several towns and cities. We study the Steiner tree problem using six-pin soap films. Experimentally, we observe spanning trees as well as Steiner trees partly by varying the pin diameter. We propose a possibly exact expression for the length of a spanning tree or a Steiner tree, which fails mysteriously in certain cases.

Fault-Tree Compiler

NASA Technical Reports Server (NTRS)

Butler, Ricky W.; Boerschlein, David P.

1993-01-01

Fault-Tree Compiler (FTC) program, is software tool used to calculate probability of top event in fault tree. Gates of five different types allowed in fault tree: AND, OR, EXCLUSIVE OR, INVERT, and M OF N. High-level input language easy to understand and use. In addition, program supports hierarchical fault-tree definition feature, which simplifies tree-description process and reduces execution time. Set of programs created forming basis for reliability-analysis workstation: SURE, ASSIST, PAWS/STEM, and FTC fault-tree tool (LAR-14586). Written in PASCAL, ANSI-compliant C language, and FORTRAN 77. Other versions available upon request.

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

USGS Publications Warehouse

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

2016-01-01

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

Dominance of an alien shrub Rhus typhina over a native shrub Vitex negundo var. heterophylla under variable water supply patterns

PubMed Central

Du, Ning; Tan, Xiangfeng; Li, Qiang; Liu, Xiao; Zhang, Wenxin; Wang, Renqing; Liu, Jian; Guo, Weihua

2017-01-01

Temporal heterogeneity of a resource supply can have a profound effect on the interactions between alien and native plant species and their potential invasiveness. Precipitation patterns may be variable and result in a higher heterogeneity of water supply with global climate change. In this study, an alien shrub species, Rhus typhina, introduced to China from North America and a native shrub species, Vitex negundo var. heterophylla, were grown in monoculture and mixed culture under different water supply regimes, with four levels of water supply frequencies but with a constant level of total supplied water. After 60 days of treatments, the alien species was found to be the superior competitor in the mixed culture and was unaffected by changes in the water supply pattern. The dominance of R. typhina was mainly owing to its greater biomass and effective modulation of leaf physiology. However, in the mixed culture, V. negundo var. heterophylla exhibited both leaf- and whole-plant-level acclimations, including higher leaf length to petiole length and root to shoot biomass ratios, and lower specific leaf weight and leaf length to leaf width ratio. Plant height of V. negundo var. heterophylla was comparable to that of R. typhina in the mixed culture, which is a strategy to escape shading. Although water treatments had little effect on most traits in both species, the possible influence of water regimes should not be neglected. Compared with high-frequency water supply treatments, more individuals of V. negundo var. heterophylla died in low-water-frequency treatments when in competition with R. typhina, which may lead to species turnover in the field. The authors recommended that caution should be exercised when introducing R. typhina to non-native areas in the context of global climate change. PMID:28445505

Dominance of an alien shrub Rhus typhina over a native shrub Vitex negundo var. heterophylla under variable water supply patterns.

PubMed

Du, Ning; Tan, Xiangfeng; Li, Qiang; Liu, Xiao; Zhang, Wenxin; Wang, Renqing; Liu, Jian; Guo, Weihua

2017-01-01

Temporal heterogeneity of a resource supply can have a profound effect on the interactions between alien and native plant species and their potential invasiveness. Precipitation patterns may be variable and result in a higher heterogeneity of water supply with global climate change. In this study, an alien shrub species, Rhus typhina, introduced to China from North America and a native shrub species, Vitex negundo var. heterophylla, were grown in monoculture and mixed culture under different water supply regimes, with four levels of water supply frequencies but with a constant level of total supplied water. After 60 days of treatments, the alien species was found to be the superior competitor in the mixed culture and was unaffected by changes in the water supply pattern. The dominance of R. typhina was mainly owing to its greater biomass and effective modulation of leaf physiology. However, in the mixed culture, V. negundo var. heterophylla exhibited both leaf- and whole-plant-level acclimations, including higher leaf length to petiole length and root to shoot biomass ratios, and lower specific leaf weight and leaf length to leaf width ratio. Plant height of V. negundo var. heterophylla was comparable to that of R. typhina in the mixed culture, which is a strategy to escape shading. Although water treatments had little effect on most traits in both species, the possible influence of water regimes should not be neglected. Compared with high-frequency water supply treatments, more individuals of V. negundo var. heterophylla died in low-water-frequency treatments when in competition with R. typhina, which may lead to species turnover in the field. The authors recommended that caution should be exercised when introducing R. typhina to non-native areas in the context of global climate change.

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.

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

PubMed

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

2008-07-01

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

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.

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

PubMed

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

2016-02-24

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

Trees are good, but…

Treesearch

E.G. McPherson; F. Ferrini

2010-01-01

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

Cavity tree selection by red-cockaded woodpeckers in relation to tree age

Treesearch

D. Craig Rudolph; Richard N. Conner

1991-01-01

We aged over 1350 Red-cockaded Woodpecker (Picoides borealis) cavity trees and a comparable number of randomly selected trees. Resulting data strongly support the hypothesis that Red-cockaded Woodpeckers preferentially select older trees. Ages of recently initiated cavity trees in the Texas study areas generally were similar to those of cavity trees...

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

PubMed

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

2016-10-01

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

Trees in the Landscape.

ERIC Educational Resources Information Center

Webb, Richard; Forbatha, Ann

1982-01-01

Strategies for using trees in classroom instruction are provided. Includes: (1) activities (such as tree identification, mapping, measuring tree height/width); (2) list of asthetic, architectural, engineering, climate, and wildlife functions of trees; (3) tree discussion questions; and (4) references. (JN)

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

PubMed Central

2013-01-01

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

Looking for trees in the forest: summary tree from posterior samples.

PubMed

Heled, Joseph; Bouckaert, Remco R

2013-10-04

Bayesian phylogenetic analysis generates a set of trees which are often condensed into a single tree representing the whole set. Many methods exist for selecting a representative topology for a set of unrooted trees, few exist for assigning branch lengths to a fixed topology, and even fewer for simultaneously setting the topology and branch lengths. However, there is very little research into locating a good representative for a set of rooted time trees like the ones obtained from a BEAST analysis. We empirically compare new and known methods for generating a summary tree. Some new methods are motivated by mathematical constructions such as tree metrics, while the rest employ tree concepts which work well in practice. These use more of the posterior than existing methods, which discard information not directly mapped to the chosen topology. Using results from a large number of simulations we assess the quality of a summary tree, measuring (a) how well it explains the sequence data under the model and (b) how close it is to the "truth", i.e to the tree used to generate the sequences. Our simulations indicate that no single method is "best". Methods producing good divergence time estimates have poor branch lengths and lower model fit, and vice versa. Using the results presented here, a user can choose the appropriate method based on the purpose of the summary tree.

Trees

ERIC Educational Resources Information Center

Al-Khaja, Nawal

2007-01-01

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

Transpiration and whole-tree conductance in ponderosa pine trees of different heights.

PubMed

Ryan, M G; Bond, B J; Law, B E; Hubbard, R M; Woodruff, D; Cienciala, E; Kucera, J

2000-09-01

Changes in leaf physiology with tree age and size could alter forest growth, water yield, and carbon fluxes. We measured tree water flux (Q) for 14 ponderosa pine trees in two size classes (12 m tall and ∼40 years old, and 36 m tall and ∼ 290 years old) to determine if transpiration (E) and whole-tree conductance (g t ) differed between the two sizes of trees. For both size classes, E was approximately equal to Q measured 2 m above the ground: Q was most highly correlated with current, not lagged, water vapor pressure deficit, and night Q was <12% of total daily flux. E for days 165-195 and 240-260 averaged 0.97 mmol m -2 (leaf area, projected) s -1 for the 12-m trees and 0.57 mmol m -2 (leaf area) s -1 for the 36-m trees. When photosynthetically active radiation (I P ) exceeded the light saturation for photosynthesis in ponderosa pine (900 µmol m -2 (ground) s -1 ), differences in E were more pronounced: 2.4 mmol m -2 (leaf area) s -1 for the 12-m trees and 1.2 mmol m -2 s -1 for the 36-m trees, yielding g t of 140 mmol m -2 (leaf area) s -1 for the 12-m trees and 72 mmol m -2 s -1 for the 36-m trees. Extrapolated to forests with leaf area index =1, the 36-m trees would transpire 117 mm between 1 June and 31 August compared to 170 mm for the 12-m trees, a difference of 15% of average annual precipitation. Lower g t in the taller trees also likely lowers photosynthesis during the growing season.

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

PubMed

Mai, Uyen; Sayyari, Erfan; Mirarab, Siavash

2017-01-01

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

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

PubMed Central

Sayyari, Erfan; Mirarab, Siavash

2017-01-01

Phylogenetic trees inferred using commonly-used models of sequence evolution are unrooted, but the root position matters both for interpretation and downstream applications. This issue has been long recognized; however, whether the potential for discordance between the species tree and gene trees impacts methods of rooting a phylogenetic tree has not been extensively studied. In this paper, we introduce a new method of rooting a tree based on its branch length distribution; our method, which minimizes the variance of root to tip distances, is inspired by the traditional midpoint rerooting and is justified when deviations from the strict molecular clock are random. Like midpoint rerooting, the method can be implemented in a linear time algorithm. In extensive simulations that consider discordance between gene trees and the species tree, we show that the new method is more accurate than midpoint rerooting, but its relative accuracy compared to using outgroups to root gene trees depends on the size of the dataset and levels of deviations from the strict clock. We show high levels of error for all methods of rooting estimated gene trees due to factors that include effects of gene tree discordance, deviations from the clock, and gene tree estimation error. Our simulations, however, did not reveal significant differences between two equivalent methods for species tree estimation that use rooted and unrooted input, namely, STAR and NJst. Nevertheless, our results point to limitations of existing scalable rooting methods. PMID:28800608

Looking for trees in the forest: summary tree from posterior samples

PubMed Central

2013-01-01

Background Bayesian phylogenetic analysis generates a set of trees which are often condensed into a single tree representing the whole set. Many methods exist for selecting a representative topology for a set of unrooted trees, few exist for assigning branch lengths to a fixed topology, and even fewer for simultaneously setting the topology and branch lengths. However, there is very little research into locating a good representative for a set of rooted time trees like the ones obtained from a BEAST analysis. Results We empirically compare new and known methods for generating a summary tree. Some new methods are motivated by mathematical constructions such as tree metrics, while the rest employ tree concepts which work well in practice. These use more of the posterior than existing methods, which discard information not directly mapped to the chosen topology. Using results from a large number of simulations we assess the quality of a summary tree, measuring (a) how well it explains the sequence data under the model and (b) how close it is to the “truth”, i.e to the tree used to generate the sequences. Conclusions Our simulations indicate that no single method is “best”. Methods producing good divergence time estimates have poor branch lengths and lower model fit, and vice versa. Using the results presented here, a user can choose the appropriate method based on the purpose of the summary tree. PMID:24093883

Tree diversity in relation to tree height: alternative perspectives.

PubMed

Givnish, Thomas J

2017-03-01

Marks et al. (Ecol. Lett., 19, 2016, 743-751) show that tree diversity increases with tree height in North America and argue it reflects habitat 'suitability'. This finding conflicts with classical results, lacks controls for covariates of tree height, and can be explained alternatively using the modified Janzen-Connell effect and regional variance in habitats. © 2017 John Wiley & Sons Ltd/CNRS.

TreePlus: interactive exploration of networks with enhanced tree layouts.

PubMed

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

2006-01-01

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

Distributed Contour Trees

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

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 erent problems that rely on contour trees can be solved in parallel with minimal communication.

Tree mortality rates and tree population projections in Baltimore, Maryland, USA

Treesearch

David J. Nowak; Miki Kuroda; Daniel E. Crane

2004-01-01

Based on re-measurements (1999 and 2001) of randomly-distributed permanent plots within the city boundaries of Baltimore, Maryland, trees are estimated to have an annual mortality rate of 6.6% with an overall annual net change in the number of live trees of -4.2%. Tree mortality rates were significantly different based on tree size, condition, species, and Land use....

Urban park tree inventories

Treesearch

Joe R. McBride; David J. Nowak

1989-01-01

A survey of published reports on urban park tree inventories in the United States and the United Kingdom reveal two types of inventories: (1) Tree Location Inventories and (2) Generalized Information Inventories. Tree location inventories permit managers to relocate specific park trees, along with providing individual tree characteristics and condition data. In...

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…

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.

Simple street tree sampling

Treesearch

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

2015-01-01

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

Folding Automaton for Trees

NASA Astrophysics Data System (ADS)

Subashini, N.; Thiagarajan, K.

2018-04-01

In this paper we observed the definition of folding technique in graph theory and we derived the corresponding automaton for trees. Also derived some propositions on symmetrical structure tree, non-symmetrical structure tree, point symmetrical structure tree, edge symmetrical structure tree along with finite number of points. This approach provides to derive one edge after n’ number of foldings.

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.

Decision-Tree Program

NASA Technical Reports Server (NTRS)

Buntine, Wray

1994-01-01

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

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

PubMed

Eilmann, Britta; Rigling, Andreas

2012-02-01

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

Community Tree Planting Guide

Treesearch

Katie Himanga; Douglas Jones; Jean Miller; Janette Monear; Gail Steinman; Katherine Widin

2001-01-01

Tree Trust has been helping people plant trees in their communities since 1976. Our goal is to educate people about the importance of trees in their community and guide them through the process of successful tree-planting projects. Franklin Delano Roosevelt once said ?to exist as a nation, to prosper as a state, and to live as a people, we must have trees?....

Are trees long-lived?

Treesearch

Kevin T. Smith

2009-01-01

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

There's Life in Hazard Trees

Treesearch

Mary Torsello; Toni McLellan

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

Tree nut allergens.

PubMed

Geiselhart, Sabine; Hoffmann-Sommergruber, Karin; Bublin, Merima

2018-04-18

Tree nuts are considered as part of a healthy diet due to their high nutritional quality. However, they are also a potent source of allergenic proteins inducing IgE mediated hypersensitivity often causing serious, life-threatening reactions. The reported prevalence of tree nut allergy is up to 4.9% worldwide. The general term "tree nuts" comprises a number of nuts, seeds, and drupes, derived from trees from different botanical families. For hazelnut and walnut several allergens have been identified which are already partly applied in component resolved diagnosis, while for other tree nuts such as macadamia, coconut, and Brazil nut only individual allergens were identified and data on additional allergenic proteins are missing. This review summarizes the current knowledge on tree nut allergens and describes their physicochemical and immunological characterization and clinical relevance. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

National Christmas Tree Association > Education > White House Tree

Science.gov Websites

Vander Velden, owners of Whispering Pines Tree Farm in Octonto, Wisconsin. The tree, a 19 foot Douglas Visitors Office and Jim Adams with the National Park Service. This 19 foot Balsam fir will be displayed in

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

PubMed

Hughes, Joseph

2011-05-20

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

On Determining if Tree-based Networks Contain Fixed Trees.

PubMed

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

2016-05-01

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

Tree leaf trade-offs are stronger for sub-canopy trees: leaf traits reveal little about growth rates in canopy trees.

PubMed

Wills, Jarrah; Herbohn, John; Hu, Jing; Sohel, Shawkat; Baynes, Jack; Firn, Jennifer

2018-06-01

Can morphological plant functional traits predict demographic rates (e.g., growth) within plant communities as diverse as tropical forests? This is one of the most important next-step questions in trait-based ecology and particularly for global reforestation efforts. Due to the diversity of tropical tree species and their longevity, it is difficult to predict their performance prior to reforestation efforts. In this study, we investigate if simple leaf traits are predictors of the more complex ecological process of plant growth in regenerating selectively logged natural forest within the Wet Tropics (WTs) bioregion of Australia. This study used a rich historical data set to quantify tree growth within plots located at Danbulla National Park and State Forest on the Atherton Tableland. Leaf traits were collected from trees that have exhibited fast or slow growth over the last ~50 yr of measurement. Leaf traits were found to be poor predictors of tree growth for trees that have entered the canopy; however, for sub-canopy trees, leaf traits had a stronger association with growth rates. Leaf phosphorus concentrations were the strongest predictor of Periodic Annual Increment (PAI) for trees growing within the sub-canopy, with trees with higher leaf phosphorus levels showing a higher PAI. Sub-canopy tree leaves also exhibited stronger trade-offs between leaf traits and adhere to theoretical predictions more so than for canopy trees. We suggest that, in order for leaf traits to be more applicable to reforestation, size dependence of traits and growth relationships need to be more carefully considered, particularly when reforestation practitioners assign mean trait values to tropical tree species from multiple canopy strata. © 2018 by the Ecological Society of America.

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

PubMed

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

2018-04-01

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

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

PubMed

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

2017-09-30

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

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

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

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

Although savanna trees and forest trees are thought to represent distinct functional groups with different effects on ecosystem processes, few empirical studies have examined these effects. In particular, it remains unclear if savanna and forest trees differ in their ability to coexist with understory plants, which comprise the majority of plant diversity in most savannas. We used structural equation modeling (SEM) and data from 157 sites across three locations in the southeastern United States to understand the effects of broadleaf savanna trees, broadleaf forest trees, and pine trees on savanna understory plant communities. After accounting for underlying gradients in firemore » frequency and soil moisture, abundances (i.e., basal area and stem density) of forest trees and pines, but not savanna trees, were negatively correlated with the cover and density (i.e., local-scale species richness) of C4 graminoid species, a defining savanna understory functional group that is linked to ecosystem flammability. In analyses of the full understory community, abundances of trees from all functional groups were negatively correlated with species density and cover. For both the C4 and full communities, fire frequency promoted understory plants directly, and indirectly by limiting forest tree abundance. There was little indirect influence of fire on the understory mediated through savanna trees and pines, which are more fire tolerant than forest trees. We conclude that tree functional identity is an important factor that influences overstory tree relationships with savanna understory plant communities. In particular, distinct relationships between trees and C4 graminoids have implications for grass-tree coexistence and vegetation-fire feedbacks that maintain savanna environments and their associated understory plant diversity.« less

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

PubMed

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

2011-06-01

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

Whole-tree canopy enclosures: why cage a tree?

Treesearch

Jerome F. Grant; Abdul Hakeem; Paris L. Lambdin; Gregory J. Wiggins; Rusty J. Rhea

2011-01-01

The use of whole-tree canopy enclosures (i.e., cages) is not a typical approach to assessing biological parameters and interactions in a forest setting. However, the successful application of this technology may enable researchers to better understand certain types of tree/organismal interactions.

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…

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

Treesearch

G.H. Donovan; D.T. Butry

2010-01-01

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

Urban tree growth modeling

Treesearch

E. Gregory McPherson; Paula J. Peper

2012-01-01

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

Decoding tree DNA

Treesearch

M. Thompson Conkle

1986-01-01

Check the laboratory reports after your next physical. You'll find information on a number of biochemical processes. Procedures like those used in the medical sciences are yielding valuable information about genetic differences among trees and tree pests. New procedures that provide ways to isolate and move genes are advancing progress in tree improvement. These...

Benefit-based tree valuation

Treesearch

E.G. McPherson

2007-01-01

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

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…

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…

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 or...

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

Treesearch

Lara A. Roman

2014-01-01

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

Keeping trees as assets

Treesearch

Kevin T. Smith

2009-01-01

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

Fault-Tree Compiler Program

NASA Technical Reports Server (NTRS)

Butler, Ricky W.; Martensen, Anna L.

1992-01-01

FTC, Fault-Tree Compiler program, is reliability-analysis software tool used to calculate probability of top event of fault tree. Five different types of gates allowed in fault tree: AND, OR, EXCLUSIVE OR, INVERT, and M OF N. High-level input language of FTC easy to understand and use. Program supports hierarchical fault-tree-definition feature simplifying process of description of tree and reduces execution time. Solution technique implemented in FORTRAN, and user interface in Pascal. Written to run on DEC VAX computer operating under VMS operating system.

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…

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

Treesearch

E. Gregory McPherson

2014-01-01

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

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.

Characterizing the phylogenetic tree-search problem.

PubMed

Money, Daniel; Whelan, Simon

2012-03-01

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

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

PubMed

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

2014-12-11

To investigate tree-related injuries in Solomon Islands by the types of trees involved, who is affected and the types of injuries caused. Descriptive case series of all cases of injuries related to trees presenting to the National Referral Hospital in Honiara from 1994 to 2011. Data were collected by the attending clinician using a Trauma Epidemiology form, which provides information on age, sex, cause of injury and type of fracture. Number of injuries by tree type, sex and age. Of the 7651 injuries in the database, 1107 (14%) were caused by falls from trees. Falls from coconut trees led to the highest number of injuries, followed by falls from mango, guava, apple and nut trees. Overall, 85% of injuries occurred in individuals aged < 20 years. For injuries involving guava trees, 77% of patients were aged < 10 years, compared with 46% for the five most commonly involved tree types. Overall, 71% of injuries occurred among males. Of all injuries, 92% were fractures, 3% were dislocations and 5% were non-fracture, non-dislocation injuries. The arm (including wrist, elbow and hand) was the most common location of injury across all tree types. Distal radius fractures in the forearm were particularly common, as were ulna fractures. While mangos and guavas are undeniably delicious, the quest for their flesh can be hazardous. Children will always climb trees, but the search for food among children in lower-income settings may lead to higher rates of injury.

High-Frequency Measurements of Tree Methane Fluxes Indicate a Primary Souce Inside Tree Tissue

NASA Astrophysics Data System (ADS)

Brewer, P.; Megonigal, P.

2017-12-01

Methane emissions from the boles and shoots of living upland trees is a recent discovery with significant implications for methane budgets. Forest soil methane uptake is the greatest terrestrial methane sink, but studies have shown this may be partially for fully offset by tree methane sources. However, our ability to quantify the tree source has been hampered because the ultimate biological source(s) of methane is unclear. We measured methane fluxes from two species of living tree boles in an Eastern North American deciduous forest over 100 consecutive days. Our two hour sampling intervals allowed us to characterize diurnal patterns and seasonal dynamics. We observed wide intraspecific differences in average flux rates and diurnal dynamics, even between adjacent individuals. This and other properties of the fluxes indicates the primary methane source is likely within the tree tissues, not in soil or groundwater. Emissions of methane from trees offset approximately 10% of soil uptake on average, but at times tree fluxes were much higher. Preliminary analyses indicate the highest rates are related to tree life history, tree growth, temperature, ground-water depth, and soil moisture.

Diameter-Constrained Steiner Tree

NASA Astrophysics Data System (ADS)

Ding, Wei; Lin, Guohui; Xue, Guoliang

Given an edge-weighted undirected graph G = (V,E,c,w), where each edge e ∈ E has a cost c(e) and a weight w(e), a set S ⊆ V of terminals and a positive constant D 0, we seek a minimum cost Steiner tree where all terminals appear as leaves and its diameter is bounded by D 0. Note that the diameter of a tree represents the maximum weight of path connecting two different leaves in the tree. Such problem is called the minimum cost diameter-constrained Steiner tree problem. This problem is NP-hard even when the topology of Steiner tree is fixed. In present paper we focus on this restricted version and present a fully polynomial time approximation scheme (FPTAS) for computing a minimum cost diameter-constrained Steiner tree under a fixed topology.

On Tree-Based Phylogenetic Networks.

PubMed

Zhang, Louxin

2016-07-01

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

A Metric on Phylogenetic Tree Shapes.

PubMed

Colijn, C; Plazzotta, G

2018-01-01

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

A Metric on Phylogenetic Tree Shapes

PubMed Central

Plazzotta, G.

2018-01-01

Abstract The shapes of evolutionary trees are influenced by the nature of the evolutionary process but comparisons of trees from different processes are hindered by the challenge of completely describing tree shape. We present a full characterization of the shapes of rooted branching trees in a form that lends itself to natural tree comparisons. We use this characterization to define a metric, in the sense of a true distance function, on tree shapes. The metric distinguishes trees from random models known to produce different tree shapes. It separates trees derived from tropical versus USA influenza A sequences, which reflect the differing epidemiology of tropical and seasonal flu. We describe several metrics based on the same core characterization, and illustrate how to extend the metric to incorporate trees’ branch lengths or other features such as overall imbalance. Our approach allows us to construct addition and multiplication on trees, and to create a convex metric on tree shapes which formally allows computation of average tree shapes. PMID:28472435

Visualizing phylogenetic tree landscapes.

PubMed

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

2017-02-02

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

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

Treesearch

Thomas B. Lynch; Robert F. Wittwer

2002-01-01

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

TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees.

PubMed

Mai, Uyen; Mirarab, Siavash

2018-05-08

Sequence data used in reconstructing phylogenetic trees may include various sources of error. Typically errors are detected at the sequence level, but when missed, the erroneous sequences often appear as unexpectedly long branches in the inferred phylogeny. We propose an automatic method to detect such errors. We build a phylogeny including all the data then detect sequences that artificially inflate the tree diameter. We formulate an optimization problem, called the k-shrink problem, that seeks to find k leaves that could be removed to maximally reduce the tree diameter. We present an algorithm to find the exact solution for this problem in polynomial time. We then use several statistical tests to find outlier species that have an unexpectedly high impact on the tree diameter. These tests can use a single tree or a set of related gene trees and can also adjust to species-specific patterns of branch length. The resulting method is called TreeShrink. We test our method on six phylogenomic biological datasets and an HIV dataset and show that the method successfully detects and removes long branches. TreeShrink removes sequences more conservatively than rogue taxon removal and often reduces gene tree discordance more than rogue taxon removal once the amount of filtering is controlled. TreeShrink is an effective method for detecting sequences that lead to unrealistically long branch lengths in phylogenetic trees. The tool is publicly available at https://github.com/uym2/TreeShrink .

Effects of a triplex mixture of Peganum harmala, Rhus coriaria, and Urtica dioica aqueous extracts on metabolic and histological parameters in diabetic rats.

PubMed

Abedi Gaballu, Fereydoon; Abedi Gaballu, Yousef; Moazenzade Khyavy, Omid; Mardomi, Alireza; Ghahremanzadeh, Kazem; Shokouhi, Behrooz; Mamandy, Himan

2015-08-01

Several therapeutic effects such as antioxidant and blood glucose-lowering activities have been reported for Peganum harmala L (Zygophyllaceae) (PH) seeds, Rhus coriaria L (Anacardiaceae) (RC) fruits, and Urtica dioica L (Urticaceae) (UD) leaves. This study investigates the effects of a triplex mixture (1:1:1) of these medicinal plants on metabolic and histological parameters in diabetic rats. Aqueous extracts of PH, RC and UD were administered as either monotherapy or in combination at a final dose of 200 mg/kg to alloxan-induced diabetic rats by daily gavage. Biochemical parameters including blood glucose, liver function-related enzymes, lipid profile, and creatinine were estimated by spectrophotometric methods. Tissues from the liver and kidney stained with hematoxylin/eosin were histologically examined. The results obtained from the exposure groups were compared to either healthy or diabetic control groups. Compared with the diabetic control rats, all aqueous extracts (ED50 = 11.5 ± 2.57 mg/ml) led to significant decreases in the levels of ALP (1.39-2.23-fold, p < 0.05), low-density lipoprotein cholesterol (LDL-C) (1.79-3.26-fold, p < 0.05), and blood glucose (1.27-4.16-fold, p < 0.05). The serum concentrations of TG was decreased only by treatment with UD and triplex mixture (1.25- and 1.20-fold, respectively, p < 0.05). Among the studied parameters, alanine aminotransferase (ALT), LDL-C, TG, and creatinine recovered to healthy control levels after 4 weeks of treatment with the extract mixture. This study showed that PH, RC, and UD extracts, especially their combination, had significant antidiabetic, hypolipidemic, and liver and renal damage recovering effects.

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

PubMed

Letunic, Ivica; Bork, Peer

2011-07-01

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

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…

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…

Tree Amigos.

ERIC Educational Resources Information Center

Center for Environmental Study, Grand Rapids, MI.

Tree Amigos is a special cross-cultural program that uses trees as a common bond to bring the people of the Americas together in unique partnerships to preserve and protect the shared global environment. It is a tangible program that embodies the philosophy that individuals, acting together, can make a difference. This resource book contains…

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

PubMed Central

2012-01-01

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

Phylogenetic trees in bioinformatics

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

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 themore » 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.« less

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…

Surface storage of rainfall in tree crowns: not all trees are equal

Treesearch

E. Gregory McPherson; Q. Xiao; Natalie van Doorn; P. Peper; E. Teach

2017-01-01

Urban forests can be an effective strategy for managing stormwater. The soil that supports tree growth acts like a reservoir that reduces runoff. The tree crown intercepts rainfall on leaves and stems and its evaporation reduces water reaching the ground below. Until now surface storage capacities have been studied only for forest trees. Based on forest research, green...

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.

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

PubMed

Castillo-Ramírez, Santiago; González, Víctor

2008-10-30

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. 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. 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

The fault-tree compiler

NASA Technical Reports Server (NTRS)

Martensen, Anna L.; Butler, Ricky W.

1987-01-01

The Fault Tree Compiler Program is a new reliability tool used to predict the top event probability for a fault tree. Five different gate types are allowed in the fault tree: AND, OR, EXCLUSIVE OR, INVERT, and M OF N gates. The high level input language is easy to understand and use when describing the system tree. In addition, the use of the hierarchical fault tree capability can simplify the tree description and decrease program execution time. The current solution technique provides an answer precise (within the limits of double precision floating point arithmetic) to the five digits in the answer. The user may vary one failure rate or failure probability over a range of values and plot the results for sensitivity analyses. The solution technique is implemented in FORTRAN; the remaining program code is implemented in Pascal. The program is written to run on a Digital Corporation VAX with the VMS operation system.

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

Treesearch

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

1997-01-01

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

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

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-20

...] WisdomTree Asset Management, Inc., and WisdomTree Trust; Notice of Application August 13, 2010. AGENCY... subadvisory agreements without shareholder approval. Applicants: WisdomTree Asset Management, Inc (``WTAM'' or ``Adviser'') and WisdomTree Trust (``Trust''). Filing Dates: The application was filed on December 23, 2009...

iTREE: Long-term variability of tree growth in a changing environment - identifying physiological mechanisms using stable C and O isotopes in tree rings.

NASA Astrophysics Data System (ADS)

Siegwolf, R. T. W.; Buchmann, N.; Frank, D.; Joos, F.; Kahmen, A.; Treydte, K.; Leuenberger, M.; Saurer, M.

2012-04-01

Trees play are a critical role in the carbon cycle - their photosynthetic assimilation is one of the largest terrestrial carbon fluxes and their standing biomass represents the largest carbon pool of the terrestrial biosphere. Understanding how tree physiology and growth respond to long-term environmental change is pivotal to predict the magnitude and direction of the terrestrial carbon sink. iTREE is an interdisciplinary research framework to capitalize on synergies among leading dendroclimatologists, plant physiologists, isotope specialists, and global carbon cycle modelers with the objectives of reducing uncertainties related to tree/forest growth in the context of changing natural environments. Cross-cutting themes in our project are tree rings, stable isotopes, and mechanistic modelling. We will (i) establish a European network of tree-ring based isotope time-series to retrodict interannual to long-term tree physiological changes, (ii) conduct laboratory and field experiments to adapt a mechanistic isotope model to derive plant physiological variables from tree-ring isotopes, (iii) implement this model into a dynamic global vegetation model, and perform subsequent model-data validation exercises to refine model representation of plant physiological processes and (iv) attribute long-term variation in tree growth to plant physiological and environmental drivers, and identify how our refined knowledge revises predictions of the coupled carbon-cycle climate system. We will contribute to i) advanced quantifications of long-term variation in tree growth across Central Europe, ii) novel long-term information on key physiological processes that underlie variations in tree growth, and iii) improved carbon cycle models that can be employed to revise predictions of the coupled carbon-cycle climate system. Hence iTREE will significantly contribute towards a seamless understanding of the responses of terrestrial ecosystems to long-term environmental change, and ultimately

Binary partition tree analysis based on region evolution and its application to tree simplification.

PubMed

Lu, Huihai; Woods, John C; Ghanbari, Mohammed

2007-04-01

Pyramid image representations via tree structures are recognized methods for region-based image analysis. Binary partition trees can be applied which document the merging process with small details found at the bottom levels and larger ones close to the root. Hindsight of the merging process is stored within the tree structure and provides the change histories of an image property from the leaf to the root node. In this work, the change histories are modelled by evolvement functions and their second order statistics are analyzed by using a knee function. Knee values show the reluctancy of each merge. We have systematically formulated these findings to provide a novel framework for binary partition tree analysis, where tree simplification is demonstrated. Based on an evolvement function, for each upward path in a tree, the tree node associated with the first reluctant merge is considered as a pruning candidate. The result is a simplified version providing a reduced solution space and still complying with the definition of a binary tree. The experiments show that image details are preserved whilst the number of nodes is dramatically reduced. An image filtering tool also results which preserves object boundaries and has applications for segmentation.

Recursive algorithms for phylogenetic tree counting.

PubMed

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

2013-10-28

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

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

PubMed

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

2018-04-06

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

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)

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

PubMed

Wu, Yufeng

2012-03-01

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

Effects of hydroalcoholic extract of Rhus coriaria seed on glucose and insulin related biomarkers, lipid profile, and hepatic enzymes in nicotinamide-streptozotocin-induced type II diabetic male mice.

PubMed

Ahangarpour, Akram; Heidari, Hamid; Junghani, Majid Salehizade; Absari, Reza; Khoogar, Mehdi; Ghaedi, Ehsan

2017-10-01

Type 2 diabetes often leads to dislipidemia and abnormal activity of hepatic enzymes. The purpose of this study was to evaluate the antidiabetic and hypolipidemic properties of Rhus coriaria ( R. coriaria ) seed extrac on nicotinamide-streptozotocin induced type 2 diabetic mice. In this experimental study, 56 male Naval Medical Research Institute mice (30-35 g) were randomly separated into seven groups: control, diabetic group, diabetic mice treated with glibenclamide (0.25 mg/kg, as standard antidiabetic drug) or R. coriaria seed extract in doses of 200 and 300 mg/kg, and control groups received these two doses of extract orally for 28 days. Induction of diabetes was done by intraperitoneal injection of nicotinamide and streptozotocin. Ultimately, body weight of mice, blood levels of glucose, insulin, hepatic enzymes, leptin, and lipid profile were assayed. After induction of type 2 diabetes, level of glucose, cholesterol, low density lipoprotein, serum glutamic oxaloacetic transaminase, and serum glutamic pyruvic transaminase increased and level of insulin and high density lipoprotein decreased remarkably. Administration of both doses of extract decreased level of glucose and cholesterol significantly in diabetic mice. LDL level decreased in treated group with dose of 300 mg/kg of the extract. Although usage of the extract improved level of other lipid profiles, insulin and hepatic enzymes, changes weren't significant. This study showed R. coriaria seeds administration has a favorable effect in controlling some blood parameters in type 2 diabetes. Therefore it may be beneficial in the treatment of diabetes.

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…

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…

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…

Tree-ring isotopes reveal drought sensitivity in trees killed by spruce beetle outbreaks in south-central Alaska.

PubMed

Csank, Adam Z; Miller, Amy E; Sherriff, Rosemary L; Berg, Edward E; Welker, Jeffrey M

2016-10-01

Increasing temperatures have resulted in reduced growth and increased tree mortality across large areas of western North American forests. We use tree-ring isotope chronologies (δ 13 C and δ 18 O) from live and dead trees from four locations in south-central Alaska, USA, to test whether white spruce trees killed by recent spruce beetle (Dendroctonus rufipennis Kirby) outbreaks showed evidence of drought stress prior to death. Trees that were killed were more sensitive to spring/summer temperature and/or precipitation than trees that survived. At two of our sites, we found greater correlations between the δ 13 C and δ 18 O chronologies and spring/summer temperatures in dead trees than in live trees, suggesting that trees that are more sensitive to temperature-induced drought stress are more likely to be killed. At one site, the difference between δ 13 C in live and dead trees was related to winter/spring precipitation, with dead trees showing stronger correlations between δ 13 C and precipitation, again suggesting increased water stress in dead trees. At all sites where δ 18 O was measured, δ 18 O chronologies showed the greatest difference in climate response between live and dead groups, with δ 18 O in live trees correlating more strongly with late winter precipitation than dead trees. Our results indicate that sites where trees are already sensitive to warm or dry early growing-season conditions experienced the most beetle-kill, which has important implications for forecasting future mortality events in Alaska. © 2016 by the Ecological Society of America.

NE-TWIGS update: Incorporating tree quality

Treesearch

Daniel A. Yaussy

1993-01-01

A method to distribute tree quality was incorporated into the NE-TWIGS individual-tree growth and yield simulator. The program uses potential tree grade to allow changes in actual tree grade over time. Volume is reported by grade and value is calculated using tree grades. Example screens are shown.

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

NASA Astrophysics Data System (ADS)

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

2012-02-01

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

Depth of soil water uptake by tropical rainforest trees during dry periods: does tree dimension matter?

PubMed

Stahl, Clément; Hérault, Bruno; Rossi, Vivien; Burban, Benoit; Bréchet, Claude; Bonal, Damien

2013-12-01

Though the root biomass of tropical rainforest trees is concentrated in the upper soil layers, soil water uptake by deep roots has been shown to contribute to tree transpiration. A precise evaluation of the relationship between tree dimensions and depth of water uptake would be useful in tree-based modelling approaches designed to anticipate the response of tropical rainforest ecosystems to future changes in environmental conditions. We used an innovative dual-isotope labelling approach (deuterium in surface soil and oxygen at 120-cm depth) coupled with a modelling approach to investigate the role of tree dimensions in soil water uptake in a tropical rainforest exposed to seasonal drought. We studied 65 trees of varying diameter and height and with a wide range of predawn leaf water potential (Ψpd) values. We confirmed that about half of the studied trees relied on soil water below 100-cm depth during dry periods. Ψpd was negatively correlated with depth of water extraction and can be taken as a rough proxy of this depth. Some trees showed considerable plasticity in their depth of water uptake, exhibiting an efficient adaptive strategy for water and nutrient resource acquisition. We did not find a strong relationship between tree dimensions and depth of water uptake. While tall trees preferentially extract water from layers below 100-cm depth, shorter trees show broad variations in mean depth of water uptake. This precludes the use of tree dimensions to parameterize functional models.

Reinforcement Learning Trees

PubMed Central

Zhu, Ruoqing; Zeng, Donglin; Kosorok, Michael R.

2015-01-01

In this paper, we introduce a new type of tree-based method, reinforcement learning trees (RLT), which exhibits significantly improved performance over traditional methods such as random forests (Breiman, 2001) under high-dimensional settings. The innovations are three-fold. First, the new method implements reinforcement learning at each selection of a splitting variable during the tree construction processes. By splitting on the variable that brings the greatest future improvement in later splits, rather than choosing the one with largest marginal effect from the immediate split, the constructed tree utilizes the available samples in a more efficient way. Moreover, such an approach enables linear combination cuts at little extra computational cost. Second, we propose a variable muting procedure that progressively eliminates noise variables during the construction of each individual tree. The muting procedure also takes advantage of reinforcement learning and prevents noise variables from being considered in the search for splitting rules, so that towards terminal nodes, where the sample size is small, the splitting rules are still constructed from only strong variables. Last, we investigate asymptotic properties of the proposed method under basic assumptions and discuss rationale in general settings. PMID:26903687

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…

Faster Bit-Parallel Algorithms for Unordered Pseudo-tree Matching and Tree Homeomorphism

NASA Astrophysics Data System (ADS)

Kaneta, Yusaku; Arimura, Hiroki

In this paper, we consider the unordered pseudo-tree matching problem, which is a problem of, given two unordered labeled trees P and T, finding all occurrences of P in T via such many-one embeddings that preserve node labels and parent-child relationship. This problem is closely related to tree pattern matching problem for XPath queries with child axis only. If m > w , we present an efficient algorithm that solves the problem in O(nm log(w)/w) time using O(hm/w + mlog(w)/w) space and O(m log(w)) preprocessing on a unit-cost arithmetic RAM model with addition, where m is the number of nodes in P, n is the number of nodes in T, h is the height of T, and w is the word length. We also discuss a modification of our algorithm for the unordered tree homeomorphism problem, which corresponds to a tree pattern matching problem for XPath queries with descendant axis only.

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)

Tree Defects: A Photo Guide

Treesearch

Alex L Shigo

1983-01-01

This guide shows, in 110 photos, how discoloration and decay form in trees. An expanded concept of tree decay is given. After wounding, trees form boundaries to resist the spread of pathogens. The boundary-setting defense process is called compartmentalization, and model of the process is CODIT. The expanded concept and the model are used to reexamine many other tree...

The national tree-list layer

Treesearch

Stacy A. Drury; Jason M. Herynk

2011-01-01

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

On the Number of Non-equivalent Ancestral Configurations for Matching Gene Trees and Species Trees.

PubMed

Disanto, Filippo; Rosenberg, Noah A

2017-09-14

An ancestral configuration is one of the combinatorially distinct sets of gene lineages that, for a given gene tree, can reach a given node of a specified species tree. Ancestral configurations have appeared in recursive algebraic computations of the conditional probability that a gene tree topology is produced under the multispecies coalescent model for a given species tree. For matching gene trees and species trees, we study the number of ancestral configurations, considered up to an equivalence relation introduced by Wu (Evolution 66:763-775, 2012) to reduce the complexity of the recursive probability computation. We examine the largest number of non-equivalent ancestral configurations possible for a given tree size n. Whereas the smallest number of non-equivalent ancestral configurations increases polynomially with n, we show that the largest number increases with [Formula: see text], where k is a constant that satisfies [Formula: see text]. Under a uniform distribution on the set of binary labeled trees with a given size n, the mean number of non-equivalent ancestral configurations grows exponentially with n. The results refine an earlier analysis of the number of ancestral configurations considered without applying the equivalence relation, showing that use of the equivalence relation does not alter the exponential nature of the increase with tree size.

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

PubMed Central

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

2016-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Terrestrial apes and phylogenetic trees

PubMed Central

Arsuaga, Juan Luis

2010-01-01

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

Nonbinary Tree-Based Phylogenetic Networks.

PubMed

Jetten, Laura; van Iersel, Leo

2018-01-01

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

Trees of Yap: a field guide

Treesearch

Marjorie V. Cushing Falanruw

2015-01-01

Descriptions, drawings, and photographs are presented for trees found on the Yap Islands in the Federated States of Micronesia. Included are all recorded native trees and most introduced trees as well as new records of native and introduced trees. Additional information is provided on tree distribution, status, vernacular names in Micronesia, and English names when...

Wrist postures and forces in tree planters during three tree unloading conditions.

PubMed

Denbeigh, Kathleen; Slot, Tegan R; Dumas, Geneviève A

2013-01-01

The aims of this study were to investigate wrist postures and forces while operating the shovel during tree planting and to determine if different tree unloading techniques result in variations in wrist postures and forces. Experienced tree planters performed the planting task in a laboratory environment for three conditions: (1) symmetric tree unloading, and asymmetric unloading resulting in (2) right-loaded planting bags and (3) left-loaded planting bags. An optoelectric system and a shovel instrumented with strain gauges captured wrist posture and forces at the wrist, respectively. Wrist extension of up to 45° was observed, and this posture, in combination with varying degrees of wrist deviation, may be a primary risk factor for musculoskeletal pain. Average resultant forces at the wrist were moderately high (>30 N) for each unloading condition, indicating increased risk for the development of repetitive strain injuries such as carpal tunnel syndrome. No significant differences in wrist posture or forces existed between unloading conditions. Wrist pain is a major musculoskeletal complaint among tree planters. This study measured wrist postures and forces at the wrist while operating the shovel during tree planting. The wrist extension observed, in combination with deviation, may be a key risk factor for musculoskeletal pain. Forces at the wrist indicate increased risk for repetitive strain injuries.

Coalescent methods for estimating phylogenetic trees.

PubMed

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

2009-10-01

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

Modeling individual tree survial

Treesearch

Quang V. Cao

2016-01-01

Information provided by growth and yield models is the basis for forest managers to make decisions on how to manage their forests. Among different types of growth models, whole-stand models offer predictions at stand level, whereas individual-tree models give detailed information at tree level. The well-known logistic regression is commonly used to predict tree...

Decision trees in epidemiological research.

PubMed

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

2017-01-01

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

Urban tree database and allometric equations

Treesearch

E. Gregory McPherson; Natalie S. van Doorn; Paula J.  Peper

2016-01-01

Information on urban tree growth underpins models used to calculate the effects of trees on the environment and human well-being. Maximum tree size and other growth data are used by urban forest managers, landscape architects, and planners to select trees most suitable to the amount of growing space, thereby reducing costly future conflicts between trees and...

Non-unique key B-Tree implementation

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

Ries, D.R.

1980-12-23

The B-Trees are an indexed method to allow fast retrieval and order preserving updates to a FRAMIS relation based on a designated set of keys in the relation. A B-Tree access method is being implemented to provide indexed and sequential (in index order) access to FRAMIS relations. The implementation modifies the basic B-Tree structure to correctly allow multiple key values and still maintain the balanced page fill property of B-Trees. The data structures of the B-Tree are presented first, including the FRAMIS solution to the duplicate key value problem. Then the access level routines and utilities are presented. These routinesmore » include the original B-Tree creation; searching the B-Tree; and inserting, deleting, and replacing tuples on the B-Tree. In conclusion, the uses of the B-Tree access structures at the semantic level to enhance the FRAMIS performance are discussed. 10 figures.« less

Common allometric response of open-grown leader shoots to tree height in co-occurring deciduous broadleaved trees

PubMed Central

Miyata, Rie; Kubo, Takuya; Nabeshima, Eri; Kohyama, Takashi S.

2011-01-01

Background and Aims Morphology of crown shoots changes with tree height. The height of forest trees is usually correlated with the light environment and this makes it difficult to separate the effects of tree size and of light conditions on the morphological plasticity of crown shoots. This paper addresses the tree-height dependence of shoot traits under full-light conditions where a tree crown is not shaded by other crowns. Methods Focus is given to relationships between tree height and top-shoot traits, which include the shoot's leaf-blades and non-leafy mass, its total leaf-blade area and the length and basal diameter of the shoot's stem. We examine the allometric characteristics of open-grown current-year leader shoots at the tops of forest tree crowns up to 24 m high and quantify their responses to tree height in 13 co-occurring deciduous hardwood species in a cool-temperate forest in northern Japan. Key Results Dry mass allocated to leaf blades in a leader shoot increased with tree height in all 13 species. Specific leaf area decreased with tree height. Stem basal area was almost proportional to total leaf area in a leader shoot, where the proportionality constant did not depend on tree height, irrespective of species. Stem length for a given stem diameter decreased with tree height. Conclusions In the 13 species observed, height-dependent changes in allometry of leader shoots were convergent. This finding suggests that there is a common functional constraint in tree-height development. Under full-light conditions, leader shoots of tall trees naturally experience more severe water stress than those of short trees. We hypothesize that the height dependence of shoot allometry detected reflects an integrated response to height-associated water stress, which contributes to successful crown expansion and height gain. PMID:21914698

PhyloTreePruner: A Phylogenetic Tree-Based Approach for Selection of Orthologous Sequences for Phylogenomics.

PubMed

Kocot, Kevin M; Citarella, Mathew R; Moroz, Leonid L; Halanych, Kenneth M

2013-01-01

Molecular phylogenetics relies on accurate identification of orthologous sequences among the taxa of interest. Most orthology inference programs available for use in phylogenomics rely on small sets of pre-defined orthologs from model organisms or phenetic approaches such as all-versus-all sequence comparisons followed by Markov graph-based clustering. Such approaches have high sensitivity but may erroneously include paralogous sequences. We developed PhyloTreePruner, a software utility that uses a phylogenetic approach to refine orthology inferences made using phenetic methods. PhyloTreePruner checks single-gene trees for evidence of paralogy and generates a new alignment for each group containing only sequences inferred to be orthologs. Importantly, PhyloTreePruner takes into account support values on the tree and avoids unnecessarily deleting sequences in cases where a weakly supported tree topology incorrectly indicates paralogy. A test of PhyloTreePruner on a dataset generated from 11 completely sequenced arthropod genomes identified 2,027 orthologous groups sampled for all taxa. Phylogenetic analysis of the concatenated supermatrix yielded a generally well-supported topology that was consistent with the current understanding of arthropod phylogeny. PhyloTreePruner is freely available from http://sourceforge.net/projects/phylotreepruner/.

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.

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.

Influence of sumac (Rhus Coriaria L.) and ginger (Zingiber officinale) on egg yolk fatty acid, cholesterol and blood parameters in laying hens.

PubMed

Gurbuz, Y; Salih, Y G

2017-12-01

The aim of the study was to evaluate the potential effect of different levels of sumac (Rhus coriaria L.) seed powder and ginger (Zingiber officinale) root powder on egg yolk fatty acid composition, blood/yolk cholesterol in laying hen. A total of 63 (ATAK-S: Domestic Turkish Laying Hens) laying hens (average weight: 1470 g each hen, 25-weeks of age) were assigned to seven treatment diets including sumac seed (S) and ginger root powder (G) at 0 g/kg (control), 10 g/kg (S1), 20 g/kg (S2), and 30 g/kg (S3); 10 g/kg (G1), 20 g/kg (G2), or 30 g/kg in rations respectively, for 8 weeks. After a two-week adaptation period to cages, the hens were allocated to 7 groups with 9 replicates of 1 hen in per cage each. The replications were allotted equally into the upper and lower cages to minimize the effects of cage level. In this study, egg yolk cholesterol had a decrease (p <0.05) in supplemented diet( sumac seed and ginger root powder). Fatty acid content in yolk; saturated fatty acid, monounsaturated fatty acids, polyunsaturated fatty acids and rate of n6/n3 were not significant (p <0.05). However, dietary supplementation with sumac and ginger powder reduced and yolk/blood cholesterol concentrations in laying hens. Supplementation of sumac and ginger affected on HDL, there was found a significant effect (p < 0.05) in treatment groups. Moreover, LDL positively decreased in all treatment groups compared with the control group. The findings of this study suggested that feeding sumac and ginger tend to be decreasing cholesterol levels in both yolk and blood on laying hens. It can be concluded that ginger root and sumac seed powder can be used as an effective feed additive to improve fatty acid composition and yolk and blood cholesterol in ATAK-S laying hens. Journal of Animal Physiology and Animal Nutrition © 2017 Blackwell Verlag GmbH.

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

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

PubMed

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

2017-11-01

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

Tree nut oils

USDA-ARS?s Scientific Manuscript database

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...

Fault Tree Analysis.

PubMed

McElroy, Lisa M; Khorzad, Rebeca; Rowe, Theresa A; Abecassis, Zachary A; Apley, Daniel W; Barnard, Cynthia; Holl, Jane L

The purpose of this study was to use fault tree analysis to evaluate the adequacy of quality reporting programs in identifying root causes of postoperative bloodstream infection (BSI). A systematic review of the literature was used to construct a fault tree to evaluate 3 postoperative BSI reporting programs: National Surgical Quality Improvement Program (NSQIP), Centers for Medicare and Medicaid Services (CMS), and The Joint Commission (JC). The literature review revealed 699 eligible publications, 90 of which were used to create the fault tree containing 105 faults. A total of 14 identified faults are currently mandated for reporting to NSQIP, 5 to CMS, and 3 to JC; 2 or more programs require 4 identified faults. The fault tree identifies numerous contributing faults to postoperative BSI and reveals substantial variation in the requirements and ability of national quality data reporting programs to capture these potential faults. Efforts to prevent postoperative BSI require more comprehensive data collection to identify the root causes and develop high-reliability improvement strategies.

Felling small trees with a drive-to-tree feller-buncher

Treesearch

Dana Mitchell

2008-01-01

Conventional forestry equipment is often used to harvest small-diameter trees. The typical ground-based logging operation is highly mechanized, with the most common using feller-bunchers, grapple skidders, and a chipper or grinder. But these machines may not be economical when used in pre-commercial or unmerchantable thinning operations in which the number of trees to...

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.; Güntner, A.

2012-04-01

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

The potential of the tree water potential.

PubMed

Steppe, Kathy

2018-06-12

Non-invasive quantification of tree water potential is one of the grand challenges for assessing the fate of trees and forests in the coming decades. Tree water potential is a robust and direct indicator of tree water status and is preferably used to track how trees, forests and vegetation in general respond to changes in climate and drought. In this issue of Tree Physiology, Dietrich et al. (2018) predict the daily canopy water potential of mature temperate trees from tree water deficit derived from stem diameter variation measurements.

Complementarity effects on tree growth are contingent on tree size and climatic conditions across Europe

PubMed Central

Madrigal-González, Jaime; Ruiz-Benito, Paloma; Ratcliffe, Sophia; Calatayud, Joaquín; Kändler, Gerald; Lehtonen, Aleksi; Dahlgren, Jonas; Wirth, Christian; Zavala, Miguel A.

2016-01-01

Neglecting tree size and stand structure dynamics might bias the interpretation of the diversity-productivity relationship in forests. Here we show evidence that complementarity is contingent on tree size across large-scale climatic gradients in Europe. We compiled growth data of the 14 most dominant tree species in 32,628 permanent plots covering boreal, temperate and Mediterranean forest biomes. Niche complementarity is expected to result in significant growth increments of trees surrounded by a larger proportion of functionally dissimilar neighbours. Functional dissimilarity at the tree level was assessed using four functional types: i.e. broad-leaved deciduous, broad-leaved evergreen, needle-leaved deciduous and needle-leaved evergreen. Using Linear Mixed Models we show that, complementarity effects depend on tree size along an energy availability gradient across Europe. Specifically: (i) complementarity effects at low and intermediate positions of the gradient (coldest-temperate areas) were stronger for small than for large trees; (ii) in contrast, at the upper end of the gradient (warmer regions), complementarity is more widespread in larger than smaller trees, which in turn showed negative growth responses to increased functional dissimilarity. Our findings suggest that the outcome of species mixing on stand productivity might critically depend on individual size distribution structure along gradients of environmental variation. PMID:27571971

Size matters a lot: tree height and prior growth predict drought-induced tree death in Italian oak forests

NASA Astrophysics Data System (ADS)

Ripullone, F.; Colangelo, M.; Camarero, J. J.; Gazol, A.; Borghetti, M.; Gentilesca, T.

2016-12-01

Climate warming is expected to amplify drought stress resulting in the occurrence of more widespread dieback episodes and increasing mortality rates. This has pushed the search of reliable and robust early-warning indicators of impending drought-triggered tree death. Recent studies highlight how level of defoliation or age of trees strictly coact with drought in leading to forest decline. In addition, tree size and the tree-to-tree competition for water could also contribute to tree death in drought-prone sites. In this regard, it has been predicted that tall trees with isohydric stomatal regulation are most likely to die due to drought stress. Here, we test this hypothesis by analyzing size, age, competition and growth data in a Mediterranean oak species characterized by anisohydric behaviour, showing recent drought-induced mortality in two Italian forest sites. At both study sites, tree height was associated to the probability of dying. However, this association was opposite to published predictions because living trees were taller than dead trees at both sites. Neither age nor competition intensity played significant roles as drivers of tree mortality. Regarding growth data, trends in basal area increment were significantly smaller in dead than in living trees. Differences were most marked at mid (15 years prior to death) than at short (10 years) or long-term (35 year) scales. This is probably not related to intrinsic growth features of the study species but it can be explained because the most severe drought since 1950 occurred in 2000 at the study area, i.e. 15 years prior to the increase of tree mortality and when growth of living and dead trees started diverging. Lastly, we discuss potential factors which may explain why smaller individuals of anisohydric tree species such as Mediterranean oaks are prone to drought-induced tree death.

Influence of Tree-Scale Environmental Variability on Tree-Ring Reconstructions of Temperature at Sonora Pass, CA

NASA Astrophysics Data System (ADS)

Ma, L.; Stine, A.

2016-12-01

Tree-ring width from treeline environments tend to covary with local interannual temperature variabilities. However, other environmental factors such as moisture and light availability may further modulate tree growth in cold climates. We investigate the influence of various environmental factors on a tree-ring record from a research plot near Sonora Pass, CA (38.32N, 119.64W; elev. 3130 m). This treeline ecotone is dominated by whitebark pine (Pinus albicaulis) growing as individuals and as stands, and at the transition between tree form and krummholtz. We surveyed all trees in the 160m x 90m site, mapping and coring all trees with a diameter at breast height greater than 10 cm. We use survey data to test for an influence of inter-tree competition on growth. We also test for modulation of growth by variation in distance from surface water, aspect and slope, and soil types. Initial result shows a relationship between tree ring width and local May-July temperature (R = 0.33, p < 0.01), suggesting summer temperature as a large-scale control on growth. Incorporating the tree-level metadata, we test for the effect of spatial variability on mean growth rate and on reconstructed temperatures. Trees that have larger or closer neighboring trees experience greater competition, and we hypothesize that competition will be inversely related to average growth rate. Further, we test the sensitivity of ring-width interannual variability to other non-temperature environmental drivers such as moisture availability, light competition, and spatial relations in the microenvironment. We hypothesize that trees that have ready access to light and water will likely produce ring records more closely correlated with the temperature record, and thus will produce a temperature reconstruction with a higher signal-to-noise ratio; whereas trees that experience more microenvironment limitations or competition will produce ring records resembling temperature and additional environmental factors or

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

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

PubMed

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

2014-01-01

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

New tree-measurement concepts: height accumulation, giant tree, taper and shape

Treesearch

L. R. Grosenbaugh

1954-01-01

An entirely new concept of tree measurment was announced by the author in 1948 (11). Since the original theory and applications have subsequently been b roadened considerably, it seems advisable to publish the entire development in readily usable form, along with other material helpful in tree measurement.

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…

Extended Full Computation-Tree Logic with Sequence Modal Operator: Representing Hierarchical Tree Structures

NASA Astrophysics Data System (ADS)

Kamide, Norihiro; Kaneiwa, Ken

An extended full computation-tree logic, CTLS*, is introduced as a Kripke semantics with a sequence modal operator. This logic can appropriately represent hierarchical tree structures where sequence modal operators in CTLS* are applied to tree structures. An embedding theorem of CTLS* into CTL* is proved. The validity, satisfiability and model-checking problems of CTLS* are shown to be decidable. An illustrative example of biological taxonomy is presented using CTLS* formulas.

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. © The Author 2014. Published by Oxford University Press. All rights reserved

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

PubMed

Wein, Annika; Bauhus, Jürgen; Bilodeau-Gauthier, Simon; Scherer-Lorenzen, Michael; Nock, Charles; Staab, Michael

2016-01-01

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

Anatomical modeling of the bronchial tree

NASA Astrophysics Data System (ADS)

Hentschel, Gerrit; Klinder, Tobias; Blaffert, Thomas; Bülow, 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 naïve 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.

Tree colonization by the Asian longhorn beetle, Anoplophora glabripennis (Coleoptera: Cerambycidae): effect of habitat and tree suitability.

PubMed

Faccoli, Massimo; Favaro, Riccardo; Concheri, Giuseppe; Squartini, Andrea; Battisti, Andrea

2016-04-01

Tree colonization and feeding activity of the invasive wood-borer Asian longhorn beetle (Anoplophora glabripennis), an Asian pest introduced into North America and Europe, was studied in a newly invaded area in Italy. The hypothesis being tested was that the reproductive success of the insect depend on habitat type and tree suitability. Adult beetles were caged on branches of host and nonhost species, in both urban and forest habitats. Two months later, number and size of feeding patches on plant tissues, eggs laid, and surviving larvae were assessed. Bark concentration of C and N was also measured from the same trees. Results indicated that the mean area of plant tissues consumed by adult feeding was significantly larger on trees growing in forest than in urban habitat, although within the same habitat there were no differences between susceptible and nonsusceptible trees. ALB tree colonization, in terms of number of eggs laid and young larvae survival, was not affected by habitat while it was higher on susceptible trees. Although trees growing in forests had a lower nitrogen concentration, they allowed colonization rates similar to those of trees growing in the urban habitat. Hence, the amount of carbon and nitrogen did not fully explain tree suitability or habitat selection. We suggest compensatory feeding as a potential mechanism that might explain this peculiar situation, as supported by a more intensive feeding activity recorded on trees in the forest. Suitability of different trees may be due to other factors, such as secondary chemical compounds. © 2014 Institute of Zoology, Chinese Academy of Sciences.

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…

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

PubMed

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

2007-11-01

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

Remeasuring tree heights on permanent plots using rectangular coordinates and one angle per tree

Treesearch

Robert L. Neal

1973-01-01

Heights of permanent sample trees with tops visible from any point can be measured from that point with any clinometer, measuring one vertical angle per tree. Two horizontal angles and one additional vertical angle per observation point are necessary to orient the point to the plot. Permanently recorded coordinates and elevations of tree locations are used with the...

Moon tree ceremony

NASA Image and Video Library

2011-02-03

Apollo 13 astronaut Fred Haise stands with Rosemary Roosa, daughter of late Apollo 14 astronaut Stuart Roosa, beside a 'moon tree' planted at the INFINITY science center on Feb. 3, 2011. The moon tree is a descendent of seeds carried into space by Stuart Roosa on the Apollo 14 mission in 1971.

Individual tree control

Treesearch

Harvey A. Holt

1989-01-01

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

Tree growth visualization

Treesearch

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

2005-01-01

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

iGLASS: An Improvement to the GLASS Method for Estimating Species Trees from Gene Trees

PubMed Central

Rosenberg, Noah A.

2012-01-01

Abstract Several methods have been designed to infer species trees from gene trees while taking into account gene tree/species tree discordance. Although some of these methods provide consistent species tree topology estimates under a standard model, most either do not estimate branch lengths or are computationally slow. An exception, the GLASS method of Mossel and Roch, is consistent for the species tree topology, estimates branch lengths, and is computationally fast. However, GLASS systematically overestimates divergence times, leading to biased estimates of species tree branch lengths. By assuming a multispecies coalescent model in which multiple lineages are sampled from each of two taxa at L independent loci, we derive the distribution of the waiting time until the first interspecific coalescence occurs between the two taxa, considering all loci and measuring from the divergence time. We then use the mean of this distribution to derive a correction to the GLASS estimator of pairwise divergence times. We show that our improved estimator, which we call iGLASS, consistently estimates the divergence time between a pair of taxa as the number of loci approaches infinity, and that it is an unbiased estimator of divergence times when one lineage is sampled per taxon. We also show that many commonly used clustering methods can be combined with the iGLASS estimator of pairwise divergence times to produce a consistent estimator of the species tree topology. Through simulations, we show that iGLASS can greatly reduce the bias and mean squared error in obtaining estimates of divergence times in a species tree. PMID:22216756

Using tree diversity to compare phylogenetic heuristics.

PubMed

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

2009-04-29

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

Measuring (bio)physical tree properties using accelerometers

NASA Astrophysics Data System (ADS)

van Emmerik, Tim; Steele-Dunne, Susan; Hut, Rolf; Gentine, Pierre; Selker, John; van de Giesen, Nick

2017-04-01

Trees play a crucial role in the water, carbon and nitrogen cycle on local, regional and global scales. Understanding the exchange of heat, water, and CO2 between trees and the atmosphere is important to assess the impact of drought, deforestation and climate change. Unfortunately, ground measurements of tree dynamics are often expensive, or difficult due to challenging environments. We demonstrate the potential of measuring (bio)physical properties of trees using robust and affordable acceleration sensors. Tree sway is dependent on e.g. mass and wind energy absorption of the tree. By measuring tree acceleration we can relate the tree motion to external loads (e.g. precipitation), and tree (bio)physical properties (e.g. mass). Using five months of acceleration data of 19 trees in the Brazilian Amazon, we show that the frequency spectrum of tree sway is related to mass, precipitation, and canopy drag. This presentation aims to show the concept of using accelerometers to measure tree dynamics, and we acknowledge that the presented example applications is not an exhaustive list. Further analyses are the scope of current research, and we hope to inspire others to explore additional applications.

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

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

PubMed

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

2012-11-15

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

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

NASA Astrophysics Data System (ADS)

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

2010-05-01

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

Individual tree crown delineation using localized contour tree method and airborne LiDAR data in coniferous forests

NASA Astrophysics Data System (ADS)

Wu, Bin; Yu, Bailang; Wu, Qiusheng; Huang, Yan; Chen, Zuoqi; Wu, Jianping

2016-10-01

Individual tree crown delineation is of great importance for forest inventory and management. The increasing availability of high-resolution airborne light detection and ranging (LiDAR) data makes it possible to delineate the crown structure of individual trees and deduce their geometric properties with high accuracy. In this study, we developed an automated segmentation method that is able to fully utilize high-resolution LiDAR data for detecting, extracting, and characterizing individual tree crowns with a multitude of geometric and topological properties. The proposed approach captures topological structure of forest and quantifies topological relationships of tree crowns by using a graph theory-based localized contour tree method, and finally segments individual tree crowns by analogy of recognizing hills from a topographic map. This approach consists of five key technical components: (1) derivation of canopy height model from airborne LiDAR data; (2) generation of contours based on the canopy height model; (3) extraction of hierarchical structures of tree crowns using the localized contour tree method; (4) delineation of individual tree crowns by segmenting hierarchical crown structure; and (5) calculation of geometric and topological properties of individual trees. We applied our new method to the Medicine Bow National Forest in the southwest of Laramie, Wyoming and the HJ Andrews Experimental Forest in the central portion of the Cascade Range of Oregon, U.S. The results reveal that the overall accuracy of individual tree crown delineation for the two study areas achieved 94.21% and 75.07%, respectively. Our method holds great potential for segmenting individual tree crowns under various forest conditions. Furthermore, the geometric and topological attributes derived from our method provide comprehensive and essential information for forest management.

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

NASA Astrophysics Data System (ADS)

Masson, Josiane; Soille, Pierre; Mueller, Rick

2004-10-01

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

Voxel-Based 3-D Tree Modeling from Lidar Images for Extracting Tree Structual Information

NASA Astrophysics Data System (ADS)

Hosoi, F.

2014-12-01

Recently, lidar (light detection and ranging) has been used to extracting tree structural information. Portable scanning lidar systems can capture the complex shape of individual trees as a 3-D point-cloud image. 3-D tree models reproduced from the lidar-derived 3-D image can be used to estimate tree structural parameters. We have proposed the voxel-based 3-D modeling for extracting tree structural parameters. One of the tree parameters derived from the voxel modeling is leaf area density (LAD). We refer to the method as the voxel-based canopy profiling (VCP) method. In this method, several measurement points surrounding the canopy and optimally inclined laser beams are adopted for full laser beam illumination of whole canopy up to the internal. From obtained lidar image, the 3-D information is reproduced as the voxel attributes in the 3-D voxel array. Based on the voxel attributes, contact frequency of laser beams on leaves is computed and LAD in each horizontal layer is obtained. This method offered accurate LAD estimation for individual trees and woody canopy trees. For more accurate LAD estimation, the voxel model was constructed by combining airborne and portable ground-based lidar data. The profiles obtained by the two types of lidar complemented each other, thus eliminating blind regions and yielding more accurate LAD profiles than could be obtained by using each type of lidar alone. Based on the estimation results, we proposed an index named laser beam coverage index, Ω, which relates to the lidar's laser beam settings and a laser beam attenuation factor. It was shown that this index can be used for adjusting measurement set-up of lidar systems and also used for explaining the LAD estimation error using different types of lidar systems. Moreover, we proposed a method to estimate woody material volume as another application of the voxel tree modeling. In this method, voxel solid model of a target tree was produced from the lidar image, which is composed of

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)

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…

Christmas Tree Pest Manual, Third Edition

Treesearch

Steven Katovich; Deborah McCullough; Michael Ostry; Jill O’Donnell; Isabel Munck; Cliff Sadof

2014-01-01

Continuing mortality of red pine from an unknown cause has been observed in 30 to 40 year old plantations in southern and west central Wisconsin. A single tree or small group of trees die, followed by mortality of adjacent trees. These circular pockets of dead trees expand up to 0.3 acre per year.

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.

Grading hardwood trees

Treesearch

Robert L. Brisbin

1989-01-01

Tree grading provides a way to evaluate the quality characteristics and value of standing hardwood trees. This is important because the differences in price between high-quality and low-quality end products can be very large. Since hardwood timber varies greatly in quality and value among species, within species, and even within specific geographic areas, timber...

Factors that influence Christmas tree sales

Treesearch

Thomas H. Pendleton; Lawrence D. Garrett

1970-01-01

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

Pocket guide to Christmas tree diseases

Treesearch

Thomas H. Nicholls; Robert D. Wray

1989-01-01

Each year more than 30 million American families bring a live Christmas tree into their homes to become the warm and glowing center of their Christmas celebration. Years ago, most Christmas trees were cut wild. But, as demand increased and the supply of suitable wild trees decreased, growing Christmas trees in plantations became more and more common.

Imaging tree roots with borehole radar

Treesearch

John R. Butnor; Kurt H. Johnsen; Per Wikstrom; Tomas Lundmark; Sune Linder

2006-01-01

Ground-penetrating radar has been used to de-tect and map tree roots using surface-based antennas in reflection mode. On amenable soils these methods can accurately detect lateral tree roots. In some tree species (e.g. Pinus taeda, Pinus palustris), vertically orientated tap roots directly beneath the tree, comprise most of the root mass. It is...

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

PubMed Central

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

2018-01-01

Solitary foraging ants commonly use visual cues from their environment for navigation. Foragers are known to store visual scenes from the surrounding panorama for later guidance to known resources and to return successfully back to the nest. Several ant species travel not only on the ground, but also climb trees to locate resources. The navigational information that guides animals back home during their descent, while their body is perpendicular to the ground, is largely unknown. Here, we investigate in a nocturnal ant, Myrmecia midas, whether foragers travelling down a tree use visual information to return home. These ants establish nests at the base of a tree on which they forage and in addition, they also forage on nearby trees. We collected foragers and placed them on the trunk of the nest tree or a foraging tree in multiple compass directions. Regardless of the displacement location, upon release ants immediately moved to the side of the trunk facing the nest during their descent. When ants were released on non-foraging trees near the nest, displaced foragers again travelled around the tree to the side facing the nest. All the displaced foragers reached the correct side of the tree well before reaching the ground. However, when the terrestrial cues around the tree were blocked, foragers were unable to orient correctly, suggesting that the surrounding panorama is critical to successful orientation on the tree. Through analysis of panoramic pictures, we show that views acquired at the base of the foraging tree nest can provide reliable nest-ward orientation up to 1.75 m above the ground. We discuss, how animals descending from trees compare their current scene to a memorised scene and report on the similarities in visually guided behaviour while navigating on the ground and descending from trees. PMID:29422880

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

PubMed

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

2018-01-01

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

Encoding phylogenetic trees in terms of weighted quartets.

PubMed

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

2008-04-01

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

The relationship between tree growth patterns and likelihood of mortality: A study of two tree species in the Sierra Nevada

USGS Publications Warehouse

Das, A.J.; Battles, J.J.; Stephenson, N.L.; van Mantgem, P.J.

2007-01-01

We examined mortality of Abies concolor (Gord. & Glend.) Lindl. (white fir) and Pinus lambertiana Dougl. (sugar pine) by developing logistic models using three growth indices obtained from tree rings: average growth, growth trend, and count of abrupt growth declines. For P. lambertiana, models with average growth, growth trend, and count of abrupt declines improved overall prediction (78.6% dead trees correctly classified, 83.7% live trees correctly classified) compared with a model with average recent growth alone (69.6% dead trees correctly classified, 67.3% live trees correctly classified). For A. concolor, counts of abrupt declines and longer time intervals improved overall classification (trees with DBH ???20 cm: 78.9% dead trees correctly classified and 76.7% live trees correctly classified vs. 64.9% dead trees correctly classified and 77.9% live trees correctly classified; trees with DBH <20 cm: 71.6% dead trees correctly classified and 71.0% live trees correctly classified vs. 67.2% dead trees correctly classified and 66.7% live trees correctly classified). In general, count of abrupt declines improved live-tree classification. External validation of A. concolor models showed that they functioned well at stands not used in model development, and the development of size-specific models demonstrated important differences in mortality risk between understory and canopy trees. Population-level mortality-risk models were developed for A. concolor and generated realistic mortality rates at two sites. Our results support the contention that a more comprehensive use of the growth record yields a more robust assessment of mortality risk. ?? 2007 NRC.

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

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

PubMed

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

2018-03-05

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

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

PubMed

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

2011-09-01

Shrubs and trees are expected to expand in the sub-Arctic due to global warming. Our study was conducted in Abisko, sub-arctic Sweden. We recorded the change in coverage of shrub and tree species over a 32- to 34-year period, in three 50 x 50 m plots; in the alpine-tree-line ecotone. The cover of shrubs and trees (<3.5 cm diameter at breast height) were estimated during 2009-2010 and compared with historical documentation from 1976 to 1977. Similarly, all tree stems (> or =3.5 cm) were noted and positions determined. There has been a substantial increase of cover of shrubs and trees, particularly dwarf birch (Betula nana), and mountain birch (Betula pubescens ssp. czerepanovii), and an establishment of aspen (Populus tremula). The other species willows (Salix spp.), juniper (Juniperus communis), and rowan (Sorbus aucuparia) revealed inconsistent changes among the plots. Although this study was unable to identify the causes for the change in shrubs and small trees, they are consistent with anticipated changes due to climate change and reduced herbivory.

Tree-Based Unrooted Phylogenetic Networks.

PubMed

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

2018-02-01

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

Tree Height and DBH Growth Model Establishment of Main Tree Species in Wuling Mountain Small Watershed

NASA Astrophysics Data System (ADS)

Luo, Jia; Zhang, Min; Zhou, Xiaoling; Chen, Jianhua; Tian, Yuxin

2018-01-01

Taken 4 main tree species in the Wuling mountain small watershed as research objects, 57 typical sample plots were set up according to the stand type, site conditions and community structure. 311 goal diameter-class sample trees were selected according to diameter-class groups of different tree-height grades, and the optimal fitting models of tree height and DBH growth of main tree species were obtained by stem analysis using Richard, Logistic, Korf, Mitscherlich, Schumacher, Weibull theoretical growth equations, and the correlation coefficient of all optimal fitting models reached above 0.9. Through the evaluation and test, the optimal fitting models possessed rather good fitting precision and forecast dependability.

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.

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.

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

Treesearch

David W. MacFarlane; Neil R. Ver Planck

2012-01-01

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

Atmospheric carbon reduction by urban trees

Treesearch

David J. Nowak

1993-01-01

Trees, because they sequester atmospheric carbon through their growth process and conserve energy in urban areas, have been suggested as one means to combat increasing levels of atmospheric carbon. Analysis of the urban forest in Oakland, California (21% tree cover), reveals a tree carbon storage level of 11.0 metric tons/hectare. Trees in the area of the 1991 fire in...

Hardwood Regeneration After Seed Tree Cutting

Treesearch

Robert L. Johnson; R. M. Krinard

1976-01-01

Seed trees left at two sites did not appear to influence the establishment or development of reproduction . Seed trees were mainly sweetgum and red oaks. Most reproduction was from sprouting of the stumps and roots of cut trees or from advanced seedlings present in the understory at the time of cutting. Eighteen years after cutting, dominant trees of the reproduction...

Guide to the measurement of tree characteristics important to the quality classification for young hardwood trees

Treesearch

David L. Sonderman

1979-01-01

A procedure is shown for measuring external tree characteristics that are important in determining the current and future quality of young hardwood trees. This guide supplements a precious study which describes the quality classification system for young hardwood trees

Prioritizing trees for global conservation action: BGCI’s tree conservation agenda

Treesearch

K. Shaw; M. Rivers; E. Beech

2017-01-01

Botanic Gardens Conservation International (BGCI) is a global voice for plant conservation via its worldwide network of botanic gardens and partners. Tree conservation has been a strong focus of BGCI’s program for many years. In collaboration with Fauna & Flora International, BGCI runs the Global Trees Campaign (GTC, www.globaltrees.org), the only international...

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.

Inferences from growing trees backwards

Treesearch

David W. Green; Kent A. McDonald

1997-01-01

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

The 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:…

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,…

The stopping rules for winsorized tree

NASA Astrophysics Data System (ADS)

Ch'ng, Chee Keong; Mahat, Nor Idayu

2017-11-01

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

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.…

Accounting for Uncertainty in Gene Tree Estimation: Summary-Coalescent Species Tree Inference in a Challenging Radiation of Australian Lizards.

PubMed

Blom, Mozes P K; Bragg, Jason G; Potter, Sally; Moritz, Craig

2017-05-01

Accurate gene tree inference is an important aspect of species tree estimation in a summary-coalescent framework. Yet, in empirical studies, inferred gene trees differ in accuracy due to stochastic variation in phylogenetic signal between targeted loci. Empiricists should, therefore, examine the consistency of species tree inference, while accounting for the observed heterogeneity in gene tree resolution of phylogenomic data sets. Here, we assess the impact of gene tree estimation error on summary-coalescent species tree inference by screening ${\\sim}2000$ exonic loci based on gene tree resolution prior to phylogenetic inference. We focus on a phylogenetically challenging radiation of Australian lizards (genus Cryptoblepharus, Scincidae) and explore effects on topology and support. We identify a well-supported topology based on all loci and find that a relatively small number of high-resolution gene trees can be sufficient to converge on the same topology. Adding gene trees with decreasing resolution produced a generally consistent topology, and increased confidence for specific bipartitions that were poorly supported when using a small number of informative loci. This corroborates coalescent-based simulation studies that have highlighted the need for a large number of loci to confidently resolve challenging relationships and refutes the notion that low-resolution gene trees introduce phylogenetic noise. Further, our study also highlights the value of quantifying changes in nodal support across locus subsets of increasing size (but decreasing gene tree resolution). Such detailed analyses can reveal anomalous fluctuations in support at some nodes, suggesting the possibility of model violation. By characterizing the heterogeneity in phylogenetic signal among loci, we can account for uncertainty in gene tree estimation and assess its effect on the consistency of the species tree estimate. We suggest that the evaluation of gene tree resolution should be incorporated

Phylogenetic trees and Euclidean embeddings.

PubMed

Layer, Mark; Rhodes, John A

2017-01-01

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

Mapping Tree Density at the Global Scale

NASA Astrophysics Data System (ADS)

Covey, K. R.; Crowther, T. W.; Glick, H.; Bettigole, C.; Bradford, M.

2015-12-01

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 regions, with 0.74, and 0.61 trillion in boreal and temperate regions, respectively. 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 impact of humans across most of the world. Based on our projected tree densities, we estimate that deforestation is currently responsible for removing over 15 billion trees each year, and the global number of trees has fallen by approximately 46% since the start of human civilization.

Utility of tree crown condition indicators to predict tree survival using remeasured Forest Inventory and Analysis data

Treesearch

Randall S. Morin; Jim Steinman; KaDonna C. Randolph

2012-01-01

The condition of tree crowns is an important indicator of tree and forest health. Crown conditions have been evaluated during surveys of Forest Inventory and Analysis (FIA) Phase 3 (P3) plots since 1999. In this study, remeasured data from 39,357 trees in the northern United States were used to assess the probability of survival among various tree species using the...

Anatomy of the Pythagoras' Tree

ERIC Educational Resources Information Center

Teia, Luis

2016-01-01

The architecture of nature can be seen at play in a tree: no two are alike. The Pythagoras' tree behaves just as a "tree" in that the root plus the same movement repeated over and over again grows from a seed, to a plant, to a tree. In human life, this movement is termed cell division. With triples, this movement is a geometrical and…

Tree diversity and the role of non-host neighbour tree species in reducing fungal pathogen infestation

PubMed Central

Hantsch, Lydia; Bien, Steffen; Radatz, Stine; Braun, Uwe; Auge, Harald; Bruelheide, Helge

2014-01-01

The degree to which plant pathogen infestation occurs in a host plant is expected to be strongly influenced by the level of species diversity among neighbouring host and non-host plant species. Since pathogen infestation can negatively affect host plant performance, it can mediate the effects of local biodiversity on ecosystem functioning. We tested the effects of tree diversity and the proportion of neighbouring host and non-host species with respect to the foliar fungal pathogens of Tilia cordata and Quercus petraea in the Kreinitz tree diversity experiment in Germany. We hypothesized that fungal pathogen richness increases while infestation decreases with increasing local tree diversity. In addition, we tested whether fungal pathogen richness and infestation are dependent on the proportion of host plant species present or on the proportion of particular non-host neighbouring tree species. Leaves of the two target species were sampled across three consecutive years with visible foliar fungal pathogens on the leaf surface being identified macro- and microscopically. Effects of diversity among neighbouring trees were analysed: (i) for total fungal species richness and fungal infestation on host trees and (ii) for infestation by individual fungal species. We detected four and five fungal species on T. cordata and Q. petraea, respectively. High local tree diversity reduced (i) total fungal species richness and infestation of T. cordata and fungal infestation of Q. petraea and (ii) infestation by three host-specialized fungal pathogen species. These effects were brought about by local tree diversity and were independent of host species proportion. In general, host species proportion had almost no effect on fungal species richness and infestation. Strong effects associated with the proportion of particular non-host neighbouring tree species on fungal species richness and infestation were, however, recorded. Synthesis. For the first time, we experimentally

Tree diversity and the role of non-host neighbour tree species in reducing fungal pathogen infestation.

PubMed

Hantsch, Lydia; Bien, Steffen; Radatz, Stine; Braun, Uwe; Auge, Harald; Bruelheide, Helge

2014-11-01

The degree to which plant pathogen infestation occurs in a host plant is expected to be strongly influenced by the level of species diversity among neighbouring host and non-host plant species. Since pathogen infestation can negatively affect host plant performance, it can mediate the effects of local biodiversity on ecosystem functioning.We tested the effects of tree diversity and the proportion of neighbouring host and non-host species with respect to the foliar fungal pathogens of Tilia cordata and Quercus petraea in the Kreinitz tree diversity experiment in Germany. We hypothesized that fungal pathogen richness increases while infestation decreases with increasing local tree diversity. In addition, we tested whether fungal pathogen richness and infestation are dependent on the proportion of host plant species present or on the proportion of particular non-host neighbouring tree species.Leaves of the two target species were sampled across three consecutive years with visible foliar fungal pathogens on the leaf surface being identified macro- and microscopically. Effects of diversity among neighbouring trees were analysed: (i) for total fungal species richness and fungal infestation on host trees and (ii) for infestation by individual fungal species.We detected four and five fungal species on T. cordata and Q. petraea , respectively. High local tree diversity reduced (i) total fungal species richness and infestation of T. cordata and fungal infestation of Q. petraea and (ii) infestation by three host-specialized fungal pathogen species. These effects were brought about by local tree diversity and were independent of host species proportion. In general, host species proportion had almost no effect on fungal species richness and infestation. Strong effects associated with the proportion of particular non-host neighbouring tree species on fungal species richness and infestation were, however, recorded. Synthesis . For the first time, we experimentally

Application of cosmetic nail varnish does not affect the antifungal efficacy of amorolfine 5% nail lacquer in the treatment of distal subungual toenail onychomycosis: results of a randomised active-controlled study and in vitro assays.

PubMed

Sigurgeirsson, B; Ghannoum, M A; Osman-Ponchet, H; Kerrouche, N; Sidou, F

2016-05-01

As onychomycosis is unsightly, this study clinically evaluated whether the antifungal efficacy of amorolfine 5% nail lacquer (NL) was affected by a masking, natural-coloured, cosmetic nail varnish applied 24 h later; in vitro investigations were also performed. Subjects with mild-to-moderate distal subungual toenail onychomycosis were randomised to receive amorolfine 5% NL once weekly with or without cosmetic nail varnish applied 24 h later. After 12-week treatment, antifungal activity of affected toenail clippings was assessed by measurement of zones of inhibition (ZOIs) on Trichophyton mentagrophytes seeded agar plates. Mean diameters were 53.5 mm for the amorolfine 5% NL-alone group (n = 23) and 53.6 mm for amorolfine 5% NL plus cosmetic nail varnish group (n = 25). Also, mycological cultures of subungual debris at week 12 were negative for all subjects in both groups. Most subjects (88%) reported that cosmetic nail varnish masked their infected toenails. Additionally, cadaver human nails coated in vitro with or without cosmetic nail varnish 10 min or 24 h post amorolfine NL application all gave ZOIs on Trichophyton rubrum agar plates representing potent antifungal activity. In conclusion, cosmetic nail varnish applied post amorolfine had no effect on the subungual antifungal activity of amorolfine 5% NL or its penetration through toenails. © 2016 The Authors Mycoses published by Blackwell Verlag GmbH.

Are There Infinite Irrigation Trees?

NASA Astrophysics Data System (ADS)

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

2006-08-01

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

Trees and highway safety.

DOT National Transportation Integrated Search

2011-03-01

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

Interim hardwood tree grades for factory lumber

Treesearch

Leland F. Hanks; Leland F. Hanks

1971-01-01

Hardwood trees have for many years been measured in such a way that tree volume could be estimated; and in recent years the prediction of tree quality by using tree grades has become of interest to owners, sellers, and buyers of timber. Several tree-grading systems have been developed, but none has been publicized and used on a widespread scale. The Forest Service...

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

PubMed

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

2016-05-01

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

VC-dimension of univariate decision trees.

PubMed

Yildiz, Olcay Taner

2015-02-01

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

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

USGS Publications Warehouse

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

2013-01-01

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

Tree decay an expanded concept

Treesearch

Alex L. Shigo

1979-01-01

This publication is the final one in a series on tree decay developed in cooperation with Harold G. Marx, Research Application Staff Assistant, U.S. Department of Agriculture, Forest Service, Washington, D.C. The purpose of this publication is to clarify further the tree decay concept that expands the classical concept to include the orderly response of the tree to...

Rx for wounded trees

Treesearch

Hal Marx

1976-01-01

This booklet offers guidelines on how to care for trees to keep them healthy and to protect them from wounds. It also prescribes ways to prevent, recognize, and minimize damage by decay that most often sets in after tree wounding.

Fuzzy tree automata and syntactic pattern recognition.

PubMed

Lee, E T

1982-04-01

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

Folding and unfolding phylogenetic trees and networks.

PubMed

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

2016-12-01

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

Estimating phylogenetic trees from genome-scale data.

PubMed

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

2015-12-01

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

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

PubMed

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

2015-02-01

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

Long tree-ring chronologies provide evidence of recent tree growth decrease in a Central African tropical forest.

PubMed

Battipaglia, Giovanna; Zalloni, Enrica; Castaldi, Simona; Marzaioli, Fabio; Cazzolla-Gatti, Roberto; Lasserre, Bruno; Tognetti, Roberto; Marchetti, Marco; Valentini, Riccardo

2015-01-01

It is still unclear whether the exponential rise of atmospheric CO2 concentration has produced a fertilization effect on tropical forests, thus incrementing their growth rate, in the last two centuries. As many factors affect tree growth patterns, short -term studies might be influenced by the confounding effect of several interacting environmental variables on plant growth. Long-term analyses of tree growth can elucidate long-term trends of plant growth response to dominant drivers. The study of annual rings, applied to long tree-ring chronologies in tropical forest trees enables such analysis. Long-term tree-ring chronologies of three widespread African species were measured in Central Africa to analyze the growth of trees over the last two centuries. Growth trends were correlated to changes in global atmospheric CO2 concentration and local variations in the main climatic drivers, temperature and rainfall. Our results provided no evidence for a fertilization effect of CO2 on tree growth. On the contrary, an overall growth decline was observed for all three species in the last century, which appears to be significantly correlated to the increase in local temperature. These findings provide additional support to the global observations of a slowing down of C sequestration in the trunks of forest trees in recent decades. Data indicate that the CO2 increase alone has not been sufficient to obtain a tree growth increase in tropical trees. The effect of other changing environmental factors, like temperature, may have overridden the fertilization effect of CO2.

Long Tree-Ring Chronologies Provide Evidence of Recent Tree Growth Decrease in a Central African Tropical Forest

PubMed Central

Battipaglia, Giovanna; Zalloni, Enrica; Castaldi, Simona; Marzaioli, Fabio; Cazzolla- Gatti, Roberto; Lasserre, Bruno; Tognetti, Roberto; Marchetti, Marco; Valentini, Riccardo

2015-01-01

It is still unclear whether the exponential rise of atmospheric CO2 concentration has produced a fertilization effect on tropical forests, thus incrementing their growth rate, in the last two centuries. As many factors affect tree growth patterns, short -term studies might be influenced by the confounding effect of several interacting environmental variables on plant growth. Long-term analyses of tree growth can elucidate long-term trends of plant growth response to dominant drivers. The study of annual rings, applied to long tree-ring chronologies in tropical forest trees enables such analysis. Long-term tree-ring chronologies of three widespread African species were measured in Central Africa to analyze the growth of trees over the last two centuries. Growth trends were correlated to changes in global atmospheric CO2 concentration and local variations in the main climatic drivers, temperature and rainfall. Our results provided no evidence for a fertilization effect of CO2 on tree growth. On the contrary, an overall growth decline was observed for all three species in the last century, which appears to be significantly correlated to the increase in local temperature. These findings provide additional support to the global observations of a slowing down of C sequestration in the trunks of forest trees in recent decades. Data indicate that the CO2 increase alone has not been sufficient to obtain a tree growth increase in tropical trees. The effect of other changing environmental factors, like temperature, may have overridden the fertilization effect of CO2. PMID:25806946

Decision Tree Phytoremediation

DTIC Science & Technology

1999-12-01

aromatic hydrocarbons, and landfill leachates . Phytoremediation has been used for point and nonpoint source hazardous waste control. 1.2 Types of... Phytoremediation Prepared by Interstate Technology and Regulatory Cooperation Work Group Phytoremediation Work Team December 1999 Decision Tree...1999 2. REPORT TYPE N/A 3. DATES COVERED - 4. TITLE AND SUBTITLE Phytoremediation Decision Tree 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c

ETE: a python Environment for Tree Exploration.

PubMed

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

2010-01-13

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

ETE: a python Environment for Tree Exploration

PubMed Central

2010-01-01

Background Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale. Results Here we present the Environment for Tree Exploration (ETE), a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations. Conclusions ETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org. PMID:20070885

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

PubMed

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

2018-03-01

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

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

PubMed Central

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

2018-01-01

Abstract Consensus trees are required to summarize trees obtained through MCMC sampling of a posterior distribution, providing an overview of the distribution of estimated parameters such as topology, branch lengths, and divergence times. Numerous consensus tree construction methods are available, each presenting a different interpretation of the tree sample. The rise of morphological clock and sampled-ancestor methods of divergence time estimation, in which times and topology are coestimated, has increased the popularity of the maximum clade credibility (MCC) consensus tree method. The MCC method assumes that the sampled, fully resolved topology with the highest clade credibility is an adequate summary of the most probable clades, with parameter estimates from compatible sampled trees used to obtain the marginal distributions of parameters such as clade ages and branch lengths. Using both simulated and empirical data, we demonstrate that MCC trees, and trees constructed using the similar maximum a posteriori (MAP) method, often include poorly supported and incorrect clades when summarizing diffuse posterior samples of trees. We demonstrate that the paucity of information in morphological data sets contributes to the inability of MCC and MAP trees to accurately summarise of the posterior distribution. Conversely, majority-rule consensus (MRC) trees represent a lower proportion of incorrect nodes when summarizing the same posterior samples of trees. Thus, we advocate the use of MRC trees, in place of MCC or MAP trees, in attempts to summarize the results of Bayesian phylogenetic analyses of morphological data. PMID:29106675

Irrational exuberance for resolved species trees.

PubMed

Hahn, Matthew W; Nakhleh, Luay

2016-01-01

Phylogenomics has largely succeeded in its aim of accurately inferring species trees, even when there are high levels of discordance among individual gene trees. These resolved species trees can be used to ask many questions about trait evolution, including the direction of change and number of times traits have evolved. However, the mapping of traits onto trees generally uses only a single representation of the species tree, ignoring variation in the gene trees used to construct it. Recognizing that genes underlie traits, these results imply that many traits follow topologies that are discordant with the species topology. As a consequence, standard methods for character mapping will incorrectly infer the number of times a trait has evolved. This phenomenon, dubbed "hemiplasy," poses many problems in analyses of character evolution. Here we outline these problems, explaining where and when they are likely to occur. We offer several ways in which the possible presence of hemiplasy can be diagnosed, and discuss multiple approaches to dealing with the problems presented by underlying gene tree discordance when carrying out character mapping. Finally, we discuss the implications of hemiplasy for general phylogenetic inference, including the possible drawbacks of the widespread push for "resolved" species trees. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

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

Treesearch

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

2015-01-01

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

Nodal distances for rooted phylogenetic trees.

PubMed

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

2010-08-01

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

Compartmentalization of decay in trees

Treesearch

Alex L. Shigo

1985-01-01

Trees have a spectacular survival record. Over a period of more than 400 million years they have evolved as the tallest, most massive and longest-lived organisms ever to inhabit the earth. Yet trees lack a means of defense that almost every animal has: trees cannot move away from destructive forces. Because they cannot move, all types of living and nonliving enemies—...

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.…

Tree growth and management in Ugandan agroforestry systems: effects of root pruning on tree growth and crop yield.

PubMed

Wajja-Musukwe, Tellie-Nelson; Wilson, Julia; Sprent, Janet I; Ong, Chin K; Deans, J Douglas; Okorio, John

2008-02-01

Tree root pruning is a potential tool for managing belowground competition when trees and crops are grown together in agroforestry systems. We investigated the effects of tree root pruning on shoot growth and root distribution of Alnus acuminata (H.B. & K.), Casuarina equisetifolia L., Grevillea robusta A. Cunn. ex R. Br., Maesopsis eminii Engl. and Markhamia lutea (Benth.) K. Schum. and on yield of adjacent crops in sub-humid Uganda. The trees were 3 years old at the commencement of the study, and most species were competing strongly with crops. Tree roots were pruned 41 months after planting by cutting and back-filling a trench to a depth of 0.3 m, at a distance of 0.3 m from the trees, on one side of the tree row. The trench was reopened and roots recut at 50 and 62 months after planting. We assessed the effects on tree growth and root distribution over a 3 year period, and crop yield after the third root pruning at 62 months. Overall, root pruning had only a slight effect on aboveground tree growth: height growth was unaffected and diameter growth was reduced by only 4%. A substantial amount of root regrowth was observed by 11 months after pruning. Tree species varied in the number and distribution of roots, and C. equisetifolia and M. lutea had considerably more roots per unit of trunk volume than the other species, especially in the surface soil layers. Casuarina equisetifolia and M. eminii were the tree species most competitive with crops and G. robusta and M. lutea the least competitive. Crop yield data provided strong evidence of the redistribution of root activity following root pruning, with competition increasing on the unpruned side of tree rows. Thus, one-sided root pruning will be useful in only a few circumstances.

Hydraulic limits on tree performance: transpiration, carbon gain and growth of trees

Treesearch

Melvin T. Tyree

2003-01-01

The state of knowledge concerning the influences of tree size, xylem dysfunction, growth conditions, and within-species and between species genetics is reviewed. It is concluded that high plant hydraulic conductance is necessary for high productivity in forest trees, and this being the case, the implications for commercial forestry require further study.

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

Treesearch

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

1989-01-01

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

Simulating Urban Tree Effects on Air, Water, and Heat Pollution Mitigation: iTree-Hydro Model

NASA Astrophysics Data System (ADS)

Yang, Y.; Endreny, T. A.; Nowak, D.

2011-12-01

Urban and suburban development changes land surface thermal, radiative, porous, and roughness properties and pollutant loading rates, with the combined effect leading to increased air, water, and heat pollution (e.g., urban heat islands). In this research we present the USDA Forest Service urban forest ecosystem and hydrology model, iTree Eco and Hydro, used to analyze how tree cover can deliver valuable ecosystem services to mitigate air, water, and heat pollution. Air pollution mitigation is simulated by dry deposition processes based on detected pollutant levels for CO, NO2, SO2, O3 and atmospheric stability and leaf area indices. Water quality mitigation is simulated with event mean concentration loading algorithms for N, P, metals, and TSS, and by green infrastructure pollutant filtering algorithms that consider flow path dispersal areas. Urban cooling considers direct shading and indirect evapotranspiration. Spatially distributed estimates of hourly tree evapotranspiration during the growing season are used to estimate human thermal comfort. Two main factors regulating evapotranspiration are soil moisture and canopy radiation. Spatial variation of soil moisture is represented by a modified urban topographic index and radiation for each tree is modified by considering aspect, slope and shade from surrounding buildings or hills. We compare the urban cooling algorithms used in iTree-Hydro with the urban canopy and land surface physics schemes used in the Weather Research and Forecasting model. We conclude by identifying biophysical feedbacks between tree-modulated air and water quality environmental services and how these may respond to urban heating and cooling. Improvements to this iTree model are intended to assist managers identify valuable tree services for urban living.

Tree demography dominates long-term growth trends inferred from tree rings.

PubMed

Brienen, Roel J W; Gloor, Manuel; Ziv, Guy

2017-02-01

Understanding responses of forests to increasing CO 2 and temperature is an important challenge, but no easy task. Tree rings are increasingly used to study such responses. In a recent study, van der Sleen et al. (2014) Nature Geoscience, 8, 4 used tree rings from 12 tropical tree species and find that despite increases in intrinsic water use efficiency, no growth stimulation is observed. This challenges the idea that increasing CO 2 would stimulate growth. Unfortunately, tree ring analysis can be plagued by biases, resulting in spurious growth trends. While their study evaluated several biases, it does not account for all. In particular, one bias may have seriously affected their results. Several of the species have recruitment patterns, which are not uniform, but clustered around one specific year. This results in spurious negative growth trends if growth rates are calculated in fixed size classes, as 'fast-growing' trees reach the sampling diameter earlier compared to slow growers and thus fast growth rates tend to have earlier calendar dates. We assessed the effect of this 'nonuniform age bias' on observed growth trends and find that van der Sleen's conclusions of a lack of growth stimulation do not hold. Growth trends are - at least partially - driven by underlying recruitment or age distributions. Species with more clustered age distributions show more negative growth trends, and simulations to estimate the effect of species' age distributions show growth trends close to those observed. Re-evaluation of the growth data and correction for the bias result in significant positive growth trends of 1-2% per decade for the full period, and 3-7% since 1950. These observations, however, should be taken cautiously as multiple biases affect these trend estimates. In all, our results highlight that tree ring studies of long-term growth trends can be strongly influenced by biases if demographic processes are not carefully accounted for. © 2016 The Authors. Global

Comparative Use of Tree Leaves, Needles, Tree Barks and Lichens for Air Pollution Biomonitoring

NASA Astrophysics Data System (ADS)

El Khoukhi, T.; Cherkaoui El Moursli, R.; Chouak, A.; Moutia, Z.; Lferde, M.; Senhou, A.; Gaudry, A.; Ayrault, S.; Chakir, M.

2005-01-01

The aim of this work is to determine the most suitable bioaccumulators for air pollution survey in Morocco. For this, we compare in this paper heavy metals uptake efficiencies for different types of biomonitors: leaves of oak and eucalyptus trees, needles of coniferous trees, tree-barks and lichens collected at the same site. Instrumental neutron activation analysis using the k0 method (INAA-k0) was used for its adequate characteristics to analyze accurately a wide number of elements. Reference materials were analyzed to check the reliability and the accuracy of this technique. The results obtained for all these bioaccumulators lead to the following conclusions. For the major elements, leaves and needles are more accumulating than tree barks and lichens. While for the intermediate and trace elements, there is an obvious accumulation in lichens in comparison with tree barks, leaves and needles. This work shows the possibility to use these four bioaccumulators according to their availability in an area. It will be useful however to set up an inter calibration between these bioaccumulators.

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

PubMed

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

2012-10-01

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

The dynamics of strangling among forest trees.

PubMed

Okamoto, Kenichi W

2015-11-07

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

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.

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

PubMed

Vaniya, Arpana; Fiehn, Oliver

2015-06-01

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

Flow around a Living Tree

NASA Astrophysics Data System (ADS)

Ishikawa, Hitoshi; Amano, Suguru; Yakushiji, Kenta

Flow around a living tree was investigated as basic research of a windbreak forest. A type of conifer, which is named “goldcrest, ” was used as the test piece in a wind tunnel experiment. The drag coefficient of the living tree was measured in the range of a mean flow velocity of 5˜15m/s. The drag coefficient of the living tree was less than that of a two-dimensional circular cylinder. Because flow passes through the tree’s crown which has the permeability of branches and leaves, the drag coefficient was decreased as the flow velocity was increased. Moreover, the flexibility is that the bole of a living tree also plays an important role in drag reduction, bending itself so as to decrease the projected area. In the wake behind the living tree, reverse flow was found at further downstream region than the case of a circular cylinder.

An efficient and extensible approach for compressing phylogenetic trees.

PubMed

Matthews, Suzanne J; Williams, Tiffani L

2011-10-18

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

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 § 1214.3...

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 § 1214.3...

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 § 1214.3...

Tree injuries from mechanized logging

Treesearch

Richard M. Godman

1992-01-01

Small trees in even-aged northern hardwood stands suffer the most mechanical damage when stands are thinned for the first time. From 15 to 35 percent of the trees may be damaged; a quarter of the trees (but usually less than 20 per acre) can be seriously damaged by having at least 50 square inches of the cambium exposed. Bole damage is most common, followed by root and...

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

PubMed Central

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

2015-01-01

Emamectin benzoate, an insecticide derived from the avermectin family of natural products, has a unique translocation behavior in trees when applied by tree micro injection (TMI), which can result in protection from insect pests (foliar and borers) for several years. Active ingredient imported into leaves was measured at the end of season in the fallen leaves of treated horse chestnut (Aesculus hippocastanum) trees. The dissipation of emamectin benzoate in these leaves seems to be biphasic and depends on the decomposition of the leaf. In compost piles, where decomposition of leaves was fastest, a cumulative emamectin benzoate degradation half-life time of 20 d was measured. In leaves immersed in water, where decomposition was much slower, the degradation half-life time was 94 d, and in leaves left on the ground in contact with soil, where decomposition was slowest, the degradation half-life time was 212 d. The biphasic decline and the correlation with leaf decomposition might be attributed to an extensive sorption of emamectin benzoate residues to leaf macromolecules. This may also explain why earthworms ingesting leaves from injected trees take up very little emamectin benzoate and excrete it with the feces. Furthermore, no emamectin benzoate was found in water containing decomposing leaves from injected trees. It is concluded, that emamectin benzoate present in abscised leaves from horse chestnut trees injected with the insecticide is not available to nontarget organisms present in soil or water bodies. Environ Toxicol Chem 2014;9999:1–6. © 2014 The Authors. Published 2014 SETAC PMID:25363584

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

NASA Astrophysics Data System (ADS)

Pawlik, Łukasz; Kasprzak, Marek

2018-01-01

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

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)

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)

The space of ultrametric phylogenetic trees.

PubMed

Gavryushkin, Alex; Drummond, Alexei J

2016-08-21

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

Differences in xylogenesis between dominant and suppressed trees.

PubMed

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

2018-05-01

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

75 FR 25103 - Tree Assistance Program

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-07

... 1416 RIN 0560-AH96 Tree Assistance Program AGENCY: Farm Service Agency and Commodity Credit Corporation, USDA. ACTION: Final rule. SUMMARY: This rule implements specific requirements for the Tree Assistance... provides disaster assistance to eligible orchardists and nursery tree growers to replant or rehabilitate...

Genomics of Tropical Fruit Tree Crops

USDA-ARS?s Scientific Manuscript database

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...

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

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

Gu, Shengyin; Anderson, Iain; Kunin, Victor

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.

Objective consensus from decision trees.

PubMed

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

2014-12-05

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

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

PubMed

Leekitcharoenphon, Pimlapas; Kaas, Rolf S; Thomsen, Martin Christen Frølund; Friis, Carsten; Rasmussen, Simon; Aarestrup, Frank M

2012-01-01

The advances and decreasing economical cost of whole genome sequencing (WGS), will soon make this technology available for routine infectious disease epidemiology. In epidemiological studies, outbreak isolates have very little diversity and require extensive genomic analysis to differentiate and classify isolates. One of the successfully and broadly used methods is analysis of single nucletide polymorphisms (SNPs). Currently, there are different tools and methods to identify SNPs including various options and cut-off values. Furthermore, all current methods require bioinformatic skills. Thus, we lack a standard and simple automatic tool to determine SNPs and construct phylogenetic tree from WGS data. Here we introduce snpTree, a server for online-automatic SNPs analysis. This tool is composed of different SNPs analysis suites, perl and python scripts. snpTree can identify SNPs and construct phylogenetic trees from WGS as well as from assembled genomes or contigs. WGS data in fastq format are aligned to reference genomes by BWA while contigs in fasta format are processed by Nucmer. SNPs are concatenated based on position on reference genome and a tree is constructed from concatenated SNPs using FastTree and a perl script. The online server was implemented by HTML, Java and python script.The server was evaluated using four published bacterial WGS data sets (V. cholerae, S. aureus CC398, S. Typhimurium and M. tuberculosis). The evaluation results for the first three cases was consistent and concordant for both raw reads and assembled genomes. In the latter case the original publication involved extensive filtering of SNPs, which could not be repeated using snpTree. The snpTree server is an easy to use option for rapid standardised and automatic SNP analysis in epidemiological studies also for users with limited bioinformatic experience. The web server is freely accessible at http://www.cbs.dtu.dk/services/snpTree-1.0/.

Reconciliation of Gene and Species Trees

PubMed Central

Rusin, L. Y.; Lyubetskaya, E. V.; Gorbunov, K. Y.; Lyubetsky, V. A.

2014-01-01

The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating horizontal gene transfers, binarization and reconciliation of polytomous trees, and construction of species trees and scenarios. The review does not intend to cover the vast diversity of literature published on these subjects. Instead, the authors strived to overview the problem of the evolutionary scenario as a central concept in many areas of evolutionary research. The second part provides detailed mathematical proofs for the solutions of two problems: (i) inferring a gene evolution along a species tree accounting for various types of evolutionary events and (ii) trees reconciliation into a single species tree when only gene duplications and losses are allowed. All proposed algorithms have a cubic time complexity and are mathematically proved to find exact solutions. Solving algorithms for problem (ii) can be naturally extended to incorporate horizontal transfers, other evolutionary events, and time scales on the species tree. PMID:24800245

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

PubMed

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

2018-01-01

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

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)…

Single-tree nut immunotherapy attenuates allergic reactions in mice with hypersensitivity to multiple tree nuts.

PubMed

Kulis, Mike; Li, Yifan; Lane, Hannah; Pons, Laurent; Burks, Wesley

2011-01-01

Allergic reactions to tree nuts are often severe and are outgrown in less than 10% of diagnosed patients. To determine whether treatment of underlying tree nut sensitization will prevent allergic reactions to cross-reacting tree nuts and to determine the effects of single-tree nut immunotherapy on true multi-tree nut sensitization. Cross-reactivity model: Cashew-sensitized mice underwent immunotherapy with cashew and were subsequently challenged with cashew and pistachio. Multisensitization model: Cashew plus walnut-sensitized mice were treated with cashew alone, walnut alone, or both cashew and walnut and then underwent challenges to cashew and walnut. Challenges were assessed on the basis of symptoms, changes in body temperature, and mouse mast cell protease-1 release. In the cross-reactivity model, cashew immunotherapy completely prevented allergic reactions on challenges with cashew or the cross-reactive pistachio. In the multisensitization model, mice with cashew plus walnut allergy were significantly protected from anaphylactic reactions on cashew challenge in both the cashew-alone and walnut-alone immunotherapy groups. Results from the walnut challenge demonstrated significantly decreased allergic responses in the walnut immunotherapy group, whereas mice in the cashew immunotherapy group experienced significantly lower symptoms. In the cross-reactivity model, immunotherapy effectively decreased IL-4 and IL-5 production and increased IL-12 relative to placebo while also inducing a 5-fold increase in specific IgG(1). Single-tree nut immunotherapy can effectively decrease allergic responses in both the cross-reactivity and multisensitization mouse models. Further studies are needed to determine which single-tree nut immunotherapies will be most effective for specific multi-tree nut allergy profiles. Copyright © 2010 American Academy of Allergy, Asthma & Immunology. Published by Mosby, Inc. All rights reserved.

Sampling the quality of hardwood trees

Treesearch

Adrian M. Gilbert

1959-01-01

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

Clustering Tree-structured Data on Manifold

PubMed Central

Lu, Na; Miao, Hongyu

2016-01-01

Tree-structured data usually contain both topological and geometrical information, and are necessarily considered on manifold instead of Euclidean space for appropriate data parameterization and analysis. In this study, we propose a novel tree-structured data parameterization, called Topology-Attribute matrix (T-A matrix), so the data clustering task can be conducted on matrix manifold. We incorporate the structure constraints embedded in data into the non-negative matrix factorization method to determine meta-trees from the T-A matrix, and the signature vector of each single tree can then be extracted by meta-tree decomposition. The meta-tree space turns out to be a cone space, in which we explore the distance metric and implement the clustering algorithm based on the concepts like Fréchet mean. Finally, the T-A matrix based clustering (TAMBAC) framework is evaluated and compared using both simulated data and real retinal images to illus trate its efficiency and accuracy. PMID:26660696

An efficient and extensible approach for compressing phylogenetic trees

PubMed Central

2011-01-01

Background Biologists require new algorithms to efficiently compress and store their large collections of phylogenetic trees. Our previous work showed that TreeZip is a promising approach for compressing phylogenetic trees. In this paper, we extend our TreeZip algorithm by handling trees with weighted branches. Furthermore, by using the compressed TreeZip file as input, we have designed an extensible decompressor that can extract subcollections of trees, compute majority and strict consensus trees, and merge tree collections using set operations such as union, intersection, and set difference. Results On unweighted phylogenetic trees, TreeZip is able to compress Newick files in excess of 98%. On weighted phylogenetic trees, TreeZip is able to compress a Newick file by at least 73%. TreeZip can be combined with 7zip with little overhead, allowing space savings in excess of 99% (unweighted) and 92%(weighted). Unlike TreeZip, 7zip is not immune to branch rotations, and performs worse as the level of variability in the Newick string representation increases. Finally, since the TreeZip compressed text (TRZ) file contains all the semantic information in a collection of trees, we can easily filter and decompress a subset of trees of interest (such as the set of unique trees), or build the resulting consensus tree in a matter of seconds. We also show the ease of which set operations can be performed on TRZ files, at speeds quicker than those performed on Newick or 7zip compressed Newick files, and without loss of space savings. Conclusions TreeZip is an efficient approach for compressing large collections of phylogenetic trees. The semantic and compact nature of the TRZ file allow it to be operated upon directly and quickly, without a need to decompress the original Newick file. We believe that TreeZip will be vital for compressing and archiving trees in the biological community. PMID:22165819

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

Treesearch

Christopher Woodall; James Westfall

2009-01-01

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

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

NASA Astrophysics Data System (ADS)

Wang, Le

2003-10-01

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

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

PubMed Central

Neupane, Prem R.

2017-01-01

The world’s forests play a pivotal role in the mitigation of global climate change. By photosynthesis they remove CO2 from the atmosphere and store carbon in their biomass. While old trees are generally acknowledged for a long carbon residence time, there is no consensus on their contribution to carbon accumulation due to a lack of long-term individual tree data. Tree ring analyses, which use anatomical differences in the annual formation of wood for dating growth zones, are a retrospective approach that provides growth patterns of individual trees over their entire lifetime. We developed time series of diameter growth and related annual carbon accumulation for 61 trees of the species Cedrela odorata L. (Meliacea), Hymenaea courbaril L. (Fabacea) and Goupia glabra Aubl. (Goupiacea). The trees grew in unmanaged tropical wet-forests of Suriname and reached ages from 84 to 255 years. Most of the trees show positive trends of diameter growth and carbon accumulation over time. For some trees we observed fluctuating growth—periods of lower growth alternate with periods of increased growth. In the last quarter of their lifetime trees accumulate on average between 39 percent (C. odorata) and 50 percent (G. glabra) of their final carbon stock. This suggests that old-growth trees in tropical forests do not only contribute to carbon stocks by long carbon resistance times, but maintain high rates of carbon accumulation at later stages of their life time. PMID:28813429

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

PubMed

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

2017-01-01

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

The gravity apple tree

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.

Relationships between tree size, crown shape, gender segregation and sex allocation in Pinus halepensis, a Mediterranean pine tree.

PubMed

Ne'eman, Gidi; Goubitz, Shirrinka; Werger, Marinus J A; Shmida, Avi

2011-07-01

Sex allocation has been studied mainly in small herbaceous plants but much less in monoecious wind-pollinated trees. The aim of this study was to explore changes in gender segregation and sex allocation by Pinus halepensis, a Mediterranean lowland pine tree, within tree crowns and between trees differing in their size or crown shape. The production of new male and female cones and sex allocation of biomass, nitrogen and phosphorus were studied. The relationship between branch location, its reproductive status and proxies of branch vigour was also studied. Small trees produced only female cones, but, as trees grew, they produced both male and female cones. Female cones were produced mainly in the upper part of the crown, and male cones in its middle and lower parts. Lateral branch density was correlated with the number of male but not female cones; lateral branches were more dense in large than in small trees and even denser in hemispherical trees. Apical branches grew faster, were thicker and their phosphorus concentration was higher than in lateral shoots. Nitrogen concentration was higher in cone-bearing apical branches than in apical vegetative branches and in lateral branches with or without cones. Allocation to male relative to female function increased with tree size as predicted by sex allocation theory. The adaptive values of sex allocation and gender segregation patterns in P. halepensis, in relation to its unique life history, are demonstrated and discussed. Small trees produce only female cones that have a higher probability of being pollinated than the probability of male cones pollinating; the female-first strategy enhances population spread. Hemispherical old trees are loaded with serotinous cones that supply enough seeds for post-fire germination; thus, allocation to males is more beneficial than to females.

Trees as templates for tropical litter arthropod diversity.

PubMed

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

2010-09-01

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

Tree biology and dendrochemistry

Treesearch

Kevin T. Smith; Walter C. Shortle

1996-01-01

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

Does predation contribute to tree diversity?

Treesearch

Brian Beckage; James S. Clark

2005-01-01

Seed and seedling predation may differentially affect competitively superior tree species to increase the relative recruitment success of poor competitors and contribute to the coexistence of tree species. We examined the effect of seed and seedling predation on the seedling recruitment of three tree species, Acer rubrum (red maple), ...

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

PubMed

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

2017-03-01

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

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

PubMed

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

2006-09-01

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

7 CFR 1437.306 - Christmas tree crops.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 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 crop and may generate a claim for benefits under this part only if the tree was grown exclusively for...

Molecular basis of angiosperm tree architecture.

PubMed

Hollender, Courtney A; Dardick, Chris

2015-04-01

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

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

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

PubMed Central

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

2018-01-01

Mensuration of tree growth habits is of considerable importance for understanding forest ecosystem processes and forest biophysical responses to climate changes. However, the complexity of tree crown morphology that is typically formed after many years of growth tends to render it a non-trivial task, even for the state-of-the-art 3D forest mapping technology—light detection and ranging (LiDAR). Fortunately, botanists have deduced the large structural diversity of tree forms into only a limited number of tree architecture models, which can present a-priori knowledge about tree structure, growth, and other attributes for different species. This study attempted to recruit Hallé architecture models (HAMs) into LiDAR mapping to investigate tree growth habits in structure. First, following the HAM-characterized tree structure organization rules, we run the kernel procedure of tree species classification based on the LiDAR-collected point clouds using a support vector machine classifier in the leave-one-out-for-cross-validation mode. Then, the HAM corresponding to each of the classified tree species was identified based on expert knowledge, assisted by the comparison of the LiDAR-derived feature parameters. Next, the tree growth habits in structure for each of the tree species were derived from the determined HAM. In the case of four tree species growing in the boreal environment, the tests indicated that the classification accuracy reached 85.0%, and their growth habits could be derived by qualitative and quantitative means. Overall, the strategy of recruiting conventional HAMs into LiDAR mapping for investigating tree growth habits in structure was validated, thereby paving a new way for efficiently reflecting tree growth habits and projecting forest structure dynamics. PMID:29515616

Decision tree modeling using R.

PubMed

Zhang, Zhongheng

2016-08-01

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

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

Treesearch

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

2003-01-01

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

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

Treesearch

Thomas Brandeis; KaDonna Randolph; Mike Strub

2009-01-01

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

Field guide to red tree vole nests

Treesearch

Damon B. Lesmeister; James K. Swingle

2017-01-01

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

Visualization of time-varying natural tree data

Treesearch

S. Brasch; L. Linsen; E.G. McPherson

2007-01-01

Given a set of global (natural) tree parameters measured for many specimens of different ages for a range of species, we have developed a tool that visualizes these parameters over time. The parameters include measures of tree dimensions like heights, diameters, and crown shape, and measures of costs and benefits for growing the tree. We visualize the tree dimensions...

7 CFR 1437.306 - Christmas tree crops.

Code of Federal Regulations, 2014 CFR

2014-01-01

... commercial use as a Christmas tree, and only if other requirements of this section are met. (b) The unit of... 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...

7 CFR 1437.306 - Christmas tree crops.

Code of Federal Regulations, 2013 CFR

2013-01-01

... commercial use as a Christmas tree, and only if other requirements of this section are met. (b) The unit of... 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...

7 CFR 1437.306 - Christmas tree crops.

Code of Federal Regulations, 2011 CFR

2011-01-01

... commercial use as a Christmas tree, and only if other requirements of this section are met. (b) The unit of... 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...

7 CFR 1437.306 - Christmas tree crops.

Code of Federal Regulations, 2012 CFR

2012-01-01

... commercial use as a Christmas tree, and only if other requirements of this section are met. (b) The unit of... 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...

The '06 trap trees in '07

Treesearch

Andrea C. Anulewicz; Deborah G. McCullough; Therese M. Poland; David Cappaert

2008-01-01

To date, use of girdled trap trees remain the most effective method employed by regulatory and resource management agencies for detecting low-density populations of emerald ash borer (EAB), Agrilus planipennis Fairmaire. Locating suitable trees can be difficult, and felling and debarking trap trees is expensive. Alternative options for EAB detection...

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…

California tree seed zones

Treesearch

John M. Buck; Ronald S. Adams; Jerrold Cone; M. Thompson Conkle; William J. Libby; Cecil J. Eden; Michel J. Knight

1970-01-01

California forest tree seed zones were established originally by Fowells (1946), with revisions proposed by Roy (1963) and Schubert (1966). The Forest Tree Seed Committee of the Northern California Section, Society of American Foresters, has revised the original zones and updated the recording system described in the earlier reports. Fowells' (1946) Research Note...

The tree BVOC index

Treesearch

J.R. Simpson; E.G. McPherson

2011-01-01

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

Dependency Tree Annotation Software

DTIC Science & Technology

2015-11-01

formats, and it provides numerous options for customizing how dependency trees are displayed. Built entirely in Java , it can run on a wide range of...tree can be saved as an image, .mxe (a mxGraph editing file), a .conll file, and several other file formats. DTE uses the open source Java version

Uncertain decision tree inductive inference

NASA Astrophysics Data System (ADS)

Zarban, L.; Jafari, S.; Fakhrahmad, S. M.

2011-10-01

Induction is the process of reasoning in which general rules are formulated based on limited observations of recurring phenomenal patterns. Decision tree learning is one of the most widely used and practical inductive methods, which represents the results in a tree scheme. Various decision tree algorithms have already been proposed such as CLS, ID3, Assistant C4.5, REPTree and Random Tree. These algorithms suffer from some major shortcomings. In this article, after discussing the main limitations of the existing methods, we introduce a new decision tree induction algorithm, which overcomes all the problems existing in its counterparts. The new method uses bit strings and maintains important information on them. This use of bit strings and logical operation on them causes high speed during the induction process. Therefore, it has several important features: it deals with inconsistencies in data, avoids overfitting and handles uncertainty. We also illustrate more advantages and the new features of the proposed method. The experimental results show the effectiveness of the method in comparison with other methods existing in the literature.

Nitrogen nutrition of poplar trees.

PubMed

Rennenberg, H; Wildhagen, H; Ehlting, B

2010-03-01

Many forest ecosystems have evolved at sites with growth-limiting nitrogen (N) availability, low N input from external sources and high ecosystem internal cycling of N. By contrast, many poplar species are frequent constituents of floodplain forests where they are exposed to a significant ecosystem external supply of N, mainly nitrate, in the moving water table. Therefore, nitrate is much more important for N nutrition of these poplar species than for many other tree species. We summarise current knowledge of nitrate uptake and its regulation by tree internal signals, as well as acquisition of ammonium and organic N from the soil. Unlike herbaceous plants, N nutrition of trees is sustained by seasonal, tree internal cycling. Recent advances in the understanding of seasonal storage and mobilisation in poplar bark and regulation of these processes by temperature and daylength are addressed. To explore consequences of global climate change on N nutrition of poplar trees, responses of N uptake and metabolism to increased atmospheric CO(2) and O(3) concentrations, increased air and soil temperatures, drought and salt stress are highlighted.

Clarifying the effects of dwarfing rootstock on vegetative and reproductive growth during tree development: a study on apple trees.

PubMed

Costes, E; García-Villanueva, E

2007-08-01

Despite the widespread use of dwarfing rootstocks in the fruit-tree industry, their impact on tree architectural development and possible role in the within-tree balance between growth and flowering are still poorly understood, in particular during the early years of growth. The present study addressed this question in apple trees, through a detailed analysis of shoot populations, i.e. both vegetative and flowering shoots, during tree development. Architectural databases were constructed for trees of two cultivars that were either own-rooted or grafted on dwarfing rootstock. Within-tree shoot demographics and annual shoot characteristics, i.e. their dimensions, number of laterals and flowering, were observed from the first to the fifth year of growth and compared among scion/root system combinations. Differences in axis demographics appeared among scion/root system combinations after the second year of growth. Differences were found (a) in the number of long axes and (b) the number of medium axes. Dwarfing rootstock reduced the total number of axes developed in a tree, and this reduction resulted from proportionally more medium axes and spurs than long axes. The life span of spurs was also shortened. These phenomena appeared after an increase in flowering that started in the second year of growth and involved both axillary and terminal positions. Flowering regularity was also increased in grafted trees. These results confirm that the number of long shoots and flowering potential depend on the cultivar. They indicate that tree architectural plasticity in response to its root system mainly derives from the number of medium shoots developed and follows priorities within the whole tree axis population. There was also evidence for dwarfing rootstock involvement in adjusting the flowering abundance and that differences in flowering occurrence take precedence over those regarding vegetative growth during tree development.

TreeWatch.net: A Water and Carbon Monitoring and Modeling Network to Assess Instant Tree Hydraulics and Carbon Status.

PubMed

Steppe, Kathy; von der Crone, Jonas S; De Pauw, Dirk J W

2016-01-01

TreeWatch.net is an initiative that has been developed to watch trees grow and function in real-time. It is a water- and carbon-monitoring and modeling network, in which high-quality measurements of sap flow and stem diameter variation are collected on individual trees. Automated data processing using a cloud service enables instant visualization of water movement and radial stem growth. This can be used to demonstrate the sensitivity of trees to changing weather conditions, such as drought, heat waves, or heavy rain showers. But TreeWatch.net's true innovation lies in its use of these high-precision harmonized data to also parameterize process-based tree models in real-time, which makes displaying the much-needed mechanisms underlying tree responses to climate change possible. Continuous simulation of turgor to describe growth processes and long-term time series of hydraulic resistance to assess drought-vulnerability in real-time are only a few of the opportunities our approach offers. TreeWatch.net has been developed with the view to be complementary to existing forest monitoring networks and with the aim to contribute to existing dynamic global vegetation models. It provides high-quality data and real-time simulations in order to advance research on the impact of climate change on the biological response of trees and forests. Besides its application in natural forests to answer climate-change related scientific and political questions, we also envision a broader societal application of TreeWatch.net by selecting trees in nature reserves, public areas, cities, university areas, schoolyards, and parks to teach youngsters and create public awareness on the effects of changing weather conditions on trees and forests in this era of climate change.

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

Analyzing and synthesizing phylogenies using tree alignment graphs.

PubMed

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

2013-01-01

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

Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs

PubMed Central

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

2013-01-01

Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe. PMID:24086118

Epicormic branching on hardwood trees bordering forest openings

Treesearch

G.R., Jr. Trimble; Donald W. Seegrist; Donald W. Seegrist

1973-01-01

Epicormic branching in hardwoods can degrade logs and reduce the dollar returns from growing trees. A study made around clearcut openings of various sizes showed that the following variables were related to the degree of epicormic branching on trees bordering the openings: size of opening, species, tree dominance class, exposure of tree bole, and position on tree bole...

Do trees smart from ozone

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

Not Available

Douglas-firs near Eatonville, Washington - 70 miles south of Seattle - are getting doses of ozone pollution at levels regularly found in Los Angeles. Ozone levels of 220 parts per billion (ppb) can make your eyes smart and give your Aunt Edna a doozy of a headache. University of Washington researchers are now trying to find if Douglas-fir is adversely affected by 220 ppb of ozone. They are also studying whether individual branches can reveal how whole trees respond to pollutants. Studying entire trees is tough so researchers hope to take the pulse of a tree by examining its branches.more » At the university's experimental forest, researchers have placed 12-foot-tall plastic-covered corrals around six Douglas-firs, each nine or 10 years old and up to 15 feet tall. Three of the trees receive filtered air while three others are blasted with 220 ppb of ozone for eight hours each day. Four individual branches on each tree are encased in their own plastic chambers. Two are dosed with filtered air and two with ozone. To date, the UW research is the only study in the US combining branch chambers with whole tree measurements. Now in its second year, the experiment is expected to yield information about growth and foliage health by measuring respiration, chlorophyll, photosynthesis, and nutrient uptake. Loss of tree vigor could lead to increased problems with pathogens and insects. In the summer of '88, surprisingly high levels of ozone - up to 196 ppb - were detected in forests downwind from Seattle, worse than the urban areas themselves.« less

Climate variability drives recent tree mortality in Europe.

PubMed

Neumann, Mathias; Mues, Volker; Moreno, Adam; Hasenauer, Hubert; Seidl, Rupert

2017-11-01

Tree mortality is an important process in forest ecosystems, frequently hypothesized to be highly climate sensitive. Yet, tree death remains one of the least understood processes of forest dynamics. Recently, changes in tree mortality have been observed in forests around the globe, which could profoundly affect ecosystem functioning and services provisioning to society. We describe continental-scale patterns of recent tree mortality from the only consistent pan-European forest monitoring network, identifying recent mortality hotspots in southern and northern Europe. Analyzing 925,462 annual observations of 235,895 trees between 2000 and 2012, we determine the influence of climate variability and tree age on interannual variation in tree mortality using Cox proportional hazard models. Warm summers as well as high seasonal variability in precipitation increased the likelihood of tree death. However, our data also suggest that reduced cold-induced mortality could compensate increased mortality related to peak temperatures in a warming climate. Besides climate variability, age was an important driver of tree mortality, with individual mortality probability decreasing with age over the first century of a trees life. A considerable portion of the observed variation in tree mortality could be explained by satellite-derived net primary productivity, suggesting that widely available remote sensing products can be used as an early warning indicator of widespread tree mortality. Our findings advance the understanding of patterns of large-scale tree mortality by demonstrating the influence of seasonal and diurnal climate variation, and highlight the potential of state-of-the-art remote sensing to anticipate an increased likelihood of tree mortality in space and time. © 2017 John Wiley & Sons Ltd.

Reclamation: what about trees

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

Kolar, C.A.; Ashby, W.C.

A five-year research programme was started in 1978 in the Botany Department of Southern Illinois University to evaluate the effect of reclamation practices on tree survival and growth. The project was initiated as a direct result of reports from Illinois and Indiana of tree-planting failures on mined lands reclaimed to current regulation standards.

Northern Mountain and Prairie Community Tree Guide

Treesearch

E.G. McPherson; J.R. Simpson; P.J. Peper; S.E. Maco; Q. Xiao; P.J. Hoefer

2003-01-01

This tree guide quantifies benefits and costs for typical large-, medium-, small-stature, deciduous trees, as well as a conifer. The analysis assumed that trees were planted in a residential yard site or a public (street/park) site, under a 40-year time frame, and having a 60% survival rate. Tree care costs were based on findings from a survey of municipal and...

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.

Critical wind speed at which trees break.

PubMed

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

2016-02-01

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

Fault trees and sequence dependencies

NASA Technical Reports Server (NTRS)

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

1990-01-01

One of the frequently cited shortcomings of fault-tree models, their inability to model so-called sequence dependencies, is discussed. Several sources of such sequence dependencies are discussed, and new fault-tree gates to capture this behavior are defined. These complex behaviors can be included in present fault-tree models because they utilize a Markov solution. The utility of the new gates is demonstrated by presenting several models of the fault-tolerant parallel processor, which include both hot and cold spares.

Comprehensive decision tree models in bioinformatics.

PubMed

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

2012-01-01

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

Comprehensive Decision Tree Models in Bioinformatics

PubMed Central

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

2012-01-01

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

On estimation in k-tree sampling

Treesearch

Christoph Kleinn; Frantisek Vilcko

2007-01-01

The plot design known as k-tree sampling involves taking the k nearest trees from a selected sample point as sample trees. While this plot design is very practical and easily applied in the field for moderate values of k, unbiased estimation remains a problem. In this article, we give a brief introduction to the...

Mathematical form models of tree trunks

Treesearch

Rudolfs Ozolins

2000-01-01

Assortment structure analysis of tree trunks is a characteristic and proper problem that can be solved by using mathematical modeling and standard computer programs. Mathematical form model of tree trunks consists of tapering curve equations and their parameters. Parameters for nine species were obtained by processing measurements of 2,794 model trees and studying the...

Visual exploration of parameter influence on phylogenetic trees.

PubMed

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

2014-01-01

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

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

PubMed

Engel, Julien; Brousseau, Louise; Baraloto, Christopher

2016-01-01

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

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.

Intraspecific scaling laws of vascular trees.

PubMed

Huo, Yunlong; Kassab, Ghassan S

2012-01-07

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 volume-diameter and flow-length scaling laws of intraspecific vascular trees. In conjunction with the minimum energy hypothesis, this formulation also results in diameter-length, flow-diameter and flow-volume scaling laws. The intraspecific scaling predicts the volume-diameter 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.

Wind-Induced Reconfigurations in Flexible Branched Trees

NASA Astrophysics Data System (ADS)

Ojo, Oluwafemi; Shoele, Kourosh

2017-11-01

Wind induced stresses are the major mechanical cause of failure in trees. We know that the branching mechanism has an important effect on the stress distribution and stability of a tree in the wind. Eloy in PRL 2011, showed that Leonardo da Vinci's original observation which states the total cross section of branches is conserved across branching nodes is the best configuration for resisting wind-induced fracture in rigid trees. However, prediction of the fracture risk and pattern of a tree is also a function of their reconfiguration capabilities and how they mitigate large wind-induced stresses. In this studies through developing an efficient numerical simulation of flexible branched trees, we explore the role of the tree flexibility on the optimal branching. Our results show that the probability of a tree breaking at any point depends on both the cross-section changes in the branching nodes and the level of tree flexibility. It is found that the branching mechanism based on Leonardo da Vinci's original observation leads to a uniform stress distribution over a wide range of flexibilities but the pattern changes for more flexible systems.

i-Tree and urban FIA—what's the connection?

Treesearch

David J. Nowak

2015-01-01

The i-Tree program (www.itreetools.org) was developed to assess ecosystem services and values from trees and forests based on measured forest data. The i-Tree program is currently being integrated with FIA data to assess various ecosystem services and values from urban FIA data. This presentation will overview the history and use of i-Tree; the various tools of i-Tree...

User's Manual for Total-Tree Multiproduct Cruise Program

Treesearch

Alexander Clark; Thomas M. Burgan; Richard C. Field; Peter E. Dress

1985-01-01

This interactive computer program uses standard tree-cruise data to estimate the weight and volume of the total tree, saw logs, plylogs, chipping logs, pulpwood, crown firewood, and logging residue in timber stands.Input is cumulative cruise data for tree counts by d.b.h. and height. Output is in tables: board-foot volume by d.b.h.; total-tree and tree-component...

Basswood, linden, lime-tree,

Treesearch

John Zasada

2003-01-01

Tilia americana - to foresters, botanists, and ecologists around the world this name conjures up the picture of a very specific tree (Tilia in latin means linden tree so literally translated the scientific name means American linden). But what about basswood, linden, lime, and pu tee shu (Chinese for linden)? Common names are often confusing and may be different from...

A tree hurts, too

Treesearch

Northeastern Forest Experiment Station

1973-01-01

This booklet outlines what happens most of the time as decay develops in a living tree. The drawings are designed to give an accurate general presentation of the decay process by focusing only on the major portions of an extremely complex process that involves the interactions among microorganisms, environmental factors, and the tree. The better we understand these...

Recovery efficiency of whole-tree harvesting

Treesearch

Bryce J. Stokes; William F. Watson

1988-01-01

The recovery of total tree biomass and most components of a stand is a practical economic and management alternative to tree-length harvesting. First, the increased utilization of woody biomass provides additional revenues from the site. Second, the removal and utilization of the stems and crowns reduces site preparation costs and makes tree planting easier. Third,...

Tree planting: not a simple solution

Treesearch

Constance I. Millar; William J. Libby

1991-01-01

There's no doubt about it. Planting trees has caught the attention of the American public. In his 1990 State of the Union address, President Bush proposed planting a billion Fees annually for the next ten years. Inspired by the potential for trees to reduce greenhouse gases and mitigate global climate change, tree-planting programs such as Treepeople and Global...

Pollen dispersion of some forest trees

Treesearch

Jonathan W. Wright

1952-01-01

The distance the pollen of forest trees travels is of practical and theoretical importance not only in tree breeding, but also in silviculture. For example, one way to produce elite or hybrid tree seed where vegetative propagation is impractical is by the establishment of "seed orchards" or natural-crossing plots. The success of such orchards will depend...

Measuring and analyzing urban tree cover

Treesearch

David J. Nowak; Rowan A. Rowntree; E. Gregory McPherson; Susan M. Sisinni; Esther R. Kirkmann; Jack C. Stevens

1996-01-01

Measurement of city tree cover can aid in urban vegetation planning, management, and research by revealing characteristics of vegetation across a city. Urban tree cover in the United States ranges from 0.4% in Lancaster, California, to 55% in Baton Rouge, Louisiana. Two important factors that affect the amount of urban tree cover are the natural environment and land...

Do you believe in palm trees?

Treesearch

Kevin T. Smith

2013-01-01

Palms are real, but are they really trees? The answer depends on definitions. As usually tall, peremrial plants with roots, stems, and leaves, palms seem to qualify. Palms should also qualify because arborists care for them, and arborists care for trees, right? My introduction to botany class defined trees as plants that produce wood. Unraveling the question of whether...

On fractal properties of arterial trees.

PubMed

Zamir, M

1999-04-21

The question of fractal properties of arterial trees is considered in light of data from the extensive tree structure of the right coronary artery of a human heart. Because of the highly non-uniform structure of this tree, the study focuses on the purely geometrical rather than statistical aspects of fractal properties. The large number of arterial bifurcations comprising the tree were found to have a mixed degree of asymmetry at all levels of the tree, including the depth of the tree where it has been generally supposed that they would be symmetrical. Cross-sectional area ratios of daughter to parent vessels were also found to be highly mixed at all levels, having values both above and below 1.0, rather than consistently above as has been generally supposed in the past. Calculated values of the power law index which describes the theoretical relation between the diameters of the three vessel segments at an arterial bifurcation were found to range far beyond the two values associated with the cube and square laws, and not clearly favoring one or the other. On the whole the tree structure was found to have what we have termed "pseudo-fractal" properties, in the sense that vessels of different calibers displayed the same branching pattern but with a range of values of the branching parameters. The results suggest that a higher degree of fractal character, one in which the branching parameters are constant throughout the tree structure, is unlikely to be attained in non-uniform vascular structures. Copyright 1999 Academic Press.