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Sample records for tupaia tree shrew

  1. Identification of Glyceraldehyde 3-Phosphate Dehydrogenase Sequence and Expression Profiles in Tree Shrew (Tupaia belangeri)

    OpenAIRE

    Zheng, Yu; Wang, Qihui; Yun, Chenxia; Wang, Yingjun; Smith, Wanli W.; Leng, Jing

    2014-01-01

    The tree shrews (Tupaia belangeri) diverged from the primate order (Primates) and are classified as Scandentia, a separate taxonomic group of mammals. The tree shrew has been suggested to use an animal model to study human disease but the genomic sequences of tree shrew is largely unidentified. Here we identified the full-length cDNA sequence of a housekeeping gene, Glyceraldehyde 3-phosphate Dehydrogenase (GAPDH), in tree shrew. We further constructed a phylogenetic family tree base on GAPDH...

  2. Telemetric Study of Sleep Architecture and Sleep Homeostasis in the Day-Active Tree Shrew Tupaia belangeri

    NARCIS (Netherlands)

    Coolen, Alex; Hoffmann, Kerstin; Barf, R. Paulien; Fuchs, Eberhard; Meerlo, Peter

    2012-01-01

    Study Objectives: In this study the authors characterized sleep architecture and sleep homeostasis in the tree shrew, Tupaia belangeri, a small, omnivorous, day-active mammal that is closely related to primates. Design: Adult tree shrews were individually housed under a 12-hr light/12-hr dark cycle

  3. Experimental infection of tree shrews (Tupaia belangeri) with Coxsackie virus A16.

    Science.gov (United States)

    Li, Jian-Ping; Liao, Yun; Zhang, Ying; Wang, Jing-Jing; Wang, Li-Chun; Feng, Kai; Li, Qi-Han; Liu, Long-Ding

    2014-11-18

    Coxsackie virus A16 (CA16) is commonly recognized as one of the main human pathogens of hand-foot-mouth disease (HFMD). The clinical manifestations of HFMD include vesicles of hand, foot and mouth in young children and severe inflammatory CNS lesions. In this study, experimentally CA16 infected tree shrews (Tupaia belangeri) were used to investigate CA16 pathogenesis. The results showed that both the body temperature and the percentages of blood neutrophilic granulocytes / monocytes of CA16 infected tree shrews increased at 4-7 days post infection. Dynamic distributions of CA16 in different tissues and stools were found at different infection stages. Moreover, the pathological changes in CNS and other organs were also observed. These findings indicate that tree shrews can be used as a viable animal model to study CA16 infection.

  4. Metabolism and thermoregulation in the tree shrew, Tupaia belangeri

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    Lin Zhang

    2012-05-01

    Full Text Available Maximum metabolic rate is a physiological limitation that is an important for animals' survival, reproduction and geographic. Basal metabolic rate (BMR, nonshivering thermogenesis (NST, and maximum metabolic rate (MMR were measured was in a small mammal species, Tupaia belangeri, which is a unique species of small-bodied mammals in the Oriental realm. Thermal neutral zone (TNZ was 30 - 35°C and BMR was 1.38±0.09 ml g-1 h-1. NST and MMR were 2.64±0.08 ml g-1 h-1 and 7.14±0.38 ml g-1 h-1 in summer, respectively. The ecophysiological properties of relatively high body temperature, wide TNZ, low BMR and thermogenic capacity enable this species to adapt to its environment.

  5. Relationships between body weight, fasting blood glucose concentration, sex and age in tree shrews (Tupaia belangeri chinensis).

    Science.gov (United States)

    Wu, X; Chang, Q; Zhang, Y; Zou, X; Chen, L; Zhang, L; Lv, L; Liang, B

    2013-12-01

    The tree shrew (Tupaia belangeri chinensis) is a squirrel-like lower primate or a close relative of primates, commonly used as an animal model in biomedical research. Despite more than three decades of usage in research, the clear relationships between body weight, fasting blood glucose concentration, sex and age among tree shrews remain unclear. Based on an investigation of 992 tree shrews (454 males and 538 females) aged between 4 months and 4 years old, we found that male tree shrews have significantly higher body weight and fasting blood glucose concentration than female tree shrews (p body weight in males (r = 0.152, p body weight, concentration of fasting blood glucose and waist circumference positively increased with age (p body weight (g)*0.33*1000/body length (cm)] above 290 had significantly higher body weight, waist circumference and glycated haemoglobin A1c (HbA1c) than non-obese tree shrews with a Lee index score below 290 (p body weight, fasting blood glucose concentration, sex and age in tree shrews, further improving our understanding of this relationship in metabolic syndrome (MetS). Given the similarity of tree shrews to humans and non-human primates, this finding supports their potential use as an animal model in the research of MetS. © 2013 Blackwell Verlag GmbH.

  6. Enzyme activity, hormone concentration in tree shrew (Tupaia belangeri during cold acclimation

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    Lin Zhang

    2012-08-01

    Full Text Available Environmental factors play an important role in the seasonal adaptation of body mass and thermogenesis in wild small mammals. The tree shrew (Tupaia belangeri, is a unique species of small mammals which is origin of island in the Oriental realm. The present study was to test the hypothesis that ambient temperature was a cue to induce adjustments in body mass, energy intake, metabolism, uncoupling protein 1 (UCP1 in brown adipose tissue (BAT, and other biochemical characters of T. belangeri during cold exposure about 21 days. Our data demonstrate that cold acclimation induced a remarkable increase in body mass, a significant increase in energy intake and metabolic rate, and high expression of UCP1 in BAT of T. belangeri. Cold acclimation induced an increase in cytochrome c oxidase (COX and Thyroidhormones (T3/T4. These data supported that T. belangeri increased the body mass and increased energy intake and expenditure under cold acclimation. Increased expression of UCP1 was potentially involved in the regulation of energy metabolism and thermogenic capacity following cold acclimation. And it through changes in enzyme activity and hormone concentration under cold acclimation, and suggested temperature changes play an important role in the regulation of thermogenic capacity in tree shrew.

  7. Dynamic changes in DNA demethylation in the tree shrew (Tupaia belangeri chinensis) brain during postnatal development and aging.

    Science.gov (United States)

    Wei, Shu; Hua, Hai-Rong; Chen, Qian-Quan; Zhang, Ying; Chen, Fei; Li, Shu-Qing; Li, Fan; Li, Jia-Li

    2017-03-18

    Brain development and aging are associated with alterations in multiple epigenetic systems, including DNA methylation and demethylation patterns. Here, we observed that the levels of the 5-hydroxymethylcytosine (5hmC) ten-eleven translocation (TET) enzyme-mediated active DNA demethylation products were dynamically changed and involved in postnatal brain development and aging in tree shrews ( Tupaia belangeri chinensis ). The levels of 5hmC in multiple anatomic structures showed a gradual increase throughout postnatal development, whereas a significant decrease in 5hmC was found in several brain regions in aged tree shrews, including in the prefrontal cortex and hippocampus, but not the cerebellum. Active changes in Tet mRNA levels indicated that TET2 and TET3 predominantly contributed to the changes in 5hmC levels. Our findings provide new insight into the dynamic changes in 5hmC levels in tree shrew brains during postnatal development and aging processes.

  8. Microvascularization in trigeminal ganglion of the common tree shrew (Tupaia glis).

    Science.gov (United States)

    Kongstaponkit, S; Pradidarcheep, W; Toutip, S; Chunhabundit, P; Somana, R

    1997-01-01

    Since there is only a limited number of studies of the blood supply to the trigeminal ganglion (TG) in mammalian species, the TG from 16 common tree shrews (Tupaia glis) were investigated by light microscope, transmission electron microscope (TEM) and the corrosion cast technique in conjunction with scanning electron microscope (SEM). It was found that the TG contained clusters of neurons in the peripheral region whereas the bundles of nerve fibers were located more centrally. Each ganglionic neuron had a concentric nucleus and was ensheathed by satellite cells. It was noted that blood vessels of a continuous type were predominantly found in the area where the neurons were densely located and were much less frequently observed in the area occupied by nerve fibers. With TEM, the TG was shown to be mainly associated with large neurons containing big nuclei and prominent nucleoli. The blood supply of the TG is derived from the most rostral branch of the pontine artery, from the stapedial artery or sometimes from the supraorbital artery, and from the accessory meningeal artery which is a branch of the maxillary artery passing through the foramen ovale. These arteries give off branches and become capillary networks in the ganglion before draining blood to the peripheral region. The veins at the medial border drained into the cavernous sinus directly or through the inferior hypophyseal vein, while those at the lateral side of the ganglion carried the blood into the pterygoid plexus via an accessory meningeal vein. The veins along the trigeminal nerve root joined the posterior part of the cavernous sinus. These studies establish a unique anatomical distribution of the TG blood supply in the tree shrew and the utility of the cast/SEM technique in discerning detailed features of the blood supply in the nervous system.

  9. Tree shrew (Tupaia belangeri chinensis, a novel non-obese animal model of non-alcoholic fatty liver disease

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    Linqiang Zhang

    2016-10-01

    Full Text Available Non-alcoholic fatty liver disease (NAFLD is becoming a severe public health problem that is affecting a large proportion of the world population. Generally, NAFLD in patients is usually accompanied by obesity, hyperglycemia, insulin resistance (IR and type 2 diabetes (T2D, for which numerous animal models have been generated in order to explore the pathogenesis and therapies of NAFLD. On the contrary, quite a number of NAFLD subjects, especially in Asian regions, are non-obese and non-diabetic; however, few animal models are available for the research of non-obese NAFLD. Here, four approaches (here called approach 1 to 4 corresponding to the variable compositions of diets were used to treat tree shrews (Tupaia belangeri chinensis, which have a closer evolutionary relationship to primates than rodents. Analysis of plasma biochemical parameters, hepatic histology, and the expression of hepatic lipid metabolic genes revealed that all four approaches led to hepatic lipid accumulation, liver injury and hypercholesterolemia, but had no effect on body weight and adipose tissue generation, or glycemia. Hepatic gene expression in tree shrews treated by approach 4 might suggest a different or non-canonical pathway leading to hepatic steatosis. In conclusion, the tree shrew displays hepatic steatosis and dyslipidemia, but remains non-obese and non-diabetic under high energy diets, which suggests that the tree shrew may be useful as a novel animal model for the research of human non-obese NAFLD.

  10. Molecular cloning and characterization of the full-length cDNA encoding the tree shrew (tupaia belangeri) CD28

    Science.gov (United States)

    Huang, Xiaoyan; Yan, Yan; Wang, Sha; Wang, Qinying; Shi, Jian; Shao, Zhanshe; Dai, Jiejie

    2017-11-01

    CD28 is one of the most important co-stimulatory molecules expressed by naive and primed T cells. The tree shrews (Tupaia belangeri), as an ideal animal model for analyzing mechanism of human diseases receiving extensive attentions, demands essential research tools, in particular in the study of cellular markers and monoclonal antibodies for immunological studies. However, little is known about tree shrew CD28 (tsCD28) until now. In this study, a 663 bp of the full-length CD28 cDNA, encoding a polypeptide of 220 amino acids was cloned from tree shrew spleen lymphocytes. The nucleotide sequence of the tsCD28 showed 85%, 76%, and 75% similarities with human, rat, and mouse, respectively, which showed the affinity relationship between tree shrew and human is much closer than between human and rodents. The open reading frame (ORF) sequence of tsCD28 gene was predicted to be in correspondence with the signal sequence, immunoglobulin variable-like (IgV) domain, transmembrane domain and cytoplasmic tail, respectively.We also analyzed its molecular characteristics with other mammals by using biology software such as Clustal W 2.0 and so forth. Our results showed that tsCD28 contained many features conserved in CD28 genes from other mammals, including conserved signal peptide and glycosylation sites, and several residues responsible for binding to the CD28R, and the tsCD28 amino acid sequence were found a close genetic relationship with human and monkey. The crystal structure and surface charge revealed most regions of tree shrew CD28 molecule surface charges are similar as human. However, compared with human CD28 (hCD28) regions, in some areas, the surface positive charge of tsCD28 was less than hCD28, which may affect antibody binding. The present study is the first report of cloning and characterization of CD28 in tree shrew. This study provides a theoretical basis for the further study the structure and function of tree shrew CD28 and utilize tree shrew as an effective

  11. Distribution of 239Pu in the skeleton of the tree shrew (Tupaia belangeri) between 15 and 50 months after injection

    International Nuclear Information System (INIS)

    Sontag, W.; Seidel, A.

    1987-01-01

    The macroscopic and microscopic distribution of intramuscularly injected, essentially monomeric, 239 Pu was studied in the skeleton of the adult tree shrew (Tupaia belangeri). Data for between 15 and 50 months after injection are presented and compared with data from earlier time points. Between 83 and 500 days after injection nuclide content and wet weight of the skeleton decreased to a constant level at about 55% of maximum. The microscopic distribution was analysed in distal femora, proximal humerus, proximal tibia and lumbar vertebra over the whole time; additionally at some selected time points proximal femur, femur shaft, distal humerus and distal tibia were analysed. The initial endosteal surface activity ranged from 3.8 to 5.3 Bq/cm 2 , decreased to a minimum at about 1000 days after injection and increased thereafter. Similar behaviour was found for dose rate near bone surfaces (initially about 0.075 Gy/day on endosteal surfaces). In deep bone and deep marrow the dose rate was negligible, about 0.008 Gy/day and 0.001 Gy/day, respectively. The average cumulative dose 1500 days after injection was about 67 Gy on the endosteum; six times greater than the cumulative dose calculated from the mean concentration of plutonium in the whole skeleton. Tupaia data are compared to monkeys, dogs and rats. (author)

  12. Experimental chronic hepatitis B infection of neonatal tree shrews (Tupaia belangeri chinensis: A model to study molecular causes for susceptibility and disease progression to chronic hepatitis in humans

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    Wang Qi

    2012-08-01

    Full Text Available Abstract Background Hepatitis B virus (HBV infection continues to be an escalating global health problem. Feasible and effective animal models for HBV infection are the prerequisite for developing novel therapies for this disease. The tree shrew (Tupaia is a small animal species evolutionary closely related to humans, and thus is permissive to certain human viral pathogens. Whether tree shrews could be chronically infected with HBV in vivo has been controversial for decades. Most published research has been reported on adult tree shrews, and only small numbers of HBV infected newborn tree shrews had been observed over short time periods. We investigated susceptibility of newborn tree shrews to experimental HBV infection as well as viral clearance over a protracted time period. Results Forty-six newborn tree shrews were inoculated with the sera from HBV-infected patients or tree shrews. Serum and liver samples of the inoculated animals were periodically collected and analyzed using fluorescence quantitative polymerase chain reaction, enzyme-linked immunosorbent assay, Southern blot, and immunohistochemistry. Six tree shrews were confirmed and four were suspected as chronically HBV-infected for more than 48 (up to 228 weeks after inoculation, including three that had been inoculated with serum from a confirmed HBV-infected tree shrew. Conclusions Outbred neonatal tree shrews can be long-term chronically infected with HBV at a frequency comparable to humans. The model resembles human disease where also a smaller proportion of infected individuals develop chronic HBV related disease. This model might enable genetic and immunologic investigations which would allow determination of underlying molecular causes favoring susceptibility for chronic HBV infection and disease establishment vs. viral clearance.

  13. Characterization and phylogenetic analysis of Krüppel-like transcription factor (KLF) gene family in tree shrews (Tupaia belangeri chinensis).

    Science.gov (United States)

    Shao, Ming; Ge, Guang-Zhe; Liu, Wen-Jing; Xiao, Ji; Xia, Hou-Jun; Fan, Yu; Zhao, Feng; He, Bao-Li; Chen, Ceshi

    2017-03-07

    Krüppel-like factors (KLFs) are a family of zinc finger transcription factors regulating embryonic development and diseases. The phylogenetics of KLFs has not been studied in tree shrews, an animal lineage with a closer relationship to primates than rodents. Here, we identified 17 KLFs from Chinese tree shrew (Tupaia belangeri chinensis). KLF proteins are highly conserved among humans, monkeys, rats, mice and tree shrews compared to zebrafish and chickens. The CtBP binding site, Sin3A binding site and nuclear localization signals are largely conserved between tree shrews and human beings. Tupaia belangeri (Tb) KLF5 contains several conserved post-transcriptional modification motifs. Moreover, the mRNA and protein expression patterns of multiple tbKLFs are tissue-specific . TbKLF5, like hKLF5, significantly promotes NIH3T3 cell proliferation in vitro. These results provide insight for future studies regarding the structure and function of the tbKLF gene family.

  14. Neural Progenitors in the Developing Neocortex of the Northern Tree Shrew (Tupaia belangeri Show a Closer Relationship to Gyrencephalic Primates Than to Lissencephalic Rodents

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    Sebastian Römer

    2018-04-01

    Full Text Available The neocortex is the most complex part of the mammalian brain and as such it has undergone tremendous expansion during evolution, especially in primates. The majority of neocortical neurons originate from distinct neural stem and progenitor cells (NPCs located in the ventricular and subventricular zone (SVZ. Previous studies revealed that the SVZ thickness as well as the abundance and distribution of NPCs, especially that of basal radial glia (bRG, differ markedly between the lissencephalic rodent and gyrencephalic primate neocortex. The northern tree shrew (Tupaia belangeri is a rat-sized mammal with a high brain to body mass ratio, which stands phylogenetically mid-way between rodents and primates. Our study provides – for the first time – detailed data on the presence, abundance and distribution of bRG and other distinct NPCs in the developing neocortex of the northern tree shrew (Tupaia belangeri. We show that the developing tree shrew neocortex is characterized by an expanded SVZ, a high abundance of Pax6+ NPCs in the SVZ, and a relatively high percentage of bRG at peak of upper-layer neurogenesis. We further demonstrate that key features of tree shrew neocortex development, e.g., the presence, abundance and distribution of distinct NPCs, are closer related to those of gyrencephalic primates than to those of ferret and lissencephalic rodents. Together, our study provides novel insight into the evolution of bRG and other distinct NPCs in the neocortex development of Euarchontoglires and introduces the tree shrew as a potential novel model organism in the area of human brain development and developmental disorders.

  15. Taxonomy Icon Data: Javan tree shrew [Taxonomy Icon

    Lifescience Database Archive (English)

    Full Text Available Javan tree shrew Tupaia javanica Chordata/Vertebrata/Mammalia/Theria/Eutheria/etc. Tupaia_java...nica_L.png Tupaia_javanica_NL.png Tupaia_javanica_S.png Tupaia_javanica_NS.png http://bioscienced...bc.jp/taxonomy_icon/icon.cgi?i=Tupaia+javanica&t=L http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Tupaia+java...nica&t=NL http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Tupaia+javanica&t=S http://biosciencedbc.jp/taxonomy_icon/icon.cgi?i=Tupaia+javanica&t=NS ...

  16. Tree shrews (tupaia belangeri exhibit novelty preference in the novel location memory task with 24-hour retention periods.

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    Jayakrishnan H R Nair

    2014-04-01

    Full Text Available Novelty preference is pervasive in mammalian species, and describes an inherent tendency to preferentially explore novelty. The novel location memory task studied here assesses the ability of animals to form accurate memories of a spatial configuration, consisting of several identical objects placed within an arena. Tree shrews were first familiarized with a particular object configuration during several sessions, and then an object was displaced during a test session. Tree shrews exhibited enhanced exploration when confronted with this novel configuration. The most reliable indicator associated with novelty preference was an enhancement in directed exploration towards the novel object, although we also observed a non-specific overall increase in exploration in one experiment. During the test session, we also observed an exploration of the location, which had previously been occupied by the displaced object, an effect termed empty quadrant. Our behavioral findings suggest multiple stages of spatial memory formation in tree shrews that are associated with various forms of behavioral responses to novelty. Reduced novelty preference has been linked to major depressive disorder in human patients. Given the established social conflict depression model in tree shrews, we anticipate that the study of the neural circuits of novelty preference and their malfunction during depression may have implications for understanding or treating depression in humans.

  17. Mutualism between tree shrews and pitcher plants

    Science.gov (United States)

    Moran, Jonathan A; Chin, Lijin

    2010-01-01

    Three species of Nepenthes pitcher plants from Borneo engage in a mutualistic interaction with mountain tree shrews, the basis of which is the exchange of nutritional resources. The plants produce modified “toilet pitchers” that produce copious amounts of exudates, the latter serving as a food source for tree shrews. The exudates are only accessible to the tree shrews when they position their hindquarters over the pitcher orifice. Tree shrews mark valuable resources with feces and regularly defecate into the pitchers when they visit them to feed. Feces represent a valuable source of nitrogen for these Nepenthes species, but there are many facets of the mutualism that are yet to be investigated. These include, but are not limited to, seasonal variation in exudate production rates by the plants, behavioral ecology of visiting tree shrews and the mechanism by which the plants signal to tree shrews that their pitchers represent a food source. Further research into this extraordinary animal-plant interaction is required to gain a better understanding of the benefits to the participating species. PMID:20861680

  18. Molecular cloning and characterization of APOBEC3 family in tree shrew.

    Science.gov (United States)

    Luo, Meng-Ting; Fan, Yu; Mu, Dan; Yao, Yong-Gang; Zheng, Yong-Tang

    2018-03-10

    The APOBEC3 family is a series antiviral factors that inhibit the replication of many viruses, such as HIV-1 and HBV. Tree shrews (Tupaia belangeri) possess great potential as an animal model for human diseases and therapeutic responses. However, the APOBEC3 family is unknown in tree shrews. Recent work has showed the presence of the APOBEC3 family in tree shrews. In this work, the cDNA sequences of five APOBEC3 members were identified in tree shrews, namely, tsAPOBEC3A, -3C, -3F, -3G and -3H. The results showed that their sequences encoded a zinc (Z)-coordinating-domain as a characteristic of APOBEC3 proteins. Phylogenetic analysis revealed that the tree shrew APOBEC3 (tsAPOBEC3) genes have occurred independently and that they are clustered with other mammalian APOBEC3 members. Transcript expression analysis indicated that tsAPOBEC3 genes are constitutively expressed, and high in immune-related tissues. tsAPOBEC3 gene expression was up-regulated in hepatocytes and PBMCs by IFN-α stimulation. Finally, tsAPOBEC3 proteins could edit both sides of DNA by inserting G→A and C→T hypermutations. Overall, the results suggest that the tsAPOBEC3 family could play a key role in defense immunity through distinct editing mechanisms. Our results provided insights into the genetic basis for the development of a tree shrew model for studying viral infection. Future studies will focus on deepening our understanding on the antiviral functions of these editing enzymes in tree shrew. Copyright © 2018 Elsevier B.V. All rights reserved.

  19. Chronic clomipramine treatment reverses core symptom of depression in subordinate tree shrews.

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    Jing Wang

    Full Text Available Chronic stress is the major cause of clinical depression. The behavioral signs of depression, including anhedonia, learning and memory deficits, and sleep disruption, result from the damaging effects of stress hormones on specific neural pathways. The Chinese tree shrew (Tupaia belangeri chinensis is an aggressive non-human primate with a hierarchical social structure that has become a well-established model of the behavioral, endocrine, and neurobiological changes associated with stress-induced depression. The tricyclic antidepressant clomipramine treats many of the core symptoms of depression in humans. To further test the validity of the tree shrew model of depression, we examined the effects of clomipramine on depression-like behaviors and physiological stress responses induced by social defeat in subordinate tree shrews. Social defeat led to weight loss, anhedonia (as measured by sucrose preference, unstable fluctuations in locomotor activity, sustained urinary cortisol elevation, irregular cortisol rhythms, and deficient hippocampal long-term potentiation (LTP. Clomipramine ameliorated anhedonia and irregular locomotor activity, and partially rescued the irregular cortisol rhythm. In contrast, weight loss increased, cortisol levels were even higher, and in vitro LTP was still impaired in the clomipramine treatment group. These results demonstrate the unique advantage of the tree shrew social defeat model of depression.

  20. Starburst cholinergic amacrine cells in the tree shrew retina.

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    Sandmann, D; Engelmann, R; Peichl, L

    1997-12-08

    In all mammalian retinae studied to date, starburst cholinergic amacrine cells are a consistently occurring cell type. Here, we show that the cone-dominated retina of the tree shrew also has starburst cells with the characteristic radially symmetric branching pattern known from other species. Dendritic field sizes increase from 150 microm in the central retina to 300 microm in the retinal periphery. The characteristic morphology is established early during postnatal development. Labelling the starburst cholinergic cells with an antibody against choline acetyltransferase (ChAT) reveals two dendritic strata in the inner plexiform layer and two corresponding soma populations in the inner nuclear layer (orthotopic) and ganglion cell layer (displaced). These features are present in the adult and in early postnatal stages. In the adult, the density of the orthotopic population as well as the displaced population peaks in the central retina at about 2,200 cells/mm2 and has a peripheral minimum of 400 cells/mm2. These properties are qualitatively similar to those of starburst cells in rod-dominated retinae. In contrast to findings in other mammals, we did not see gamma-aminobutyric acid (GABA) or glutamic acid decarboxylase 65 kDa (GAD65) immunoreactivity in tree shrew starburst cells. These cells also appear to lack synaptophysin, a ubiquitous synaptic vesicle protein detected in the starburst cells of some other mammals. However, synaptoporin, a homologous synaptic vesicle protein, appears to be present in tree shrew starburst cells.

  1. Structural Analysis Of CD59 Of Chinese Tree Shrew: A New Reference Molecule For Human Immune System Specific CD59 Drug Discovery.

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    Panda, Subhamay; Kumari, Leena; Panda, Santamay

    2017-11-17

    Chinese tree shrews (Tupaia belangeri chinensis) bear several characteristics that are considered to be very crucial for utilizing in animal experimental models in biomedical research. Subsequent to the identification of key aspects and signaling pathways in nervous and immune systems, it is revealed that tree shrews acquires shared common as well as unique characteristics, and hence offers a genetic basis for employing this animal as a prospective model for biomedical research. CD59 glycoprotein, commonly referred to as MAC-inhibitory protein (MAC-IP), membrane inhibitor of reactive lysis (MIRL), or protectin, is encoded by the CD59 gene in human beings. It is the member of the LY6/uPAR/alpha-neurotoxin protein family. With this initial point the objective of this study was to determine a comparative composite based structure of CD59 of Chinese tree shrew. The additional objective of this study was to examine the distribution of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, hydrophobicity molecular surface analysis and electrostatic potential analysis with the assistance of several bioinformatical analytical tools. CD59 Amino acid sequence of Chinese tree shrew collected from the online database system of National Centre for Biotechnology Information. SignalP 4.0 online server was employed for detection of signal peptide instance within the protein sequence of CD59. Molecular model structure of CD59 protein was generated by the Iterative Threading ASSEmbly Refinement (I-TASSER) suite. The confirmation for three-dimensional structural model was evaluated by structure validation tools. Location of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, and hydrophobicity molecular surface analysis was performed with the help of Chimera tool. Electrostatic potential analysis was carried out with the adaptive Poisson

  2. Drug target mining and analysis of the Chinese tree shrew for pharmacological testing.

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    Feng Zhao

    Full Text Available The discovery of new drugs requires the development of improved animal models for drug testing. The Chinese tree shrew is considered to be a realistic candidate model. To assess the potential of the Chinese tree shrew for pharmacological testing, we performed drug target prediction and analysis on genomic and transcriptomic scales. Using our pipeline, 3,482 proteins were predicted to be drug targets. Of these predicted targets, 446 and 1,049 proteins with the highest rank and total scores, respectively, included homologs of targets for cancer chemotherapy, depression, age-related decline and cardiovascular disease. Based on comparative analyses, more than half of drug target proteins identified from the tree shrew genome were shown to be higher similarity to human targets than in the mouse. Target validation also demonstrated that the constitutive expression of the proteinase-activated receptors of tree shrew platelets is similar to that of human platelets but differs from that of mouse platelets. We developed an effective pipeline and search strategy for drug target prediction and the evaluation of model-based target identification for drug testing. This work provides useful information for future studies of the Chinese tree shrew as a source of novel targets for drug discovery research.

  3. Depletion of endogenous germ cells in tree shrews in preparation for spermatogonial transplantation.

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    Liu, Tingting; Guo, Ying; Yan, Lanzhen; Sun, Bin; Zheng, Ping; Zhao, Xudong

    2017-09-01

    To achieve successful spermatogonial transplantation, endogenous germ cells must be depleted in recipient animals to allow donor germ cells to colonize efficiently. Busulfan is commonly used for the depletion of endogenous germ cells in recipient males. However, the optimal dose of busulfan is species-specific, and the optimal dose in tree shrews is yet to be determined. The current study aimed to determine the optimal dose of busulfan for effective suppression of endogenous spermatogenesis in tree shrews. Different doses (15, 20, 25, 30, 35, 40 and 45 mg/kg) of busulfan were injected into tree shrews intraperitoneally. Survival rates of the different treatment groups were calculated at 2 weeks and body weights were measured at 4, 6, 8, 10 and 28 weeks post-busulfan treatment. The testes were also removed and weighed at 4, 6, 8, 10 and 28 weeks post-treatment, and the cross and longitude diameters of the testes and diameters of the seminiferous tubules were measured and histologically evaluated. It was observed that there were no significant differences in the survival rates between the 15-35 mg/kg treatment groups and the control group (P>0.05), while the survival rate of the 40 mg/kg treatment group significantly decreased relative to the control group (Pendogenous germ cells in tree shrews. This dose led to maximum suppression of endogenous spermatogenesis while maintaining an acceptable survival rate of >50% of the lethal dose of busulfan for tree shrews.

  4. Tuning of color contrast signals to visual sensitivity maxima of tree shrews by three Bornean highland Nepenthes species.

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    Moran, Jonathan A; Clarke, Charles; Greenwood, Melinda; Chin, Lijin

    2012-10-01

    Three species of Nepenthes pitcher plants (Nepenthes rajah, Nepenthes lowii and Nepenthes macrophylla) specialize in harvesting nutrients from tree shrew excreta in their pitchers. In all three species, nectaries on the underside of the pitcher lid are the focus of the tree shrews' attention. Tree shrews are dichromats, with visual sensitivity in the blue and green wavebands. All three Nepenthes species were shown to produce visual signals, in which the underside of the pitcher lid (the area of highest nectar production) stood out in high contrast to the adjacent area on the pitcher (i.e., was brighter), in the blue and green wavebands visible to the tree shrews. N. rajah showed the tightest degree of "tuning," notably in the green waveband. Conversely, pitchers of Nepenthes burbidgeae, a typical insectivorous species sympatric with N. rajah, did not produce a color pattern tuned to tree shrew sensitivity maxima.

  5. Long-term propagation of tree shrew spermatogonial stem cells in culture and successful generation of transgenic offspring.

    Science.gov (United States)

    Li, Chao-Hui; Yan, Lan-Zhen; Ban, Wen-Zan; Tu, Qiu; Wu, Yong; Wang, Lin; Bi, Rui; Ji, Shuang; Ma, Yu-Hua; Nie, Wen-Hui; Lv, Long-Bao; Yao, Yong-Gang; Zhao, Xu-Dong; Zheng, Ping

    2017-02-01

    Tree shrews have a close relationship to primates and have many advantages over rodents in biomedical research. However, the lack of gene manipulation methods has hindered the wider use of this animal. Spermatogonial stem cells (SSCs) have been successfully expanded in culture to permit sophisticated gene editing in the mouse and rat. Here, we describe a culture system for the long-term expansion of tree shrew SSCs without the loss of stem cell properties. In our study, thymus cell antigen 1 was used to enrich tree shrew SSCs. RNA-sequencing analysis revealed that the Wnt/β-catenin signaling pathway was active in undifferentiated SSCs, but was downregulated upon the initiation of SSC differentiation. Exposure of tree shrew primary SSCs to recombinant Wnt3a protein during the initial passages of culture enhanced the survival of SSCs. Use of tree shrew Sertoli cells, but not mouse embryonic fibroblasts, as feeder was found to be necessary for tree shrew SSC proliferation, leading to a robust cell expansion and long-term culture. The expanded tree shrew SSCs were transfected with enhanced green fluorescent protein (EGFP)-expressing lentiviral vectors. After transplantation into sterilized adult male tree shrew's testes, the EGFP-tagged SSCs were able to restore spermatogenesis and successfully generate transgenic offspring. Moreover, these SSCs were suitable for the CRISPR/Cas9-mediated gene modification. The development of a culture system to expand tree shrew SSCs in combination with a gene editing approach paves the way for precise genome manipulation using the tree shrew.

  6. Nerve growth factor promotes in vitro proliferation of neural stem cells from tree shrews

    Directory of Open Access Journals (Sweden)

    Liu-lin Xiong

    2016-01-01

    Full Text Available Neural stem cells promote neuronal regeneration and repair of brain tissue after injury, but have limited resources and proliferative ability in vivo. We hypothesized that nerve growth factor would promote in vitro proliferation of neural stem cells derived from the tree shrews, a primate-like mammal that has been proposed as an alternative to primates in biomedical translational research. We cultured neural stem cells from the hippocampus of tree shrews at embryonic day 38, and added nerve growth factor (100 µg/L to the culture medium. Neural stem cells from the hippocampus of tree shrews cultured without nerve growth factor were used as controls. After 3 days, fluorescence microscopy after DAPI and nestin staining revealed that the number of neurospheres and DAPI/nestin-positive cells was markedly greater in the nerve growth factor-treated cells than in control cells. These findings demonstrate that nerve growth factor promotes the proliferation of neural stem cells derived from tree shrews.

  7. Development of a tree shrew metabolic syndrome model and use of umbilical cord mesenchymal stem cell transplantation for treatment.

    Science.gov (United States)

    Pan, Xing-Hua; Zhu, Lu; Yao, Xiang; Liu, Ju-Fen; Li, Zi-An; Yang, Jian-Yong; Pang, Rong-Qing; Ruan, Guang-Ping

    2016-12-01

    The aim of this study was to establish a tree shrew metabolic syndrome model and demonstrate the utility of MSCs in treating metabolic syndrome. We used tree shrew umbilical cord mesenchymal stem cell (TS-UC-MSC) transplantation for the treatment of metabolic syndrome to demonstrate the clinical application of these stem cells and to provide a theoretical basis and reference methods for this treatment. Tree shrew metabolic syndrome model showed significant insulin resistance, high blood sugar, lipid metabolism disorders, and hypertension, consistent with the diagnostic criteria. TS-UC-MSC transplantation at 16 weeks significantly reduced blood sugar and lipid levels, improved insulin resistance and the regulation of insulin secretion, and reduced the expression levels of the pro-inflammatory cytokines IL-1 and IL-6 (P metabolic syndrome model and showed that MSC migrate in diseased organs and can attenuate metabolic syndrome severity in a tree shrew model.

  8. Long-term propagation of tree shrew spermatogonial stem cells in culture and successful generation of transgenic offspring

    OpenAIRE

    Li, Chao-Hui; Yan, Lan-Zhen; Ban, Wen-Zan; Tu, Qiu; Wu, Yong; Wang, Lin; Bi, Rui; Ji, Shuang; Ma, Yu-Hua; Nie, Wen-Hui; Lv, Long-Bao; Yao, Yong-Gang; Zhao, Xu-Dong; Zheng, Ping

    2016-01-01

    Tree shrews have a close relationship to primates and have many advantages over rodents in biomedical research. However, the lack of gene manipulation methods has hindered the wider use of this animal. Spermatogonial stem cells (SSCs) have been successfully expanded in culture to permit sophisticated gene editing in the mouse and rat. Here, we describe a culture system for the long-term expansion of tree shrew SSCs without the loss of stem cell properties. In our study, thymus cell antigen 1 ...

  9. Structure of corneal layers, collagen fibrils, and proteoglycans of tree shrew cornea.

    Science.gov (United States)

    Almubrad, Turki; Akhtar, Saeed

    2011-01-01

    The stroma is the major part of the cornea, in which collagen fibrils and proteoglycans are distributed uniformly. We describe the ultrastructure of corneal layers, collagen fibrils (CF), and proteoglycans (PGs) in the tree shrew cornea. Tree shrew corneas (5, 6, and 10 week old animals) and normal human corneas (24, 25, and 54 years old) were fixed in 2.5% glutaraldehyde containing cuprolinic blue in a sodium acetate buffer. The tissue was processed for electron microscopy. The 'iTEM Olympus Soft Imaging Solutions GmbH' program was used to measure the corneal layers, collagen fibril diameters and proteoglycan areas. The tree shrew cornea consists of 5 layers: the epithelium, Bowman's layer, stroma, Descemet's membrane, and endothelium. The epithelium was composed of squamous cells, wing cells and basal cells. The Bowman's layer was 5.5±1.0 µm thick and very similar to a normal human Bowman's layer. The stroma was 258±7.00 µm thick and consisted of collagen fibril lamellae. The lamellae were interlaced with one another in the anterior stroma, but ran parallel to one another in the middle and posterior stroma. Collagen fibrils were decorated with proteoglycan filaments with an area size of 390 ±438 nm(2). The collagen fibril had a minimum diameter of 39±4.25 nm. The interfibrillar spacing was 52.91±6.07 nm. Within the collagen fibrils, very small electron-dense particles were present. The structure of the tree shrew cornea is very similar to that of the normal human cornea. As is the case with the human cornea, the tree shrew cornea had a Bowman's layer, lamellar interlacing in the anterior stroma and electron-dense particles within the collagen fibrils. The similarities of the tree shrew cornea with the human cornea suggest that it could be a good structural model to use when studying changes in collagen fibrils and proteoglycans in non-genetic corneal diseases, such as ectasia caused after LASIK (laser-assisted in situ keratomileusis).

  10. Structure of corneal layers, collagen fibrils, and proteoglycans of tree shrew cornea

    Science.gov (United States)

    Almubrad, Turki

    2011-01-01

    Purpose The stroma is the major part of the cornea, in which collagen fibrils and proteoglycans are distributed uniformly. We describe the ultrastructure of corneal layers, collagen fibrils (CF), and proteoglycans (PGs) in the tree shrew cornea. Methods Tree shrew corneas (5, 6, and 10 week old animals) and normal human corneas (24, 25, and 54 years old) were fixed in 2.5% glutaraldehyde containing cuprolinic blue in a sodium acetate buffer. The tissue was processed for electron microscopy. The ‘iTEM Olympus Soft Imaging Solutions GmbH’ program was used to measure the corneal layers, collagen fibril diameters and proteoglycan areas. Results The tree shrew cornea consists of 5 layers: the epithelium, Bowman’s layer, stroma, Descemet’s membrane, and endothelium. The epithelium was composed of squamous cells, wing cells and basal cells. The Bowman’s layer was 5.5±1.0 µm thick and very similar to a normal human Bowman’s layer. The stroma was 258±7.00 µm thick and consisted of collagen fibril lamellae. The lamellae were interlaced with one another in the anterior stroma, but ran parallel to one another in the middle and posterior stroma. Collagen fibrils were decorated with proteoglycan filaments with an area size of 390 ±438 nm2. The collagen fibril had a minimum diameter of 39±4.25 nm. The interfibrillar spacing was 52.91±6.07 nm. Within the collagen fibrils, very small electron-dense particles were present. Conclusions The structure of the tree shrew cornea is very similar to that of the normal human cornea. As is the case with the human cornea, the tree shrew cornea had a Bowman's layer, lamellar interlacing in the anterior stroma and electron-dense particles within the collagen fibrils. The similarities of the tree shrew cornea with the human cornea suggest that it could be a good structural model to use when studying changes in collagen fibrils and proteoglycans in non-genetic corneal diseases, such as ectasia caused after LASIK (laser

  11. New advances in tree shrew model in experimental studies of hepatitis B virus

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    JIN Xiong

    2015-09-01

    Full Text Available Hepatitis B virus (HBV infection is the main cause of liver fibrosis, cirrhosis, and hepatocellular carcinoma, and it is also a major health problem around the world. How to establish an efficient, reliable, and standardized animal model of chronic HBV infection is essential to the study of the pathogenesis and prevention strategies for HBV infection. This review summarizes the general research and new advances in using tree shrews as the model of HBV infection. We believe that tree shrews, as lower primates, will provide a vital platform and have a huge potential for building a proper animal model in the future, and could become the essential animal model for simulating the process of HBV infection in humans.

  12. Tree shrew lavatories: a novel nitrogen sequestration strategy in a tropical pitcher plant

    Science.gov (United States)

    Clarke, Charles M.; Bauer, Ulrike; Lee, Ch'ien C.; Tuen, Andrew A.; Rembold, Katja; Moran, Jonathan A.

    2009-01-01

    Nepenthes pitcher plants are typically carnivorous, producing pitchers with varying combinations of epicuticular wax crystals, viscoelastic fluids and slippery peristomes to trap arthropod prey, especially ants. However, ant densities are low in tropical montane habitats, thereby limiting the potential benefits of the carnivorous syndrome. Nepenthes lowii, a montane species from Borneo, produces two types of pitchers that differ greatly in form and function. Pitchers produced by immature plants conform to the ‘typical’ Nepenthes pattern, catching arthropod prey. However, pitchers produced by mature N. lowii plants lack the features associated with carnivory and are instead visited by tree shrews, which defaecate into them after feeding on exudates that accumulate on the pitcher lid. We tested the hypothesis that tree shrew faeces represent a significant nitrogen (N) source for N. lowii, finding that it accounts for between 57 and 100 per cent of foliar N in mature N. lowii plants. Thus, N. lowii employs a diversified N sequestration strategy, gaining access to a N source that is not available to sympatric congeners. The interaction between N. lowii and tree shrews appears to be a mutualism based on the exchange of food sources that are scarce in their montane habitat. PMID:19515656

  13. Varied behavioral responses induced by morphine in the tree shrew: a possible model for human opiate addiction

    Directory of Open Access Journals (Sweden)

    Fang eShen

    2014-09-01

    Full Text Available Tree shrews represent a suitable animal model to study the pathogenesis of human diseases as they are phylogenetically close to primates and have a well-developed central nervous system that possesses many homologies with primates. Therefore, in our study, we investigated whether tree shrews can be used to explore the addictive behaviors induced by morphine. Firstly, to investigate the psychoactive effect of morphine on tree shrews’ behavior, the number of jumping and shuttling, which represent the vertical and horizontal locomotor activity respectively, was examined following the injection of different dosage of morphine. Our results showed intramuscular (IM injection of morphine (5 or 10 mg/kg significantly increased the locomotor activity of tree shrews 30-60 min post-injection. Then, using the conditioned place preference/aversion (CPP/CPA paradigm, we found morphine-conditioned tree shrews exhibited place preference in the morphine-paired chamber on the test day. In addition, naloxone-precipitated withdrawal induced place aversion in the chronic morphine-dependent tree shrews. We evaluated the craving for morphine drinking by assessing the break point that reflects the maximum effort animals will expend to get the drug. Our data showed the break point was significantly increased when compared to the baseline on the 1st, 7th and 14th day after the abstinence. Moreover, in the intravenous morphine self-administration experiment, tree shrews conditioned with morphine responded on the active lever significantly more frequently than on the inactive lever after training. These results suggest that tree shrew may be a potential candidate for study the addictive behaviors and the underling neurological mechanisms.

  14. Umbilical Cord-Derived Mesenchymal Stem Cells Relieve Hindlimb Ischemia through Enhancing Angiogenesis in Tree Shrews

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    Cunping Yin

    2016-01-01

    Full Text Available Hindlimb ischemia is still a clinical problem with high morbidity and mortality. Patients suffer from consequent rest pain, ulcers, cool limbs, and even amputation. Angiogenesis is a promising target for the treatment of ischemic limbs, providing extra blood for the ischemic region. In the present study, we investigated the role of umbilical cord-derived mesenchymal stem cells (UC-MSCs in regulating angiogenesis and relieving hindlimb ischemia. UC-MSCs were isolated from the umbilical cord of tree shrews. Angiography results showed that UC-MSCs injection significantly promoted angiogenesis in tree shrews. Moreover, the ankle brachial index, transcutaneous oxygen pressure, blood perfusion, and capillary/muscle fiber ratio were all markedly increased by the application of UC-MSCs. In addition, the conditioned culture of human umbilical vein endothelial cells using medium collected from UC-MSCs showed higher expression of angiogenic markers and improved migration ability. In short, the isolated UC-MSCs notably contributed to restoring blood supply and alleviating the symptoms of limb ischemia through enhancing angiogenesis.

  15. Umbilical Cord-Derived Mesenchymal Stem Cells Relieve Hindlimb Ischemia through Enhancing Angiogenesis in Tree Shrews.

    Science.gov (United States)

    Yin, Cunping; Liang, Yuan; Zhang, Jian; Ruan, Guangping; Li, Zian; Pang, Rongqing; Pan, Xinghua

    2016-01-01

    Hindlimb ischemia is still a clinical problem with high morbidity and mortality. Patients suffer from consequent rest pain, ulcers, cool limbs, and even amputation. Angiogenesis is a promising target for the treatment of ischemic limbs, providing extra blood for the ischemic region. In the present study, we investigated the role of umbilical cord-derived mesenchymal stem cells (UC-MSCs) in regulating angiogenesis and relieving hindlimb ischemia. UC-MSCs were isolated from the umbilical cord of tree shrews. Angiography results showed that UC-MSCs injection significantly promoted angiogenesis in tree shrews. Moreover, the ankle brachial index, transcutaneous oxygen pressure, blood perfusion, and capillary/muscle fiber ratio were all markedly increased by the application of UC-MSCs. In addition, the conditioned culture of human umbilical vein endothelial cells using medium collected from UC-MSCs showed higher expression of angiogenic markers and improved migration ability. In short, the isolated UC-MSCs notably contributed to restoring blood supply and alleviating the symptoms of limb ischemia through enhancing angiogenesis.

  16. A Comparative Analysis of the Endocannabinoid System in the Retina of Mice, Tree Shrews, and Monkeys

    DEFF Research Database (Denmark)

    Bouskila, Joseph; Javadi, Pasha; Elkrief, Laurent

    2016-01-01

    The endocannabinoid (eCB) system is widely expressed in various parts of the central nervous system, including the retina. The localization of the key eCB receptors, particularly CB1R and CB2R, has been recently reported in rodent and primate retinas with striking interspecies differences. Little...... is known about the distribution of the enzymes involved in the synthesis and degradation of these eCBs. We therefore examined the expression and localization of the main components of the eCB system in the retina of mice, tree shrews, and monkeys. We found that CB1R and FAAH distributions are well...... of the outer retina and in retinal neurons of the inner retina; in monkeys, CB2R is restricted to Müller cells. Finally, the expression patterns of MAGL and DAGLα are differently expressed across species. Overall, these results provide evidence that the eCB system is differently expressed in the retina...

  17. Chronic psychosocial stressors in adulthood: Studies in mice, rats and tree shrews

    Directory of Open Access Journals (Sweden)

    Christopher R. Pryce

    2017-02-01

    Full Text Available Human psychological stress is the major environmental risk factor for major depression and certain of the anxiety disorders. Psychological stressors often occur in the context of the adult social environment, and they or the memory formed of them impact on the individual across an extended period, thereby constituting chronic psychosocial stress (CPS. Psychosocial stressors often involve loss to the individual, such as the ending of a social relationship or the onset of interpersonal conflict leading to loss of social control and predictability. Given the difficulty in studying the etio-pathophysiological processes mediating between CPS and brain and behavior pathologies in human, considerable effort has been undertaken to study manipulations of the social environment that constitute adulthood chronic psychosocial stressors in other mammals. The majority of such research has been conducted in rodents; the focus for a considerable time period was on rats and more recently both rats and mice have been investigated, the latter species in particular providing the opportunity for essential gene x chronic psychosocial stressor interaction studies. Key studies in the tree shrew demonstrate that this approach should not be limited to rodents, however. The animal adult CPS paradigms are based on resident-intruder confrontations. These are typified by the intruder-subject's brief proximate interactions with and attacks by, and otherwise continuous distal exposure to, the resident stressor. In contrast to humans where cognitive capacities are such that the stressor pertains in its physical absence, the periods of continuous distal exposure are apparently essential in these species. Whilst the focus of this review is on the stressor rather than the stress response, we also describe some of the depression- and anxiety disorder-relevant effects on behavior, physiology and brain structure-function of chronic psychosocial stressors, as well as evidence for the

  18. Body mass, Thermogenesis and energy metabolism in Tupaia belangeri during cold acclimation

    Directory of Open Access Journals (Sweden)

    Wan-long Zhu

    2012-05-01

    Full Text Available In order to study the relationship between energy strategies and environmental temperature, basal metabolic rate (BMR, nonshivering thermogenesis (NST, the total protein contents, mitochondrial protein contents, state and state respiratory ability, cytochrome C oxidase activity Ⅲ Ⅳ of liver, heart, diaphragm, gastrocnemius and brown adipose tissue (BAT, serum leptin level and serum thyroid hormone levels were measured in tree shrews (Tupaia belangeri during cold exposure (5±1oC for 1 day, 7 days,14days,21 days. The results showed that body mass increased, BMR and NST increased, the change of liver mitochondrial protein content was more acutely than total protein. The mitochondrial protein content of heart and BAT were significantly increased during cold-exposed, however the skeletal muscle more moderate reaction. The state Ⅲ and state Ⅳ mitochondrial respiration of these tissues were enhanced significantly than the control. The cytochrome C oxidase activity with cold acclimation also significantly increased except the gastrocnemius. Liver, muscle, BAT, heart and other organs were concerned with thermoregulation during the thermal regulation process above cold-exposed. There is a negative correlation between leptin level and body mass. These results suggested that T. belangeri enhanced thermogenic capacity during cold acclimation, and leptin participated in the regulation of energy balance and body weight in T. belangeri.

  19. Variability and constraint of vertebral formulae and proportions in colugos, tree shrews, and rodents, with special reference to vertebral modification by aerodynamic adaptation.

    Science.gov (United States)

    Kawashima, Tomokazu; Thorington, Richard W; Bohaska, Paula W; Sato, Fumi

    2017-07-13

    The aim of the present study is to provide the first large data set on vertebral formulae and proportions, and examine their relationship with different locomotive modes in colugos (Dermoptera), tree shrews (Scandentia), and rodents (Rodentia), which have been considered less variable because they were thought to have a plesiomorphic number of 19 thoracolumbar vertebrae. The data included 33 colugos and 112 tree shrews, which are phylogenetically sister taxa, and 288 additional skeletons from 29 other mammalian species adapted to different locomotive modes, flying, gliding, arboreal, terrestrial, digging, and semi-aquatic habitats. The following results were obtained: (1) intra-/interspecies variability and geographical variation in thoracic, lumbar, and thoracolumbar counts were present in two gliding colugo species and 12 terrestrial/arboreal tree shrew species; (2) in our examined mammals, some aerodynamic mammals, such as colugos, southern flying squirrels, scaly-tailed squirrels, and bats, showed exceptionally high amounts of intraspecific variation of thoracic, lumbar, and thoracolumbar counts, and sugar gliders and some semi-aquatic rodents also showed some variation; (3) longer thoracic and shorter lumbar vertebrae were typically shared traits among the examined mammals, except for flying squirrels (Pteromyini) and scaly-tailed squirrels (Anomaluridae). Our study reveals that aerodynamic adaptation could potentially lead to strong selection and modification of vertebral formulae and/or proportions based on locomotive mode despite evolutionary and developmental constraints.

  20. Addiction: from context-induced hedonia to appetite, based on transition of micro-behaviors in morphine abstinent tree shrews

    Directory of Open Access Journals (Sweden)

    Ying eDuan

    2016-06-01

    Full Text Available AbstractDrug addiction is viewed as a maladaptive memory induced by contextual cues even in the abstinent state. However, the variations of hedonia and appetite induced by the context during the abstinence have been neglected. To distinguish the representative behaviors between hedonia and appetite, micro-behaviors in abstinent animal such as psycho-activity and drug seeking behaviors were observed in morphine conditioned place preference (CPP. To confirm the different effects of reward between drug and natural reward, a palatable food CPP paradigm was compared in current work. After a 10-day training in CPP with morphine or food, the preference was tested on day 1, 14, 28, and the changes of micro-behaviors were analyzed further. Our data showed that tree shrews treated with morphine performed more jumps on day 1 and more visits to saline paired side on day 28, which indicated a featured behavioral transition from psycho-activity to seeking behavior during drug abstinence. Meanwhile, food-conditioned animals only displayed obvious seeking behaviors in the three tests. The results suggest that the variations of micro-behaviors could imply such a transition from hedonic response to appetitive behaviors during morphine abstinence, which provided a potential behavioral basis for further neural mechanism studies.

  1. Social stress in tree shrews as an animal model of depression: an example of a behavioral model of a CNS disorder.

    Science.gov (United States)

    Fuchs, Eberhard

    2005-03-01

    Animal models are invaluable in preclinical research on human psychopathology. Valid animal models to study the pathophysiology of depression and specific biological and behavioral responses to antidepressant drug treatments are of prime interest. In order to improve our knowledge of the causal mechanisms of stress-related disorders such as depression, we need animal models that mirror the situation seen in patients. One promising model is the chronic psychosocial stress paradigm in male tree shrews. Coexistence of two males in visual and olfactory contact leads to a stable dominant/subordinate relationship, with the subordinates showing obvious changes in behavioral, neuroendocrine, and central nervous activity that are similar to the signs and symptoms observed during episodes of depression in patients. To discover whether this model, besides its "face validity" for depression, also has "predictive validity," we treated subordinate animals with the tricyclic antidepressant clomipramine and found a time-dependent recovery of both endocrine function and normal behavior. In contrast, the anxiolytic diazepam was ineffective. Chronic psychosocial stress in male tree shrews significantly decreased hippocampal volume and the proliferation rate of the granule precursor cells in the dentate gyrus. These stress-induced changes can be prevented by treating the animals with clomipramine, tianeptine, or the selective neurokinin receptor antagonist L-760,735. In addition to its apparent face and predictive validity, the tree shrew model also has a "molecular validity" due to the degradation routes of psychotropic compounds and gene sequences of receptors are very similar to those in humans. Although further research is required to validate this model fully, it provides an adequate and interesting non-rodent experimental paradigm for preclinical research on depression.

  2. Development of starburst cholinergic amacrine cells in the retina of Tupaia belangeri.

    Science.gov (United States)

    Knabe, Wolfgang; Washausen, Stefan; Happel, Nicole; Kuhn, Hans-Jürg

    2007-06-01

    "Starburst" cholinergic amacrines specify the response of direction-selective ganglion cells to image motion. Here, development of cholinergic amacrines was studied in the tree shrew Tupaia belangeri (Scandentia) by immunohistochemistry with antibodies against choline acetyltransferase (ChAT) and neurofilament proteins. Starburst amacrines expressed ChAT much earlier than previously thought. From embryonic day 34 (E34) onward, orthotopic and displaced subpopulations segregated from a single cluster of immunoreactive precursor cells. Orthotopic starburst amacrines rapidly took up positions in the inner nuclear layer. Displaced starburst amacrines were first arranged in a monocellular row in the inner plexiform layer, and, with a delay of 1 week, they descended to the ganglion cell layer. Conversely, dendritic stratification of displaced amacrines slightly preceded that of orthotopic ones. Starburst amacrines expressed the medium-molecular-weight neurofilament protein (NF-M) from E34 to postnatal day 11 (P11) and coexpressed alpha-internexin from E36.5 to P11. Consequently, neurofilaments composed of alpha-internexin and NF-M may stabilize developing dendrites of starburst amacrines. During the first 2 postnatal weeks, subpopulations of anti-NF-M-labeled ganglion cells costratified with the preexisting dendritic strata of starburst amacrines in the ON sublamina, OFF sublamina, or both. Hence, anti-NF-M-labeled ganglion cells may include direction-selective ones. Thereafter, NF-M and alpha-internexin proteins disappeared from starburst amacrines, and NF-M immunoreactivity was lost in the dendrites of ganglion cells. Our findings suggest that NF-M and alpha-internexin are important for starburst amacrines and ganglion cells to recognize each other and, thus, contribute to the formation of early developing retinal circuits in the inner plexiform layer. (c) 2007 Wiley-Liss, Inc.

  3. Bone Marrow Mesenchymal Stem-Cell Transplantation Promotes Functional Improvement Associated with CNTF-STAT3 Activation after Hemi-Sectioned Spinal Cord Injury in Tree Shrews.

    Science.gov (United States)

    Xiong, Liu-Lin; Liu, Fei; Lu, Bing-Tuan; Zhao, Wen-Ling; Dong, Xiu-Juan; Liu, Jia; Zhang, Rong-Ping; Zhang, Piao; Wang, Ting-Hua

    2017-01-01

    Hemi-sectioned spinal cord injury (hSCI) can lead to spastic paralysis on the injured side, as well as flaccid paralysis on the contralateral side, which can negatively affect a patient's daily life. Stem-cell therapy may offer an effective treatment option for individuals with hSCI. To examine the role of bone marrow mesenchymal stem cells (BMSCs) transplantation on hSCI and explore related mechanisms in the tree shrews, here, we created a model of hSCI by inducing injury at the tenth thoracic vertebra (T10). Hoechst 33342-labeled BMSCs derived from adult tree shrews were isolated, cultured, and implanted into the spinal cord around the injury site at 9 days after injury. The isolated BMSCs were able to survive, proliferate and release a variety of neurotrophic factors (NTFs) both in vitro and in vivo . At 28 days after injury, compared with the sham group, the hSCI group displayed scar formation and dramatic elevations in the mean interleukin 1 beta (IL-1β) density and cell apoptosis level, whereas the expression of signal transducer and activator of transcription 3 ( STAT3 ) and ciliary neurotrophic factor ( CNTF ) mRNA was reduced. Following BMSC transplantation, motoneurons extent of shrinkage were reduced and the animals' Basso, Beattie, and Bresnahan (BBB) locomotion scale scores were significantly higher at 21 and 28 days after injury when compared with the injured group. Moreover, the hSCI-induced elevations in scar formation, IL-1β, and cell apoptosis were reduced by BMSC transplantation to levels that were close to those of the sham group. Corresponding elevations in the expression of STAT3 and CNTF mRNA were observed in the hSCI + BMSCs group, and the levels were not significantly different from those observed in the sham group. Together, our results support that grafted BMSCs can significantly improve locomotor function in tree shrews subjected to hSCI and that this improvement is associated with the upregulation of CNTF and STAT3 signaling.

  4. Bone Marrow Mesenchymal Stem-Cell Transplantation Promotes Functional Improvement Associated with CNTF-STAT3 Activation after Hemi-Sectioned Spinal Cord Injury in Tree Shrews

    Directory of Open Access Journals (Sweden)

    Liu-Lin Xiong

    2017-06-01

    Full Text Available Hemi-sectioned spinal cord injury (hSCI can lead to spastic paralysis on the injured side, as well as flaccid paralysis on the contralateral side, which can negatively affect a patient’s daily life. Stem-cell therapy may offer an effective treatment option for individuals with hSCI. To examine the role of bone marrow mesenchymal stem cells (BMSCs transplantation on hSCI and explore related mechanisms in the tree shrews, here, we created a model of hSCI by inducing injury at the tenth thoracic vertebra (T10. Hoechst 33342-labeled BMSCs derived from adult tree shrews were isolated, cultured, and implanted into the spinal cord around the injury site at 9 days after injury. The isolated BMSCs were able to survive, proliferate and release a variety of neurotrophic factors (NTFs both in vitro and in vivo. At 28 days after injury, compared with the sham group, the hSCI group displayed scar formation and dramatic elevations in the mean interleukin 1 beta (IL-1β density and cell apoptosis level, whereas the expression of signal transducer and activator of transcription 3 (STAT3 and ciliary neurotrophic factor (CNTF mRNA was reduced. Following BMSC transplantation, motoneurons extent of shrinkage were reduced and the animals’ Basso, Beattie, and Bresnahan (BBB locomotion scale scores were significantly higher at 21 and 28 days after injury when compared with the injured group. Moreover, the hSCI-induced elevations in scar formation, IL-1β, and cell apoptosis were reduced by BMSC transplantation to levels that were close to those of the sham group. Corresponding elevations in the expression of STAT3 and CNTF mRNA were observed in the hSCI + BMSCs group, and the levels were not significantly different from those observed in the sham group. Together, our results support that grafted BMSCs can significantly improve locomotor function in tree shrews subjected to hSCI and that this improvement is associated with the upregulation of CNTF and STAT3

  5. Property of hepatitis B virus replication in Tupaia belangeri hepatocytes

    Energy Technology Data Exchange (ETDEWEB)

    Sanada, Takahiro [Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science, 2-1-6, Kamikitazawa, Setagaya-ku, Tokyo 156-8506 (Japan); Tsukiyama-Kohara, Kyoko, E-mail: kkohara@vet.kagoshima-u.ac.jp [Transboundary Animal Diseases Centre, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24, Korimoto, Kagoshima-city, Kagoshima 890-0065 (Japan); Laboratory of Animal Hygiene, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24, Korimoto, Kagoshima, Kagoshima 890-0065 (Japan); Yamamoto, Naoki [Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science, 2-1-6, Kamikitazawa, Setagaya-ku, Tokyo 156-8506 (Japan); Ezzikouri, Sayeh; Benjelloun, Soumaya [Viral Hepatitis Laboratory, Virology Unit, Institut Pasteur du Maroc, 1, Louis Pasteur, Casablanca 20360 (Morocco); Murakami, Shuko; Tanaka, Yasuhito [Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Kawasumi 1, Mizuho-ku, Nagoya, Aichi 467-8601 (Japan); Tateno, Chise [PhoenixBio Co. Ltd., 3-4-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-0046 (Japan); Kohara, Michinori, E-mail: kohara-mc@igakuken.or.jp [Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science, 2-1-6, Kamikitazawa, Setagaya-ku, Tokyo 156-8506 (Japan)

    2016-01-08

    The northern treeshrew (Tupaia belangeri) has been reported to be an effective candidate for animal infection model with hepatitis B virus (HBV). The objective of our study was to analyze the growth characteristics of HBV in tupaia hepatocytes and the host response to HBV infection. We established primary tupaia hepatocytes (3–6-week old tupaia) and infected them with HBV genotypes A, B and C, and all the genotypes proliferated as well as those in human primary hepatocytes (>10{sup 5} copies/ml in culture supernatant). We next generated a chimeric mouse with tupaia liver by transplantation of tupaia primary hepatocytes to urokinase-type plasminogen activator cDNA (cDNA-uPA)/severe combined immunodeficient (SCID) mice and the replacement ratio with tupaia hepatocytes was found to be more than 95%. Infection of chimeric mice with HBV (genotypes B, C, and D) resulted in HBV-DNA level of 10{sup 4}-10{sup 6} copies/ml after 8 weeks of infection, which were almost similar to that in humanized chimeric mouse. In contrast, serum HBV level in adult tupaia (1-year-old tupaia) was quite low (<10{sup 3} copies/ml). Understanding the differences in the response to HBV infection in primary tupaia hepatocytes, chimeric mouse, and adult tupaia will contribute to elucidating the mechanism of persistent HBV infection and viral eradication. Thus, T. belangeri was found to be efficient for studying the host response to HBV infection, thereby providing novel insight into the pathogenesis of HBV. - Highlights: • Primary hepatocytes were established from tupaia that is a novel HBV infection model. • Tupaia primary hepatocytes were susceptible for HBV infection. • The immunodeficient chimeric mice with tupaia hepatocytes were established. • The chimeric mice with tupaia hepatocytes were susceptible for HBV infection.

  6. Property of hepatitis B virus replication in Tupaia belangeri hepatocytes

    International Nuclear Information System (INIS)

    Sanada, Takahiro; Tsukiyama-Kohara, Kyoko; Yamamoto, Naoki; Ezzikouri, Sayeh; Benjelloun, Soumaya; Murakami, Shuko; Tanaka, Yasuhito; Tateno, Chise; Kohara, Michinori

    2016-01-01

    The northern treeshrew (Tupaia belangeri) has been reported to be an effective candidate for animal infection model with hepatitis B virus (HBV). The objective of our study was to analyze the growth characteristics of HBV in tupaia hepatocytes and the host response to HBV infection. We established primary tupaia hepatocytes (3–6-week old tupaia) and infected them with HBV genotypes A, B and C, and all the genotypes proliferated as well as those in human primary hepatocytes (>10 5 copies/ml in culture supernatant). We next generated a chimeric mouse with tupaia liver by transplantation of tupaia primary hepatocytes to urokinase-type plasminogen activator cDNA (cDNA-uPA)/severe combined immunodeficient (SCID) mice and the replacement ratio with tupaia hepatocytes was found to be more than 95%. Infection of chimeric mice with HBV (genotypes B, C, and D) resulted in HBV-DNA level of 10 4 -10 6 copies/ml after 8 weeks of infection, which were almost similar to that in humanized chimeric mouse. In contrast, serum HBV level in adult tupaia (1-year-old tupaia) was quite low (<10 3 copies/ml). Understanding the differences in the response to HBV infection in primary tupaia hepatocytes, chimeric mouse, and adult tupaia will contribute to elucidating the mechanism of persistent HBV infection and viral eradication. Thus, T. belangeri was found to be efficient for studying the host response to HBV infection, thereby providing novel insight into the pathogenesis of HBV. - Highlights: • Primary hepatocytes were established from tupaia that is a novel HBV infection model. • Tupaia primary hepatocytes were susceptible for HBV infection. • The immunodeficient chimeric mice with tupaia hepatocytes were established. • The chimeric mice with tupaia hepatocytes were susceptible for HBV infection.

  7. Layer 2/3 synapses in monocular and binocular regions of tree shrew visual cortex express mAChR-dependent long-term depression and long-term potentiation.

    Science.gov (United States)

    McCoy, Portia; Norton, Thomas T; McMahon, Lori L

    2008-07-01

    Acetylcholine is an important modulator of synaptic efficacy and is required for learning and memory tasks involving the visual cortex. In rodent visual cortex, activation of muscarinic acetylcholine receptors (mAChRs) induces a persistent long-term depression (LTD) of transmission at synapses recorded in layer 2/3 of acute slices. Although the rodent studies expand our knowledge of how the cholinergic system modulates synaptic function underlying learning and memory, they are not easily extrapolated to more complex visual systems. Here we used tree shrews for their similarities to primates, including a visual cortex with separate, defined regions of monocular and binocular innervation, to determine whether mAChR activation induces long-term plasticity. We find that the cholinergic agonist carbachol (CCh) not only induces long-term plasticity, but the direction of the plasticity depends on the subregion. In the monocular region, CCh application induces LTD of the postsynaptic potential recorded in layer 2/3 that requires activation of m3 mAChRs and a signaling cascade that includes activation of extracellular signal-regulated kinase (ERK) 1/2. In contrast, layer 2/3 postsynaptic potentials recorded in the binocular region express long-term potentiation (LTP) following CCh application that requires activation of m1 mAChRs and phospholipase C. Our results show that activation of mAChRs induces long-term plasticity at excitatory synapses in tree shrew visual cortex. However, depending on the ocular inputs to that region, variation exists as to the direction of plasticity, as well as to the specific mAChR and signaling mechanisms that are required.

  8. Shrew trap efficiency

    DEFF Research Database (Denmark)

    Gambalemoke, Mbalitini; Mukinzi, Itoka; Amundala, Drazo

    2008-01-01

    We investigated the efficiency of four trap types (pitfall, Sherman LFA, Victor snap and Museum Special snap traps) to capture shrews. This experiment was conducted in five inter-riverine forest blocks in the region of Kisangani. The total trapping effort was 6,300, 9,240, 5,280 and 5,460 trap......-nights for the pitfall, Sherman, Victor and Museum Special traps, respectively. In total, we captured 366 shrews. The use of pitfall traps yielded the highest trapping success (4.1) with at least 18 shrew species identified. Trapping success and the number of species collected was lower for the Sherman (0.6, at least 11...... species), Victor (0.6, at least 8 species) and Museum Special (0.5, at least 6 species) traps. Although Crocidura olivieri and C. denti were caught using all four trap types, captures with different trap types did not produce a sample with the same taxonomic composition. In agreement with previous studies...

  9. Using hand proportions to test taxonomic boundaries within the Tupaia glis species complex (Scandentia, Tupaiidae)

    Science.gov (United States)

    Sargos, Eric J.; Woodman, Neal; Reese, Aspen T.; Olson, Link E.

    2013-01-01

    Treeshrews (order Scandentia) comprise 2 families of squirrel-sized terrestrial, arboreal, and scansorial mammals distributed throughout much of tropical South and Southeast Asia. The last comprehensive taxonomic revision of treeshrews was published in 1913, and a well-supported phylogeny clarifying relationships among all currently recognized extant species within the order has only recently been published. Within the family Tupaiidae, 2 widely distributed species, the northern treeshrew, Tupaia belangeri (Wagner, 1841), and the common treeshrew, T. glis (Diard, 1820), represent a particularly vexing taxonomic complex. These 2 species are currently distinguished primarily based on their respective distributions north and south of the Isthmus of Kra on the Malay Peninsula and on their different mammae counts. This problematic species complex includes 54 published synonyms, many of which represent putative island endemics. The widespread T. glis and T. belangeri collectively comprise a monophyletic assemblage representing the sister lineage to a clade composed of the golden-bellied treeshrew, T. chrysogaster Miller, 1903 (Mentawai Islands), and the long-footed treeshrew, T. longipes (Thomas, 1893) (Borneo). As part of a morphological investigation of the T. glis–T. belangeri complex, we studied the proportions of hand bones, which have previously been shown to be useful in discriminating species of soricids (true shrews). We measured 38 variables from digital X-ray images of 148 museum study skins representing several subspecies of T. glis, T. belangeri, T. chrysogaster, and T. longipes and analyzed these data using principal components and cluster analyses. Manus proportions among these 4 species readily distinguish them, particularly in the cases of T. chrysogaster and T. longipes. We then tested the distinctiveness of several of the populations comprising T. glis and T. longipes. T. longipes longipes and T. l. salatana Lyon, 1913, are distinguishable from each

  10. Susceptibility and initial immune response of Tupaia belangeri cells to dengue virus infection.

    Science.gov (United States)

    Kayesh, Mohammad Enamul Hoque; Kitab, Bouchra; Sanada, Takahiro; Hayasaka, Daisuke; Morita, Kouichi; Kohara, Michinori; Tsukiyama-Kohara, Kyoko

    2017-07-01

    Dengue is an emerging disease of great public health significance worldwide. The lack of a suitable infection model has hampered dengue virus (DENV) pathogenesis study, and developing a suitable small animal model has been a long-standing challenge. The aim of this study was to develop a feasible experimental model of DENV infection using Tupaia belangeri. The susceptibility of tupaia to DENV infection and characteristics of its innate immune response were examined in vitro. We found that tupaia fibroblast cells support replication of DENV serotypes 1-4 with a linear increase in viral load 24-96h post-infection in both cells and culture supernatants. DENV-2 resulted in the highest viral growth among all serotypes. To characterize the innate immune response in tupaia cells during the early phase of DENV infection, we first evaluated the evolutionary relationship between tupaia Toll-like receptors (TLR1-9) and those of other mammalian species. Phylogenetic analysis showed that tupaia TLRs are evolutionarily much closer to human than they are to rodent. We next established an innate immune response measurement system by assessing the mRNA expression of TLR1-9 and four cytokines in DENV-infected tupaia cells. All serotypes induced the upregulation of TLR8 mRNA expression in infected tupaia cells. Silencing of TLR8 led to an increase in viral replication, indicating the existence of antiviral response through TLR8 on DENV infection. Although upregulation of IFN-β and IL-6 expression was only observed in DENV-1 infected cells and a significant suppression of TNF-α was observed in DENV-2 infected cells alone, IL-8 was upregulated in all DENV-1-4. Thus, this study demonstrates for the first time the susceptibility of tupaia cells to DENV infections and the role of TLR8 in the anti-viral response of tupaia cells to DENV. These findings demonstrate the potential utility of tupaia as a model for DENV research in the future. Copyright © 2017 The Authors. Published by

  11. Morphological distinctiveness of Javan Tupaia hypochrysa (Scandentia, Tupaiidae)

    Science.gov (United States)

    Sargis, Eric J.; Woodman, Neal; Morningstar, Natalie C.; Reese, Aspen T.; Olson, Link E.

    2013-01-01

    The common treeshrew, Tupaia glis, represents a species complex with a complicated taxonomic history. It is distributed mostly south of the Isthmus of Kra on the Malay Peninsula and surrounding islands. In our recent revision of a portion of this species complex, we did not fully assess the population from Java (T. “glis” hypochrysa) because of our limited sample. Herein, we revisit this taxon using multivariate analyses in comparisons with T. glis, T. chrysogaster of the Mentawai Islands, and T. ferruginea from Sumatra. Analyses of both the manus and skull of Javan T. “glis” hypochrysa show it to be most similar to T. chrysogaster and distinct from both T. glis and T. ferruginea. Yet, the Javan population and T. chrysogaster have different mammae counts, supporting recognition of T. hypochrysa as a distinct species. The change in taxonomic status of T. hypochrysa has conservation implications for both T. glis and this Javan endemic.

  12. Contiguous allopatry of the masked shrew and southeastern shrew in the Southern Appalachians: segregation along an elevational and habitat gradient

    Science.gov (United States)

    W. Mark Ford; Michael A. Menzel; Timothy S. McCay; Joshua Laerm

    2001-01-01

    Southeastern shrew. (Sorex longirostris) and masked shrew (Sorex cinereus) distributions converge in the Southern Appalachians. A 306,454-pitfall--trapnight survey in Alabama, Georgia, North Carolina, and South Carolina doc-umented the presence of southeastern shrews in the Cumberland Plateau, Ridge and Valley, Upper Piedmont, and...

  13. Muscle Aging and Oxidative Stress in Wild-Caught Shrews

    Science.gov (United States)

    Hindle, Allyson G.; Lawler, John M.; Campbell, Kevin L.; Horning, Markus

    2010-01-01

    Red-toothed shrews (Soricidae, subfamily Soricinae) are an intriguing model system to examine the free radical theory of aging in wild mammals, given their short (<18 month) lifespan and high mass-specific metabolic rates. As muscle performance underlies both foraging ability and predator avoidance, any age-related decline should be detrimental to fitness and survival. Muscle samples of water shrews (Sorex palustris) and sympatrically distributed short-tailed shrews (Blarina brevicauda) were therefore assessed for oxidative stress markers, protective antioxidant enzymes and apoptosis. Activity levels of catalase and glutathione peroxidase increased with age in both species. Similarly, Cu,Zn-superoxide dismutase isoform content was elevated significantly in older animals of both species (increases of 60% in the water shrew, 25% in the short-tailed shrew). Only one oxidative stress marker (lipid peroxidation) was age-elevated; the others were stable or declined (4-hydroxynonenal adducts and dihydroethidium oxidation). Glutathione peroxidase activity was significantly higher in the short-tailed shrew, while catalase activity was 2× higher in water shrews. Oxidative stress indicators were on average higher in short-tailed shrews. Apoptosis occurred in <1% of myocytes examined, and did not increase with age. Within the constraints of the sample size we found evidence of protection against elevated oxidative stress in wild-caught shrews. PMID:20109576

  14. Detection of shrew-borne hantavirus in Eurasian pygmy shrew (Sorex minutus) in Central Europe

    Czech Academy of Sciences Publication Activity Database

    Radosa, L.; Schlegel, M.; Gebauer, P.; Ansorge, H.; Heroldová, Marta; Jánová, Eva; Stanko, M.; Mošanský, L.; Fričová, J.; Pejčoch, M.; Suchomel, J.; Purchart, L.; Groschup, M. H.; Krüger, D. H.; Ulrich, R. G.; Klempa, B.

    2013-01-01

    Roč. 19, October (2013), s. 403-410 ISSN 1567-1348 Institutional support: RVO:68081766 Keywords : Hantavirus * shrew Sorex minutus * Asikkala virus * Cental Europe Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 3.264, year: 2013

  15. Tactile Experience Shapes Prey-Capture Behavior in Etruscan Shrews

    Directory of Open Access Journals (Sweden)

    Michael eBrecht

    2012-06-01

    Full Text Available A crucial role of tactile experience for the maturation of neural response properties in the somatosensory system is well established, but little is known about the role of tactile experience in the development of tactile behaviors. Here we study how tactile experience affects prey capture behavior in Etruscan shrews, Suncus etruscus. Prey capture in adult shrews is a high-speed behavior that relies on precise attacks guided by tactile Gestalt cues. We studied the role of tactile experience by three different approaches. First, we analyzed the hunting skills of young shrews right after weaning. We found that prey capture in young animals is most but not all aspects similar to that of adults. Second we performed whisker trimming for three to four weeks after birth. Such deprivation resulted in a lasting disruption of prey capture even after whisker re-growth: attacks lacked precise targeting and had a lower success rate. Third, we presented adult shrews with an entirely novel prey species, the giant cockroach. The shape of this roach is very different from the shrew’s normal (cricket prey and the thorax – the preferred point of attack in crickets – is protected a heavy cuticle. Initially shrews attacked giant roaches the same way they attack crickets and targeted the thoracic region. With progressive experience, however, shrews adopted a new attack strategy targeting legs and underside of the roaches while avoiding other body parts. Speed and efficiency of attacks improved. These data suggest that tactile experience shapes prey capture behavior.

  16. Skeletal morphology of the forefoot in shrews (Mammalia: Soricidae) of the genus Cryptotis, as revealed by digital x-rays

    Science.gov (United States)

    Woodman, N.; Morgan, J.P.J.

    2005-01-01

    Variation in the forefoot skeleton of small-eared shrews (family Soricidae, genus Cryptotis) has been previously documented, but the paucity of available skeletons for most taxa makes assessment of the degrees of intraspecific and interspecific variation difficult. We used a digital X-ray system to extract images of the forefoot skeleton from 101 dried skins of eight taxa (seven species, including two subspecies of one species) of these shrews. Lengths and widths of each of the four bones of digit III were measured directly from the digital images, and we used these data to quantify variation within and among taxa. Analysis of the images and measurements showed that interspecific variation exceeds intraspecific variation. In fact, most taxa could be distinguished in multivariate and some bivariate plots. Our quantitative data helped us define a number of specific forefoot characters that we subsequently used to hypothesize evolutionary relationships among the taxa using the exhaustive search option in PAUP, a computer program for phylogenetic analysis. The resulting trees generally concur with previously published evolutionary hypotheses for small-eared shrews. Cryptotis meridensis, a taxon not previously examined in recent phylogenies, is rooted at the base of the branch leading to the C. mexicana group of species. The position of this species suggests that the mostly South American C. thomasi group shares an early ancestor with the C. mexicana group.

  17. Effects of late quaternary climate change on Palearctic shrews.

    Science.gov (United States)

    Prost, Stefan; Klietmann, Johannes; van Kolfschoten, Thijs; Guralnick, Robert P; Waltari, Eric; Vrieling, Klaas; Stiller, Mathias; Nagel, Doris; Rabeder, Gernot; Hofreiter, Michael; Sommer, Robert S

    2013-06-01

    The Late Quaternary was a time of rapid climatic oscillations and drastic environmental changes. In general, species can respond to such changes by behavioral accommodation, distributional shifts, ecophenotypic modifications (nongenetic), evolution (genetic) or ultimately face local extinction. How those responses manifested in the past is essential for properly predicting future ones especially as the current warm phase is further intensified by rising levels of atmospheric carbon dioxide. Here, we use ancient DNA (aDNA) and morphological features in combination with ecological niche modeling (ENM) to investigate genetic and nongenetic responses of Central European Palearctic shrews to past climatic change. We show that a giant form of shrew, previously described as an extinct Pleistocene Sorex species, represents a large ecomorph of the common shrew (Sorex araneus), which was replaced by populations from a different gene-pool and with different morphology after the Pleistocene Holocene transition. We also report the presence of the cold-adapted tundra shrew (S. tundrensis) in Central Europe. This species is currently restricted to Siberia and was hitherto unknown as an element of the Pleistocene fauna of Europe. Finally, we show that there is no clear correlation between climatic oscillations within the last 50 000 years and body size in shrews and conclude that a special nonanalogous situation with regard to biodiversity and food supply in the Late Glacial may have caused the observed large body size. © 2013 Blackwell Publishing Ltd.

  18. Discovery of Novel Alphacoronaviruses in European Rodents and Shrews

    Directory of Open Access Journals (Sweden)

    Theocharis Tsoleridis

    2016-03-01

    Full Text Available Eight hundred and thirteen European rodents and shrews encompassing seven different species were screened for alphacoronaviruses using PCR detection. Novel alphacoronaviruses were detected in the species Rattus norvegicus, Microtus agrestis, Sorex araneus and Myodes glareolus. These, together with the recently described Lucheng virus found in China, form a distinct rodent/shrew-specific clade within the coronavirus phylogeny. Across a highly conserved region of the viral polymerase gene, the new members of this clade were up to 22% dissimilar at the nucleotide level to the previously described Lucheng virus. As such they might represent distinct species of alphacoronaviruses. These data greatly extend our knowledge of wildlife reservoirs of alphacoronaviruses.

  19. Exploring the diversity and molecular evolution of shrews (family ...

    African Journals Online (AJOL)

    By constructing the most taxonomically inclusive molecular phylogeny for this cosmopolitan family, this study aims to test the utility of the routinely used mitochondrial cytochrome b gene to resolve the higher-level relationships within the Soricidae. Given the life history characteristics of shrews (high metabolic rate in ...

  20. Sengi (elephant-shrew) observations from northern coastal Kenya ...

    African Journals Online (AJOL)

    The biodiversity of northern coastal Kenya is poorly understood because security problems and poor infrastructure have discouraged access to the area. However, the wooded areas in the region have great potential for harbouring unique and rare species, including sengis or elephant-shrews (Macroscelidea). Based on ...

  1. The Relative host status of rock elephant shrews Elephantulus ...

    African Journals Online (AJOL)

    Several tick species of medical and veterinary importance occur in the southern Orange Free State. The purpose of the present study was to determine the host status of rock elephant shrews ( Elephantulus myurus) and Namaqua rock mice ( Aethomys namaquensis) for these ticks. Infestation levels were used as a criterion.

  2. Rodents and Shrews as Vectors of Zoonotic Spirochetes and ...

    African Journals Online (AJOL)

    Clinically healthy wild rodents and shrews (Crocidura spp.) were captured from different localities in Morogoro, Tanga, Dodoma, Singida, Mbeya, Kilimanjaro and Mtwara regions of Tanzania. Blood samples were collected from the captured animals and screened for infectious agents of public health importance, including; ...

  3. Aggregations of masked shrews (Sorex cinereus): density related mating behavior?

    Science.gov (United States)

    Thomas J. Maier; Katherine L. Doyle

    2006-01-01

    Large aggregations of shrews have been reported and various explanations offered for this seemingly rare behavior; however, there has been little evidence to support any particular interpretation. We observed two small aggregations of highly active vocalizing Sorex cinereus while performing wildlife surveys in forested habitats in central...

  4. First records of smoky shrew (sorex fumeus) in Alabama

    Science.gov (United States)

    Zachary Felix; Lisa J. Gatens; Yong Wang; Callie J. Schweitzer

    2009-01-01

    Conserving biodiversity in the southeastern United States begins with documenting the distribution and natural history of all taxa. Using pitfall traps between March 2005 and January 2006, we collected the fi rst Sorex fumeus (Smoky Shrew) specimens (44) from Alabama on the Cumberland Plateau in the northeastern portion of the state....

  5. Short-tailed shrews: Toxicity and residue relationships of DDT, dieldrin, and endrin

    Science.gov (United States)

    Blus, L.J.

    1978-01-01

    Experiments involving dietary toxicity and residue relationships of DDT, dieldrin, and endrin were conducted with short-tailed shrews. Dietary concentrations of DDT dissolved in vegetable oils were usually more toxic than diets containing comparable amounts of powdered DDT. Younger shrews, particularly females, were more tolerant of powdered DDT than older animals; yet, there were no conspicuous age differences in toxicity of DDT dissolved in oils. In comparison to other mammals, short-tailed shrews are not unusually sensitive to DDT, dieldrin, or endrin on the basis of two-week feeding tests. The influence of age and sex on toxicity of DDT, endrin, and dieldrin was sometimes more important than body weight. Of those shrews of the same age and sex that were fed the same dietary dosage, heavier shrews were more tolerant than lighter individuals; and, heavier shrews tended to lose a greater percentage of body weight before death. There was a range of 15 to 105 DDT equivalents in brains of shrews dying on dietary dosages of DDT. Six shrews fed a high level of DDT seemed to have unusual metabolite capabilities and died with apparent lethal levels of DDD in their brains. Levels of dieldrin in brains of shrews that died on a dietary dosage of dieldrin ranged from 3.7 to 12.6 ppm. In the rates of gain and loss experiments where shrews were given diets containing 400 ppm DDT or 50 ppm dieldrin up to 17 days, high residues were noted in tissues of shrews after two weeks on a contaminated diet and a few died at that time. After shrews were placed on clean food, it was determined that >50% of the dieldrin residues in carcass and brain were lost in 50% of residues of DDT and metabolites in brains after 2 weeks on clean food; males lost nearly 50% of residues in carcasses after two weeks on clean food compared with a loss of only 11% in females.

  6. Fecal pellets from a commensal shrew (Suncus murinus) and a house gecko (Gekkonidae).

    Science.gov (United States)

    Olsen, A R

    1984-01-01

    Examination of excreta pellets from commensal shrew (Suncus murinus) and tropical house geckos (Gekkonidae) showed several characteristics that were useful in distinguishing these pellets from those of commensal rodents. Commensal shrew pellets contained a large number of embedded insect fragments but no embedded hairs. Each shrew pellet was associated with a distinctive circular stain on the floor or container surface where it was found. Gecko pellets were composed entirely of tightly packed insect fragments with no intervening matrix. In contrast to both shrew and rodent pellets, there was no surface mucous coating. A small white body containing uric acid adhered to one end of each gecko pellet.

  7. Leptospira spp. in Rodents and Shrews in Germany

    Directory of Open Access Journals (Sweden)

    Anne Mayer-Scholl

    2014-07-01

    Full Text Available Leptospirosis is an acute, febrile disease occurring in humans and animals worldwide. Leptospira spp. are usually transmitted through direct or indirect contact with the urine of infected reservoir animals. Among wildlife species, rodents act as the most important reservoir for both human and animal infection. To gain a better understanding of the occurrence and distribution of pathogenic leptospires in rodent and shrew populations in Germany, kidney specimens of 2973 animals from 11 of the 16 federal states were examined by PCR. Rodent species captured included five murine species (family Muridae, six vole species (family Cricetidae and six shrew species (family Soricidae. The most abundantly trapped animals were representatives of the rodent species Apodemus flavicollis, Clethrionomys glareolus and Microtus agrestis. Leptospiral DNA was amplified in 10% of all animals originating from eight of the 11 federal states. The highest carrier rate was found in Microtus spp. (13%, followed by Apodemus spp. (11% and Clethrionomys spp. (6%. The most common Leptospira genomospecies determined by duplex PCR was L. kirschneri, followed by L. interrogans and L. borgpetersenii; all identified by single locus sequence typing (SLST. Representatives of the shrew species were also carriers of Leptospira spp. In 20% of Crocidura spp. and 6% of the Sorex spp. leptospiral DNA was detected. Here, only the pathogenic genomospecies L. kirschneri was identified.

  8. Leptospira spp. in Rodents and Shrews in Germany

    Science.gov (United States)

    Mayer-Scholl, Anne; Hammerl, Jens Andre; Schmidt, Sabrina; Ulrich, Rainer G.; Pfeffer, Martin; Woll, Dietlinde; Scholz, Holger C.; Thomas, Astrid; Nöckler, Karsten

    2014-01-01

    Leptospirosis is an acute, febrile disease occurring in humans and animals worldwide. Leptospira spp. are usually transmitted through direct or indirect contact with the urine of infected reservoir animals. Among wildlife species, rodents act as the most important reservoir for both human and animal infection. To gain a better understanding of the occurrence and distribution of pathogenic leptospires in rodent and shrew populations in Germany, kidney specimens of 2973 animals from 11 of the 16 federal states were examined by PCR. Rodent species captured included five murine species (family Muridae), six vole species (family Cricetidae) and six shrew species (family Soricidae). The most abundantly trapped animals were representatives of the rodent species Apodemus flavicollis, Clethrionomys glareolus and Microtus agrestis. Leptospiral DNA was amplified in 10% of all animals originating from eight of the 11 federal states. The highest carrier rate was found in Microtus spp. (13%), followed by Apodemus spp. (11%) and Clethrionomys spp. (6%). The most common Leptospira genomospecies determined by duplex PCR was L. kirschneri, followed by L. interrogans and L. borgpetersenii; all identified by single locus sequence typing (SLST). Representatives of the shrew species were also carriers of Leptospira spp. In 20% of Crocidura spp. and 6% of the Sorex spp. leptospiral DNA was detected. Here, only the pathogenic genomospecies L. kirschneri was identified. PMID:25062275

  9. Novelties of conception in insectivorous mammals (Lipotyphla), particularly shrews.

    Science.gov (United States)

    Bedford, J Michael; Mock, Orin B; Goodman, Steven M

    2004-11-01

    In the order Lipotyphla (Insectivora), certain reproductive features differ quite distinctly from the eutherian norms, and are of interest with regard to the evolution of mammalian gamete function and perhaps for questions of lipotyphlan phylogeny. As seen in one or more members of five lipotyphlan families (shrews, moles, hedgehogs, golden moles, tenrecs), these features can involve the configuration of the male tract including the penis, the morphology of the sperm head, the anatomy of the oviduct and the patterns of sperm transport within it, the character of the cumulus oophorus, and the way in which fertilising spermatozoa interact with the eggs. However, the picture is by no means uniform within the order. Reproductive idiosyncrasies occur variously in the different lipotyphlan families, and appear consistently and strikingly in shrews--the group studied most extensively. Compared to the patterns in most Eutheria, the most interesting anomalies in soricids include (a) the regulation of sperm transport to the site of fertilisation by oviduct crypts, whose arrangement can vary even according to species, (b) a circumscribed matrix-free cumulus oophorus that appears essential for fertilisation as the inducer of the acrosome reaction, (c) barbs on the acrosome-reacted sperm head by which it may attach to the zona pellucida. With regard to the bearing such reproductive traits might have on lipotyphlan systematics, the African mouse shrew (Myosorex varius) displays a mix of traits that characterize either crocidurine or soricine shrews, consistent with the proposal that it belongs in a more primitive tribe, Myosoricinae, or subfamily, the Crocidosoricinae, from which the crocidurine and soricine lines probably evolved. Moreover, although elephant shrews are assigned now to a separate order (Macroscelidea), they display several of the unusual reproductive features seen in lipotyphlans, particularly in chrysochlorids and tenrecs. On the other hand, if used as a

  10. The Fetal Membranes of the Otter Shrews and a Synapomorphy for Afrotheria

    DEFF Research Database (Denmark)

    Carter, Anthony M.; Blankenship, T.N.; Enders, A.C.

    2006-01-01

    The otter shrews of mainland Africa are the closest relatives of the Madagascar tenrecs. We sought for similarities in placentation between the two groups and, in a wider context, with other mammals of the Afrotheria clade. Specimens of the Nimba otter shrew (Micropotamogale lamottei) were obtained...

  11. Observations on the post-natal development of the tiny musk shrew ...

    African Journals Online (AJOL)

    Observations on the post-natal development of the tiny musk shrew, Crocidura bicolor. Christine A.B. Watson, R.T. Watson. Abstract. Crocidura bicolor is the smallest of southern Africa's Crocidura shrews and little is known of its biology. A female, captured in the Kruger National Park, was observed giving birth to two young.

  12. Captures of Crawford's gray shrews (Notiosorex crawfordi) along the Rio Grande in central New Mexico

    Science.gov (United States)

    Alice Chung-MacCoubrey; Heather L. Bateman; Deborah M. Finch

    2009-01-01

    We captured >2000 Crawford's gray shrews (Notiosorex crawfordi) in a riparian forest mainly consisting of cottonwoods (Populus deltoides) along the Rio Grande in central New Mexico. Little has been published about abundance and habitat of Crawford's gray shrew throughout its distributional range. During 7 summers, we...

  13. Yersinia spp. in Wild Rodents and Shrews in Finland.

    Science.gov (United States)

    Joutsen, Suvi; Laukkanen-Ninios, Riikka; Henttonen, Heikki; Niemimaa, Jukka; Voutilainen, Liina; Kallio, Eva R; Helle, Heikki; Korkeala, Hannu; Fredriksson-Ahomaa, Maria

    2017-05-01

    Yersinia enterocolitica and Yersinia pseudotuberculosis are important zoonotic bacteria causing human enteric yersiniosis commonly reported in Europe. All Y. pseudotuberculosis strains are considered pathogenic, while Y. enterocolitica include both pathogenic and nonpathogenic strains which can be divided into six biotypes (1A, 1B, and 2-5) and about 30 serotypes. The most common types causing yersiniosis in Europe are Y. enterocolitica bioserotypes 4/O:3 and 2/O:9. Strains belonging to biotype 1A are considered as nonpathogenic because they are missing important virulence genes like the attachment-invasion-locus (ail) gene in the chromosome and the virulence plasmid. The role of wild small mammals as a reservoir of enteropathogenic Yersinia spp. is still obscure. In this study, the presence of Yersinia spp. was examined from 1840 wild small mammals, including voles, mice, and shrews, trapped in Finland during a 7-year period. We isolated seven Yersinia species. Y. enterocolitica was the most common species, isolated from 8% of the animals; while most of these isolates represented nonpathogenic biotype 1A, human pathogenic bioserotype 2/O:9 was also isolated from a field vole. Y. pseudotuberculosis of bioserotype 1/O:2 was isolated from two shrews. The ail gene, which is typically only found in the isolates of biotypes 1B and 2-5 associated with yersiniosis, was frequently (23%) detected in the nonpathogenic isolates of biotype 1A and sporadically (6%) in Yersinia kristensenii isolates. Our results suggest that wild small mammals, especially voles, may serve as carriers for ail-positive Y. enterocolitica 1A and Y. kristensenii. We also demonstrate that voles and shrews sporadically excrete pYV-positive Y. enterocolitica 2/O:9 and Y. pseudotuberculosis 1/O:2, respectively, in their feces and, thus, can serve as a contamination source for vegetables by contaminating the soil.

  14. Examples of the Motif of the Shrew in European Literature and Film

    OpenAIRE

    Vasvári, Louise O.

    2001-01-01

    In her article "Examples of the Motif of the Shrew in European Literature and Film" Louise O. Vasvári presents the shrew-taming story as a masterplot of both Eastern and Western folklore and literature concerned with establishing the appropriate power dynamic between a married couple. Vasvári firts reviews the comparative groundwork of the story she has documented in her earlier studies of the topic. In addition to tracing the bundle of motifs that make up the shrew story from medieval Arabic...

  15. Modelling hippocampal neurogenesis across the lifespan in seven species

    OpenAIRE

    Lazic, Stanley E.

    2011-01-01

    The aim of this study was to estimate the number of new cells and neurons added to the dentate gyrus across the lifespan, and to compare the rate of age-associated decline in neurogenesis across species. Data from mice (Mus musculus), rats (Rattus norvegicus), lesser hedgehog tenrecs (Echinops telfairi), macaques (Macaca mulatta), marmosets (Callithrix jacchus), tree shrews (Tupaia belangeri), and humans (Homo sapiens) were extracted from twenty one data sets published in fourteen different p...

  16. Posture does not matter!:paw usage and grasping paw preference in a small-bodied rooting quadrupedal mammal

    OpenAIRE

    Joly, Marine; Scheumann, Marina; Zimmermann, Elke

    2012-01-01

    BACKGROUND: Recent results in birds, marsupials, rodents and nonhuman primates suggest that phylogeny and ecological factors such as body size, diet and postural habit of a species influence limb usage and the direction and strength of limb laterality. To examine to which extent these findings can be generalised to small-bodied rooting quadrupedal mammals, we studied trees shrews (Tupaia belangeri). METHODOLOGY/PRINCIPAL FINDINGS: We established a behavioural test battery for examining paw us...

  17. Big insights from little animals: allosteric modulation and thermal sensitivity of shrew and mole hemoglobins

    DEFF Research Database (Denmark)

    Campbell, K.L.; Weber, Roy E.

    2007-01-01

    tissue mitochondria with sufficient O2 to fuel oxidative metabolism, such as blood with a high Bohr coefficient and half-saturation pressure (P50). However, a high P50 may drastically impede hemoglobin (Hb) saturation at low ambient PO2's and place a considerable strain on the hypoxia tolerance of shrews...... and moles. Despite these constraints, several shrew (and mole) species flourish at elevations exceeding 4500 m (where atmospheric PO2 is

  18. Biodiversity and evolution of Imjin virus and Thottapalayam virus in Crocidurinae shrews in Zhejiang Province, China.

    Science.gov (United States)

    Lin, Xian-Dan; Zhou, Run-Hong; Fan, Fei-Neng; Ying, Xu-Hua; Sun, Xiao-Yu; Wang, Wen; Holmes, Edward C; Zhang, Yong-Zhen

    2014-08-30

    The recent discovery of numerous hantaviruses in insectivores has provided a new view of hantavirus biodiversity and evolution. To determine the presence and genetic diversity of Imjin virus (MJNV) and Thottapalayam virus (TPMV) in insectivores in Zhejiang Province, China, we captured and performed virus screening of 32 Ussuri white-toothed shrews (Crocidura lasiura) and 105 Asian house shrews (Suncus murinus) in different coastal regions. Hantavirus genome (S, M, and L segments) sequences were successfully recovered from one Ussuri white-toothed shrew and seven Asian house shrews. Phylogenetic analysis revealed that the virus carried by the Ussuri white-toothed shrew was most closely related to MJNV, but with >15% nucleotide sequence difference, suggesting that it represents a new subtype. The hantaviruses carried by Asian house shrews were closely related to the TPMV variants found in the same geographic area, but more distantly related to those sampled in India and Nepal. Additionally, the TPMV sequences obtained in this study, as well as those found previously in this area, could be divided into three lineages reflecting their geographic origins, indicative of largely allopatric evolution. Overall, our data highlights the high genetic diversity of insectivore-borne hantaviruses in China, suggesting that more may be discovered in the future. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. Livestock grazing intensity affects abundance of Common shrews (Sorex araneus) in two meadows in Denmark.

    Science.gov (United States)

    Schmidt, Niels M; Olsen, Henrik; Leirs, Herwig

    2009-01-20

    Current nature conservation in semi-natural grasslands often includes grazing and hay cutting, as well as the abandonment of draining. Semi-natural grassland and in particular meadows constitute important habitat type for a large number of animal species in today's fragmented and intensively cultivated landscape of Europe. Here we focus on the population characteristics of Common shrews Sorex araneus in relation to livestock grazing intensity in two wet meadows in western Denmark. High grazing intensity had a significant negative effect on Common shrew number compared to low grazing intensity and no grazing. Common shrew abundance was generally, but not significantly, higher on the low grazing intensity plots than on the ungrazed controls. No differences in body mass, sex ratio, or reproductive output between Common shrew individuals from the various grazing treatments were found. No negative effects of low intensity grazing on Common shrew abundance were found compared to the ungrazed control. Low intensity grazing thus seems a suitable management regime for Common shrews, when grazing is needed as part of the meadow management scheme. High intensity grazing on the other hand is not a suitable management tool.

  20. Alternative exon usage creates novel transcript variants of tumor suppressor SHREW-1 gene with differential tissue expression profile

    Directory of Open Access Journals (Sweden)

    Petra A. B. Klemmt

    2016-11-01

    Full Text Available Shrew-1, also called AJAP1, is a transmembrane protein associated with E-cadherin-mediated adherence junctions and a putative tumor suppressor. Apart from its interaction with β-catenin and involvement in E-cadherin internalization, little structure or function information exists. Here we explored shrew-1 expression during postnatal differentiation of mammary gland as a model system. Immunohistological analyses with antibodies against either the extracellular or the cytoplasmic domains of shrew-1 consistently revealed the expression of full-length shrew-1 in myoepithelial cells, but only part of it in luminal cells. While shrew-1 localization remained unaltered in myoepithelial cells, nuclear localization occurred in luminal cells during lactation. Based on these observations, we identified two unknown shrew-1 transcript variants encoding N-terminally truncated proteins. The smallest shrew-1 protein lacks the extracellular domain and is most likely the only variant present in luminal cells. RNA analyses of human tissues confirmed that the novel transcript variants of shrew-1 exist in vivo and exhibit a differential tissue expression profile. We conclude that our findings are essential for the understanding and interpretation of future functional and interactome analyses of shrew-1 variants.

  1. Ariosto, Gascoigne e The Taming of the Shrew

    Directory of Open Access Journals (Sweden)

    Domenico Lovascio

    2010-04-01

    Full Text Available The essay aims to offer a thorough analysis of the influence exerted by Ludovico Ariosto’s I Suppositi on William Shakespeare’s The Taming of The Shrew through George Gascoigne’s translation, Supposes, and to underscore how crucial a painstaking study of sources can prove to the understanding, in a historical perspective, of the depth and complexity of Shakespeare’s theatre. First, the article briefly introduces the Italian commedia erudita and I Suppositi, and examines the changes to the source text made in translation by Gascoigne. Then, a survey is provided of some of the most important critical stances on the topic. Finally, an analysis of the various elements which Shakespeare borrowed from his source (characters, plot, verbal echoes shows how he refashioned them in order to expand their dramatic potential as well as to make his comedy an apt ground for reflection on ethical themes of great topicality in Elizabethan society.

  2. Composition and function of haemolymphatic tissues in the European common shrew.

    Directory of Open Access Journals (Sweden)

    Daniel P Bray

    Full Text Available BACKGROUND: Studies of wild animals responding to their native parasites are essential if we are to understand how the immune system functions in the natural environment. While immune defence may bring increased survival, this may come at a resource cost to other physiological traits, including reproduction. Here, we tested the hypothesis that wild common shrews (Sorex araneus, which produce large numbers of offspring during the one breeding season of their short life span, forgo investment in immunity and immune system maintenance, as increased longevity is unlikely to bring further opportunities for mating. In particular, we predicted that adult shrews, with shorter expected lifespans, would not respond as effectively as young animals to infection. METHODOLOGY/PRINCIPAL FINDINGS: We examined haemolymphatic tissues from wild-caught common shrews using light and transmission electron microscopy, applied in conjunction with immunohistology. We compared composition and function of these tissues in shrews of different ages, and the extent and type of inflammatory reactions observed in response to natural parasitic infections. All ages seemed able to mount systemic, specific immune responses, but adult shrews showed some signs of lymphatic tissue exhaustion: lymphatic follicles in adults (n = 21 were both smaller than those in sub-adults (n = 18; Wald = 11.1, p<0.05 and exhibited greater levels of depletion (Wald = 13.3, p<0.05. CONCLUSIONS/SIGNIFICANCE: Contrary to our expectations, shrews respond effectively to their natural parasites, and show little indication of immunosenescence as adults. The pancreas of Aselli, a unique lymphoid organ, may aid in providing efficient immune responses through the storage of large numbers of plasma cells. This may allow older animals to react effectively to previously encountered parasites, but infection by novel agents, and eventual depletion of plasma cell reserves, could both still be factors in the near

  3. The identity of the enigmatic "Black Shrew" (Sorex niger Ord, 1815)

    Science.gov (United States)

    Woodman, Neal

    2013-01-01

    The scientific name Sorex niger Ord, 1815 (Mammalia, Soricidae) was originally applied to a North American species that George Ord called the “Black Shrew.” The origin of the name “Black Shrew,” however, was obscure, and Samuel Rhoads subsequently wrote that the species represented by this name could not be determined. The names Sorex niger Ord and Black Shrew have since been mostly forgotten. Two of Ord's contemporaries, however, noted that Ord's use of these names probably alluded to Benjamin Smith Barton's Black Shrew, whose discovery near Philadelphia was announced by Barton in 1806. Examination of two unpublished illustrations of the Black Shrew made by Barton indicates that the animal depicted is Blarina brevicauda (Say, 1822). Had the connection between Ord's and Barton's names been made more clearly, one of the most common mammals in eastern North America would bear a different scientific name today. This connection also would have affected the validity of Sorex niger Horsfield, 1851. While Sorex niger Ord remains a nomen nudum, the animal it referenced can now be identified.

  4. Incidence of dental lesions in musk shrews (Suncus murinus) and their association with sex, age, body weight and diet.

    Science.gov (United States)

    Dudley, Emily S; Grunden, Beverly K; Crocker, Conan; Boivin, Gregory P

    2013-10-22

    Both wild and laboratory strains of the musk shrew (Suncus murinus) have a high incidence of periodontitis. The authors completed necropsy examinations in 51 shrews to identify dental lesions including tooth loss, mobility and fractures. Dental lesions were identified in significantly more females than males, and older animals were more likely to have lesions present. Shrews with one or more dental lesions weighed significantly less than those without lesions present. Dietary supplementation with mealworms did not significantly affect the incidence of dental lesions or the body weight of male or female shrews. The authors recommend routine body weight measurement as a simple, noninvasive method of detecting shrews with an increased likelihood of having dental lesions.

  5. Molecular evidence and high genetic diversity of shrew-borne Seewis virus in Slovenia.

    Science.gov (United States)

    Resman, Katarina; Korva, Miša; Fajs, Luka; Zidarič, Tanja; Trilar, Tomi; Zupanc, Tatjana Avšič

    2013-10-01

    Seewis virus, the shrew-borne hantavirus from Sorex araneus, has been molecularly detected in reservoir hosts in many different central European countries and Russia. Slovenia is a known endemic country for rodent-borne hantaviruses, therefore the aim of the study was to investigate the presence of shrew-borne hantaviruses in insectivores. Viral L, S and M segment have been recovered only from tissue samples of 7 S. araneus, despite several shrew species were tested. Phylogenetic analysis showed high genetic diversity of SWSV in Slovenia, ranging from 3 to 19.4% for different viral segments. The most divergent were M segment sequences, with 19.4% nucleotide divergence among Slovenian strains. Above that, different SWSV strains from Slovenia do not group into separate geographic clusters. While three separate genetic clades were determined, two of them were simultaneously present in one location at the same time. Copyright © 2013 Elsevier B.V. All rights reserved.

  6. Esterase variation in Turkish white-toothed shrews (Crocidura: Record of a trimeric esterase

    Directory of Open Access Journals (Sweden)

    Tez C.

    2009-01-01

    Full Text Available This study focuses on esterase variation of the genus Crocidura in Turkey. A total of 248 white-toothed shrews were analyzed by means of cellulose acetate gel electrophoresis. Liver tissue and alfa naphthyl acetate were used to investigate esterase variation in Turkish white-toothed shrews. A different esterase banding pattern was found in one Crocidura individual. This phenotype had four anodally migrated bands on cellulose acetate gel. The Crocidura individual displaying the given phenotype was identified as Crocidura suaveolens. The different esterase banding pattern observed in this study is considered to be a result of the trimeric structure of esterase in the lesser white-toothed shrew (Crocidura suaveolens.

  7. Muscle senescence in short-lived wild mammals, the soricine shrews Blarina brevicauda and Sorex palustris.

    Science.gov (United States)

    Hindle, Allyson G; Lawler, John M; Campbell, Kevin L; Horning, Markus

    2009-06-01

    Red-toothed (soricine) shrews are consummate predators exhibiting the highest energy turnovers and shortest life spans (ca. 18 months) of any mammal, yet virtually nothing is known regarding their physiological aging. We assessed the emerging pattern of skeletal muscle senescence (contractile/connective tissue components) in sympatric species, the semi-aquatic water shrew (WS), Sorex palustris, and the terrestrial short-tailed shrew (STS), Blarina brevicauda, to determine if muscle aging occurs in wild, short-lived mammals (H(0): shrews do not survive to an age where senescence occurs), and if so, whether these alterations are species-specific. Gracilis muscles were collected from first-year (n=17) and second-year (n=17) field-caught shrews. Consistent with typical mammalian aging, collagen content (% area) increased with age in both species (S. palustris: approximately 50%; B. brevicauda: approximately 60%). Muscle was dominated by stiffer Type I collagen, and the ratio of collagen Type I:Type III more than doubled with age. The area ratio of muscle:collagen decreased with age in both species, but was considerably lower in adult STS, suggesting species-specificity of senescence. Extracellular space was age-elevated in B. brevicauda, but was preserved in S. palustris ( approximately 50 vs. 10% elevation). Though juvenile interspecific comparisons revealed no significance, adult WS myocytes had 68% larger cross-sectional area and occurred at 28% lower fibers/area than those of adult STS. We demonstrate that age-related muscle senescence does occur in wild-caught, short-lived mammals, and we therefore reject this classic aging theory tenet. Our findings moreover illustrate that differential age adjustments in contractile/connective tissue components of muscle occur in the two species of wild-caught shrews. (c) 2009 Wiley-Liss, Inc.

  8. Muscle Senescence in Short-Lived Wild Mammals, the Soricine Shrews Blarina brevicauda and Sorex palustris

    Science.gov (United States)

    HINDLE, ALLYSON G.; LAWLER, JOHN M.; CAMPBELL, KEVIN L.; HORNING, MARKUS

    2015-01-01

    Red-toothed (soricine) shrews are consummate predators exhibiting the highest energy turnovers and shortest life spans (ca. 18 months) of any mammal, yet virtually nothing is known regarding their physiological aging. We assessed the emerging pattern of skeletal muscle senescence (contractile/connective tissue components) in sympatric species, the semi-aquatic water shrew (WS), Sorex palustris, and the terrestrial short-tailed shrew (STS), Blarina brevicauda, to determine if muscle aging occurs in wild, short-lived mammals (H0: shrews do not survive to an age where senescence occurs), and if so, whether these alterations are species-specific. Gracilis muscles were collected from first-year (n = 17) and second-year (n = 17) field-caught shrews. Consistent with typical mammalian aging, collagen content (% area) increased with age in both species (S. palustris: ~50%; B. brevicauda: ~60%). Muscle was dominated by stiffer Type I collagen, and the ratio of collagen Type I:Type III more than doubled with age. The area ratio of muscle:collagen decreased with age in both species, but was considerably lower in adult STS, suggesting species-specificity of senescence. Extracellular space was age-elevated in B. brevicauda, but was preserved in S. palustris (~50 vs. 10% elevation). Though juvenile interspecific comparisons revealed no significance, adult WS myocytes had 68% larger cross-sectional area and occurred at 28% lower fibers/area than those of adult STS. We demonstrate that age-related muscle senescence does occur in wild-caught, short-lived mammals, and we therefore reject this classic aging theory tenet. Our findings moreover illustrate that differential age adjustments in contractile/connective tissue components of muscle occur in the two species of wild-caught shrews. PMID:19296507

  9. Functional and numerical responses of shrews to competition vary with mouse density.

    Directory of Open Access Journals (Sweden)

    Carolyn A Eckrich

    Full Text Available For decades, ecologists have debated the importance of biotic interactions (e.g., competition and abiotic factors in regulating populations. Competition can influence patterns of distribution, abundance, and resource use in many systems but remains difficult to measure. We quantified competition between two sympatric small mammals, Keen's mice (Peromyscus keeni and dusky shrews (Sorex monticolus, in four habitat types on Prince of Wales Island in Southeast Alaska. We related shrew density to that of mice using standardized regression models while accounting for habitat variables in each year from 2010-2012, during which mice populations peaked (2011 and then crashed (2012. Additionally, we measured dietary overlap and segregation using stable isotope analysis and kernel utilization densities and estimated the change in whole community energy consumption among years. We observed an increase in densities of dusky shrews after mice populations crashed in 2012 as expected under competitive release. In addition, competition coefficients revealed that the influence of Keen's mice was dependent on their density. Also in 2012, shrew diets shifted, indicating that they were able to exploit resources previously used by mice. Nonetheless, increases in shrew numbers only partially compensated for the community energy consumption because, as insectivores, they are unlikely to utilize all food types consumed by their competitors. In pre-commercially thinned stands, which exhibit higher diversity of resources compared to other habitat types, shrew populations were less affected by changes in mice densities. These spatially and temporally variable interactions between unlikely competitors, observed in a relatively simple, high-latitude island ecosystem, highlight the difficulty in assessing the role of biotic factors in structuring communities.

  10. Microgeographical distribution of shrews (Mammalia, Soricidae) in the Congo River basin (Kisangani, D.R. Congo)

    DEFF Research Database (Denmark)

    Gambalemoke, Mbalitini; Mukinzi, Itoka; Amundala, Drazo

    2008-01-01

    Research on the biodiversity of shrews was conducted in eight forest blocks at eight sampling localities: Djabir, Maiko, Masako, Yoko, Yelenge, Baliko, Bomane-1 and Bomane-2. We used pitfall traps combined with Sherman LFA traps placed on transects. We collected 724 shrews from primary forests......, secondary forests, old fallow lands and old palm plantation for a total of 18,900 trap-nights. Shrews collected represent 5 genera and at least 19 species: Scutisorex (1 species), Crocidura (12 species), Paracrocidura (2 species), Sylvisorex (3 species) and Suncus (1 species). Sylvisorex nov. sp...

  11. A potentially new giant sengi (elephant-shrew) from the Udzungwa ...

    African Journals Online (AJOL)

    Based on visual sightings and camera-trap photographs, an unusual form of giant sengi or elephant-shrew in the genus Rhynchocyon is identified from the Udzungwa Mountains of south-central Tanzania, which are already known for their extremely high biodiversity and endemism. This unique sengi appears to occur only ...

  12. Abundance of Common Shrew (Sorex Araneus in Selected Forest Habitats of Moravia (Czech Republic

    Directory of Open Access Journals (Sweden)

    Martina Dokulilová

    2017-01-01

    Full Text Available Abundance of common shrew (Sorex araneus was evaluated on selected forest sites in Moravia, Czech Republic. Six types of habitats were assessed: forest clearings and mature forests in lowlands (173 – 233 m, uplands (360 – 600 m, and mountains (600 – 1200 m. Data were collected over five‑year‑long periods; 2006 – 2010 (uplands and 2007 – 2011 (lowlands and mountains. Small terrestrial mammals were captured using snap traps laid in lines. In total, 200 individuals of common shrew were trapped. Relative abundance among different habitats was statistically evaluated. The highest relative abundance was found in mountain forest clearings (n = 132, rA = 0.719. Lower abundance was in upland forest clearings (n = 15, rA = 0.384, in mature mountain forests (n = 32, rA = 0.355, and in the lowland forest clearings (n = 9, rA = 0.109. The lowest abundance was in mature upland forests (n = 9, rA = 0.031 and in mature lowland forests (n = 3, rA = 0.011. Differences between sites were statistically significant. Among all altitudes, shrew populations in plantations were significantly more numerous than those in mature forests. Mountain forest clearings with dense herb layer proved to be the most suitable habitat while mature lowland forests with less developed herbaceous layer were the least suitable. Forest clearings proved to be an important refuge for the populations of common shrew.

  13. Isolation and characterization of a novel arenavirus harbored by Rodents and Shrews in Zhejiang province, China

    International Nuclear Information System (INIS)

    Li, Kun; Lin, Xian-Dan; Wang, Wen; Shi, Mang; Guo, Wen-Ping; Zhang, Xiao-He; Xing, Jian-Guang

    2015-01-01

    To determine the biodiversity of arenaviruses in China, we captured and screened rodents and shrews in Wenzhou city, Zhejiang province, a locality where hemorrhagic fever diseases are endemic in humans. Accordingly, arenaviruses were detected in 42 of 351 rodents from eight species, and in 12 of 272 Asian house shrews (Suncus murinus), by RT-PCR targeting the L segment. From these, a single arenavirus was successfully isolated in cell culture. The virion particles exhibited a typical arenavirus morphology under transmission electron microscopy. Comparison of the S and L segment sequences revealed high levels of nucleotide (>32.2% and >39.6%) and amino acid (>28.8% and >43.8%) sequence differences from known arenaviruses, suggesting that it represents a novel arenavirus, which we designated Wenzhou virus (WENV). Phylogenetic analysis revealed that all WENV strains harbored by both rodents and Asian house shrews formed a distinct lineage most closely related to Old World arenaviruses. - Highlights: • A novel arenavirus (Wenzhou virus) was identified in Zhejiang province, China. • The virus is highly circulating in five species of rats and one species of shrews • More efforts are needed to infer whether it is pathogenic to humans or not

  14. Isolation and characterization of a novel arenavirus harbored by Rodents and Shrews in Zhejiang province, China

    Energy Technology Data Exchange (ETDEWEB)

    Li, Kun [State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing (China); Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou (China); Lin, Xian-Dan [Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang Province (China); Wang, Wen [State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing (China); Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou (China); Shi, Mang [State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing (China); Wencheng Center for Disease Control and Prevention, Wenzhou, Zhejiang Province (China); Guo, Wen-Ping [State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing (China); Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou (China); Zhang, Xiao-He [Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang Province (China); Xing, Jian-Guang [Wencheng Center for Disease Control and Prevention, Wenzhou, Zhejiang Province (China); and others

    2015-02-15

    To determine the biodiversity of arenaviruses in China, we captured and screened rodents and shrews in Wenzhou city, Zhejiang province, a locality where hemorrhagic fever diseases are endemic in humans. Accordingly, arenaviruses were detected in 42 of 351 rodents from eight species, and in 12 of 272 Asian house shrews (Suncus murinus), by RT-PCR targeting the L segment. From these, a single arenavirus was successfully isolated in cell culture. The virion particles exhibited a typical arenavirus morphology under transmission electron microscopy. Comparison of the S and L segment sequences revealed high levels of nucleotide (>32.2% and >39.6%) and amino acid (>28.8% and >43.8%) sequence differences from known arenaviruses, suggesting that it represents a novel arenavirus, which we designated Wenzhou virus (WENV). Phylogenetic analysis revealed that all WENV strains harbored by both rodents and Asian house shrews formed a distinct lineage most closely related to Old World arenaviruses. - Highlights: • A novel arenavirus (Wenzhou virus) was identified in Zhejiang province, China. • The virus is highly circulating in five species of rats and one species of shrews • More efforts are needed to infer whether it is pathogenic to humans or not.

  15. The neurobiology and behavior of the American water shrew (Sorex palustris).

    Science.gov (United States)

    Catania, Kenneth C

    2013-06-01

    American water shrews (Sorex palustris) are aggressive predators that dive into streams and ponds to find prey at night. They do not use eyesight for capturing fish or for discriminating shapes. Instead they make use of vibrissae to detect and attack water movements generated by active prey and to detect the form of stationary prey. Tactile investigations are supplemented with underwater sniffing. This remarkable behavior consists of exhalation of air bubbles that spread onto objects and are then re-inhaled. Recordings for ultrasound both above and below water provide no evidence for echolocation or sonar, and presentation of electric fields and anatomical investigations provide no evidence for electroreception. Counts of myelinated fibers show by far the largest volume of sensory information comes from the trigeminal nerve compared to optic and cochlear nerves. This is in turn reflected in the organization of the water shrew's neocortex, which contains two large somatosensory areas and much smaller visual and auditory areas. The shrew's small brain with few cortical areas may allow exceptional speed in processing sensory information and producing motor output. Water shrews can accurately attack the source of a water disturbance in only 50 ms, perhaps outpacing any other mammalian predator.

  16. Improved starch digestion of sucrase deficient shrews treated with oral glucoamylase enzyme supplements

    Science.gov (United States)

    Although named because of its sucrose hydrolytic activity, this mucosal enzyme plays a leading role in starch digestion because of its maltase and glucoamylase activities. Sucrase deficient mutant shrews, Suncus murinus, were used as a model to investigate starch digestion in patients with Congenita...

  17. Leucism in Mexican small-eared shrew Cryptotis mexicana (Mammalia : Soricomorpha), endemic to Mexico

    NARCIS (Netherlands)

    Guevara, Lazaro; Ramirez-Chaves, Hector E.; Cervantes, Fernando A.

    Leucism is the partial or complete reduction of the fur pigmentation where eyes and skin maintain their normal coloration. In this paper, we report the record of an individual of the endemic Mexican shrew Cryptotis mexicana from Veracruz, Mexico, that displays leucism. This lack of pigmentation,

  18. On a new very small Shrew from Mayotte, Crocidura (Pachyura) coquerelii, Pollen and van Dam, Ms

    NARCIS (Netherlands)

    Trouessart, E.L.

    1880-01-01

    The Insectivora from Madagascar generally belong to forms which are quite distinct from each other, such as the genera Centetes, Oryzoryctes, Geogale, etc., and which have now become the types of separate families and subfamilies. Up to 1848 the large group of Shrews, Soricidae, was looked upon as

  19. Homeostatic maintenance in excitability of tree shrew hippocampal CA3 pyramidal neurons after chronic stress

    NARCIS (Netherlands)

    Kole, Maarten H. P.; Czéh, Boldizsár; Fuchs, Eberhard

    2004-01-01

    The experience of chronic stress induces a reversible regression of hippocampal CA3 apical neuron dendrites. Although such postsynaptic membrane reduction will obviously diminish the possibility of synaptic input, the consequences for the functional membrane properties of these cells are not well

  20. Umbilical Cord-Derived Mesenchymal Stem Cells Relieve Hindlimb Ischemia through Enhancing Angiogenesis in Tree Shrews

    OpenAIRE

    Cunping Yin; Yuan Liang; Jian Zhang; Guangping Ruan; Zian Li; Rongqing Pang; Xinghua Pan

    2016-01-01

    Hindlimb ischemia is still a clinical problem with high morbidity and mortality. Patients suffer from consequent rest pain, ulcers, cool limbs, and even amputation. Angiogenesis is a promising target for the treatment of ischemic limbs, providing extra blood for the ischemic region. In the present study, we investigated the role of umbilical cord-derived mesenchymal stem cells (UC-MSCs) in regulating angiogenesis and relieving hindlimb ischemia. UC-MSCs were isolated from the umbilical cord o...

  1. The timing of the shrew: continuous melatonin treatment maintains youthful rhythmic activity in aging Crocidura russula.

    Directory of Open Access Journals (Sweden)

    Elodie Magnanou

    2009-06-01

    Full Text Available Laboratory conditions nullify the extrinsic factors that determine the wild expected lifespan and release the intrinsic or potential lifespan. Thus, wild animals reared in a laboratory often show an increased lifespan, and consequently an increased senescence phase. Senescence is associated with a broad suite of physiological changes, including a decreased responsiveness of the circadian system. The time-keeping hormone melatonin, an important chemical player in this system, is suspected to have an anti-aging role. The Greater White-toothed shrew Crocidura russula is an ideal study model to address questions related to aging and associated changes in biological functions: its lifespan is short and is substantially increased in captivity; daily and seasonal rhythms, while very marked the first year of life, are dramatically altered during the senescence process which starts during the second year. Here we report on an investigation of the effects of melatonin administration on locomotor activity of aging shrews.1 The diel fluctuations of melatonin levels in young, adult and aging shrews were quantified in the pineal gland and plasma. In both, a marked diel rhythm (low diurnal concentration; high nocturnal concentration was present in young animals but then decreased in adults, and, as a result of a loss in the nocturnal production, was absent in old animals. 2 Daily locomotor activity rhythm was monitored in pre-senescent animals that had received either a subcutaneous melatonin implant, an empty implant or no implant at all. In non-implanted and sham-implanted shrews, the rhythm was well marked in adults. A marked degradation in both period and amplitude, however, started after the age of 14-16 months. This pattern was considerably delayed in melatonin-implanted shrews who maintained the daily rhythm for significantly longer.This is the first long term study (>500 days observation of the same individuals that investigates the effects of

  2. The timing of the shrew: continuous melatonin treatment maintains youthful rhythmic activity in aging Crocidura russula.

    Science.gov (United States)

    Magnanou, Elodie; Attia, Joël; Fons, Roger; Boeuf, Gilles; Falcon, Jack

    2009-06-15

    Laboratory conditions nullify the extrinsic factors that determine the wild expected lifespan and release the intrinsic or potential lifespan. Thus, wild animals reared in a laboratory often show an increased lifespan, and consequently an increased senescence phase. Senescence is associated with a broad suite of physiological changes, including a decreased responsiveness of the circadian system. The time-keeping hormone melatonin, an important chemical player in this system, is suspected to have an anti-aging role. The Greater White-toothed shrew Crocidura russula is an ideal study model to address questions related to aging and associated changes in biological functions: its lifespan is short and is substantially increased in captivity; daily and seasonal rhythms, while very marked the first year of life, are dramatically altered during the senescence process which starts during the second year. Here we report on an investigation of the effects of melatonin administration on locomotor activity of aging shrews. 1) The diel fluctuations of melatonin levels in young, adult and aging shrews were quantified in the pineal gland and plasma. In both, a marked diel rhythm (low diurnal concentration; high nocturnal concentration) was present in young animals but then decreased in adults, and, as a result of a loss in the nocturnal production, was absent in old animals. 2) Daily locomotor activity rhythm was monitored in pre-senescent animals that had received either a subcutaneous melatonin implant, an empty implant or no implant at all. In non-implanted and sham-implanted shrews, the rhythm was well marked in adults. A marked degradation in both period and amplitude, however, started after the age of 14-16 months. This pattern was considerably delayed in melatonin-implanted shrews who maintained the daily rhythm for significantly longer. This is the first long term study (>500 days observation of the same individuals) that investigates the effects of continuous melatonin

  3. Livestock grazing intensity affects abundance of Common shrews (Sorex araneus) in two meadows in Denmark

    OpenAIRE

    Schmidt, Niels M; Olsen, Henrik; Leirs, Herwig

    2009-01-01

    Abstract Background Current nature conservation in semi-natural grasslands often includes grazing and hay cutting, as well as the abandonment of draining. Semi-natural grassland and in particular meadows constitute important habitat type for a large number of animal species in today's fragmented and intensively cultivated landscape of Europe. Here we focus on the population characteristics of Common shrews Sorex araneus in relation to livestock grazing intensity in two wet meadows in western ...

  4. Haematology, genotoxicity, enzymatic activity and histopathology as biomarkers of metal pollution in the shrew Crocidura russula

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez-Chardi, A. [Departament Biologia Animal, Facultat de Biologia, Universitat Barcelona, Av. Diagonal 645, 08028 Barcelona (Spain); Servei de Microscopia, Facultat de Ciencies, Ed. C, Universitat Autonoma de Barcelona, 08193 Bellaterra, Barcelona (Spain)], E-mail: Alejandro.Sanchez.Chardi@uab.es; Marques, C.C.; Gabriel, S.I. [Centro de Biologia Ambiental, Departamento de Biologia Animal, Faculdade de Ciencias, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa (Portugal); Capela-Silva, F. [Centro de Investigacao em Ciencias e Tecnologias da Saude, Departamento de Biologia, Universidade de Evora, 7002-552 Evora (Portugal); Cabrita, A.S. [Centro de Histofisiologia, Instituto de Patologia Experimental, Faculdade de Medicina, Universidade de Coimbra, 3004-504 Coimbra (Portugal); Lopez-Fuster, M.J.; Nadal, J. [Departament Biologia Animal, Facultat de Biologia, Universitat Barcelona, Av. Diagonal 645, 08028 Barcelona (Spain); Mathias, M.L. [Centro de Biologia Ambiental, Departamento de Biologia Animal, Faculdade de Ciencias, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa (Portugal)

    2008-12-15

    Haematological (WBC, RBC, Hgb and Hct) and genotoxicity (MNT) parameters, hepatic enzymatic activities (GST, GPx and GR), and a histopathological evaluation of liver, kidneys and gonads were assessed as general biomarkers of metal pollution in the shrew Crocidura russula inhabiting a pyrite mining area. Specimens exposed to metals presented a few significant alterations when compared with reference animals: GST activity decreased; micronuclei increased; and evident liver alterations related to metal exposure were observed. On the basis of all the parameters studied, age was an important factor that partly explained the observed variation, whereas sex was the least important factor. Significant correlations were also found between heavy metal concentrations and biomarkers evaluated, demonstrating the great influence of these metals in the metabolic alterations. To the best of our knowledge, these data constitute the first measurements of a battery of biomarkers in shrews from a mine site and are among the few available for insectivorous mammals. - Metals from an abandoned pyrite mine produce alterations in haematological parameters, GST, MNT, and histopathology in shrews.

  5. Haematology, genotoxicity, enzymatic activity and histopathology as biomarkers of metal pollution in the shrew Crocidura russula

    International Nuclear Information System (INIS)

    Sanchez-Chardi, A.; Marques, C.C.; Gabriel, S.I.; Capela-Silva, F.; Cabrita, A.S.; Lopez-Fuster, M.J.; Nadal, J.; Mathias, M.L.

    2008-01-01

    Haematological (WBC, RBC, Hgb and Hct) and genotoxicity (MNT) parameters, hepatic enzymatic activities (GST, GPx and GR), and a histopathological evaluation of liver, kidneys and gonads were assessed as general biomarkers of metal pollution in the shrew Crocidura russula inhabiting a pyrite mining area. Specimens exposed to metals presented a few significant alterations when compared with reference animals: GST activity decreased; micronuclei increased; and evident liver alterations related to metal exposure were observed. On the basis of all the parameters studied, age was an important factor that partly explained the observed variation, whereas sex was the least important factor. Significant correlations were also found between heavy metal concentrations and biomarkers evaluated, demonstrating the great influence of these metals in the metabolic alterations. To the best of our knowledge, these data constitute the first measurements of a battery of biomarkers in shrews from a mine site and are among the few available for insectivorous mammals. - Metals from an abandoned pyrite mine produce alterations in haematological parameters, GST, MNT, and histopathology in shrews

  6. Molecular Survey on Brucellosis in Rodents and Shrews - Natural Reservoirs of Novel Brucella Species in Germany?

    Science.gov (United States)

    Hammerl, J A; Ulrich, R G; Imholt, C; Scholz, H C; Jacob, J; Kratzmann, N; Nöckler, K; Al Dahouk, S

    2017-04-01

    Brucellosis is a widespread zoonotic disease introduced from animal reservoirs to humans. In Germany, bovine and ovine/caprine brucellosis were eradicated more than a decade ago and mandatory measures in livestock have been implemented to keep the officially brucellosis-free status. In contrast, surveillance of wildlife is still challenging, and reliable data on the prevalence of brucellae in small mammal populations do not exist. To assess the epidemiology of Brucella spp. in rodents and shrews, a molecular survey was carried out. A total of 537 rodents and shrews were trapped in four federal states located throughout Germany and investigated for the presence of Brucella. Using a two-step molecular assay based on the detection of the Brucella-specific bcsp31 and IS711 sequences in tissue samples, 14.2% (n = 76) of the tested animals were positive. These originated mainly from western and south-western Germany, where preliminary analyses indicate population density-dependent Brucella prevalence in voles (Myodes glareolus) and mice (Apodemus spp.). recA typing revealed a close relationship to a potentially novel Brucella species recently isolated from red foxes (Vulpes vulpes) in Austria. The molecular detection of brucellae in various rodent taxa and for the first time in shrew species shows that these animals may be naturally infected or at least have a history of exposure to Brucella spp. © 2015 Blackwell Verlag GmbH.

  7. Development and characterization of 21 polymorphic microsatellite markers for the barren-ground shrew, Sorex ugyunak (Mammalia: Sorcidae), through next-generation sequencing, and cross-species amplification in the masked shrew, S. cinereus

    Science.gov (United States)

    Sonsthagen, S.A.; Sage, G.K.; Fowler, M.; Hope, A.G.; Cook, J.A.; Talbot, S.L.

    2013-01-01

    We used next generation shotgun sequencing to develop 21 novel microsatellite markers for the barren-ground shrew (Sorex ugyunak), which were polymorphic among individuals from northern Alaska. The loci displayed moderate allelic diversity (averaging 6.81 alleles per locus) and heterozygosity (averaging 70 %). Two loci deviated from Hardy–Weinberg equilibrium (HWE) due to heterozygote deficiency. While the population did not deviate from HWE overall, it showed significant linkage disequilibrium suggesting this population is not in mutation-drift equilibrium. Nineteen of 21 loci were polymorphic in masked shrews (S. cinereus) from interior Alaska and exhibited linkage equilibrium and HWE overall. All loci yielded sufficient variability for use in population studies.

  8. Resting-associated vocalization emitted by captive Asian house shrews (Suncus murinus: acoustic structure and variability in an unusual mammalian vocalization.

    Directory of Open Access Journals (Sweden)

    Irena Schneiderová

    Full Text Available Shrews have rich vocal repertoires that include vocalizations within the human audible frequency range and ultrasonic vocalizations. Here, we recorded and analyzed in detail the acoustic structure of a vocalization with unclear functional significance that was spontaneously produced by 15 adult, captive Asian house shrews (Suncus murinus while they were lying motionless and resting in their nests. This vocalization was usually emitted repeatedly in a long series with regular intervals. It showed some structural variability; however, the shrews most frequently emitted a tonal, low-frequency vocalization with minimal frequency modulation and a low, non-vocal click that was clearly noticeable at its beginning. There was no effect of sex, but the acoustic structure of the analyzed vocalizations differed significantly between individual shrews. The encoded individuality was low, but it cannot be excluded that this individuality would allow discrimination of family members, i.e., a male and female with their young, collectively resting in a common nest. The question remains whether the Asian house shrews indeed perceive the presence of their mates, parents or young resting in a common nest via the resting-associated vocalization and whether they use it to discriminate among their family members. Additional studies are needed to explain the possible functional significance of resting-associated vocalizations emitted by captive Asian house shrews. Our study highlights that the acoustic communication of shrews is a relatively understudied topic, particularly considering that they are highly vocal mammals.

  9. Posture does not matter! Paw usage and grasping paw preference in a small-bodied rooting quadrupedal mammal.

    Science.gov (United States)

    Joly, Marine; Scheumann, Marina; Zimmermann, Elke

    2012-01-01

    Recent results in birds, marsupials, rodents and nonhuman primates suggest that phylogeny and ecological factors such as body size, diet and postural habit of a species influence limb usage and the direction and strength of limb laterality. To examine to which extent these findings can be generalised to small-bodied rooting quadrupedal mammals, we studied trees shrews (Tupaia belangeri). We established a behavioural test battery for examining paw usage comparable to small-bodied primates and tested 36 Tupaia belangeri. We studied paw usage in a natural foraging situation (simple food grasping task) and measured the influence of varying postural demands (triped, biped, cling, sit) on paw preferences by applying a forced-food grasping task similar to other small-bodied primates. Our findings suggest that rooting tree shrews prefer mouth over paw usage to catch food in a natural foraging situation. Moreover, we demonstrated that despite differences in postural demand, tree shrews show a strong and consistent individual paw preference for grasping across different tasks, but no paw preference at a population level. Tree shrews showed less paw usage than small-bodied quadrupedal and arboreal primates, but the same paw preference. Our results confirm that individual paw preferences remain constant irrespective of postural demand in some small-bodied quadrupedal non primate and primate mammals which do not require fine motoric control for manipulating food items. Our findings suggest that the lack of paw/hand preference for grasping food at a population level is a universal pattern among those species and that the influence of postural demand on manual lateralisation in quadrupeds may have evolved in large-bodied species specialised in fine manipulations of food items.

  10. Posture does not matter! Paw usage and grasping paw preference in a small-bodied rooting quadrupedal mammal.

    Directory of Open Access Journals (Sweden)

    Marine Joly

    Full Text Available BACKGROUND: Recent results in birds, marsupials, rodents and nonhuman primates suggest that phylogeny and ecological factors such as body size, diet and postural habit of a species influence limb usage and the direction and strength of limb laterality. To examine to which extent these findings can be generalised to small-bodied rooting quadrupedal mammals, we studied trees shrews (Tupaia belangeri. METHODOLOGY/PRINCIPAL FINDINGS: We established a behavioural test battery for examining paw usage comparable to small-bodied primates and tested 36 Tupaia belangeri. We studied paw usage in a natural foraging situation (simple food grasping task and measured the influence of varying postural demands (triped, biped, cling, sit on paw preferences by applying a forced-food grasping task similar to other small-bodied primates. Our findings suggest that rooting tree shrews prefer mouth over paw usage to catch food in a natural foraging situation. Moreover, we demonstrated that despite differences in postural demand, tree shrews show a strong and consistent individual paw preference for grasping across different tasks, but no paw preference at a population level. CONCLUSIONS/SIGNIFICANCE: Tree shrews showed less paw usage than small-bodied quadrupedal and arboreal primates, but the same paw preference. Our results confirm that individual paw preferences remain constant irrespective of postural demand in some small-bodied quadrupedal non primate and primate mammals which do not require fine motoric control for manipulating food items. Our findings suggest that the lack of paw/hand preference for grasping food at a population level is a universal pattern among those species and that the influence of postural demand on manual lateralisation in quadrupeds may have evolved in large-bodied species specialised in fine manipulations of food items.

  11. Seroprevalence of rickettsial infection in commensal rodents and shrews trapped in the Bangkok Metropolitan Area.

    Science.gov (United States)

    Siritantikorn, Sontana; Sangkasuwan, Vichai; Eamsila, Chirapa; Singchai, Chantra; Kantakamalakul, Wannee; Puthavathana, Pilaipan

    2003-06-01

    Murine typhus and scrub typhus are important human rickettsial diseases in Thailand. Small mammals, including many species of rodents and shrews, serve as the reservoir host of rickettsial diseases. Rickettsia typhi can be transmitted to humans by fleas causing murine typhus, while infection with Orientia tsutsugamushi causing scrub typhus in humans is transmitted by chiggers. The prevalence of rickettsial infection depends on the geographic area. The seroprevalence of antibody to R. typhi and O. tsutsugamushi was studied in commensal rodents and shrews trapped in markets in the Bangkok Metropolitan Area (BMA). R. typhi and O. tsutsugamushi antigen prepared in the yolk sac of embryonated eggs were used to determine the specific antibody in trapped animals' sera by using fluorescein isothiocyanate (FITC)-anti rat immunoglobulins as a second antibody. Antibody to R. typhi was found in 25 (5%) of 500 sera tested and no antibody to O. tsutsugamushi was detected. R. typhi antibody titer ranged from 40-1280 and was found in Rattus norvegicus (4.2%), Rattus rattus (0.4%), Rattus exulans (0.2%), and Mus musculus (0.2%) trapped in 8 of 47 markets in the BMA. R. typhi antibody was commonly found in R. norvegicus. The authors concluded that murine typhus is an important rickettsial disease and R. norvegicus is an important reservoir species of rodents found in markets of the BMA.

  12. Conditioned flavor preference and the US postexposure effect in the house musk shrew (Suncus murinus

    Directory of Open Access Journals (Sweden)

    Kosuke eSawa

    2012-07-01

    Full Text Available The house musk shrew (Suncus murinus is the only species of insectivore that can be used as a laboratory animal and is an interesting subject in terms of evolutional and comparative aspects. The present study on the learning faculties of shrews examines the possibility of acquiring a conditioned flavor preference and the effects of US postexposure. Subjects were allowed to a drink sucrose solution with flavor A and tap water with flavor B during training. Two extinction tests were administered after every four conditioning trials, and a significant preference for flavor A was observed. After each test, the animals were divided into two groups. Subjects in Group US were presented with a sucrose solution without flavor, while those in Group Water were given tap water. After these trials, all subjects received choice tests where they were presented with water containing the two flavors. The preference ratio was lower in Group US than in Group Water, suggesting a postexposure effect. The findings were discussed in terms of habituation to the US.

  13. Prevalence of zoonotic Bartonella species among rodents and shrews in Thailand.

    Science.gov (United States)

    Pangjai, Decha; Maruyama, Soichi; Boonmar, Sumalee; Kabeya, Hidenori; Sato, Shingo; Nimsuphan, Burin; Petkanchanapong, Wimol; Wootta, Wattanapong; Wangroongsarb, Piyada; Boonyareth, Maskiet; Preedakoon, Poom; Saisongkorh, Watcharee; Sawanpanyalert, Pathom

    2014-03-01

    We investigated the prevalence of Bartonella species in 10 rodent and one shrew species in Thailand. From February 2008 to May 2010, a total of 375 small animals were captured in 9 provinces in Thailand. Bartonella strains were isolated from 57 rodents (54 from Rattus species and 3 from Bandicota indica) and one shrew (Suncus murinus) in 7 of the 9 provinces, and identified to the species level. Sequence analysis of the citrate synthase and RNA polymerase β subunit genes identified the 58 isolates from each Bartonella-positive animal as B. tribocorum in 27 (46.6%) animals, B. rattimassiliensis in 17 (29.3%) animals, B. elizabethae in 10 (17.2%) animals and B. queenslandensis in 4 (6.9%) animals. R. norvegicus, R. rattus, and Suncus murinus carried B. elizabethae, which causes endocarditis in humans. The prevalence of Bartonella bacteremic animals by province was 42.9% of the animals collected in Phang Nga, 26.8% in Chiang Rai, 20.4% in Sa Kaeo, 16.7% in Nakhon Si Thammarat, 12.0% in Surat Thani, 9.1% in Mae Hong Son and Loei Provinces. These results indicate that Bartonella organisms are widely distributed in small mammals in Thailand and some animal species may serve as important reservoirs of zoonotic Bartonella species in the country. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

  14. "The Taming of the Shrew": authority and love at the origin of the modern nuclear family

    Directory of Open Access Journals (Sweden)

    Antonella Piazza

    2013-10-01

    Full Text Available The lesson on William Shakespeare’s The Taming of the Shrew was written on occasion of the day against the astonishing number of women murdered by men especially men who pretended to love them. This phenomenon is not to be associated to a sort of archaic culture, but, on the contrary, it is related to modernity. In fact, violence and conflicts in a heterosexual couple come explicitly to the fore with and after the institution of the patriarchal nuclear family which at the origins of modernity posits love as the motivation of marriage and the formation of a family. Shakespeare and the Elizabethan theatre face the question both in tragedies and in comedies as in the case of The Taming of the Shrew where the shrew’s final monologue problematically sounds as the manifesto of the acknowledgment of the inferiority of women and so of the husband’s right to the woman’s subjection to her husband.

  15. Tree Contractions and Evolutionary Trees

    OpenAIRE

    Kao, Ming-Yang

    2001-01-01

    An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of species. An agreement subtree of two evolutionary trees is an evolutionary tree which is also a topological subtree of the two given trees. We give an algorithm to determine the largest possible number of leaves in any agreement subtree of two trees T_1 and ...

  16. Colonization of Ireland: revisiting ‘the pygmy shrew syndrome' using mitochondrial, Y chromosomal and microsatellite markers

    Science.gov (United States)

    McDevitt, A D; Vega, R; Rambau, R V; Yannic, G; Herman, J S; Hayden, T J; Searle, J B

    2011-01-01

    There is great uncertainty about how Ireland attained its current fauna and flora. Long-distance human-mediated colonization from southwestern Europe has been seen as a possible way that Ireland obtained many of its species; however, Britain has (surprisingly) been neglected as a source area for Ireland. The pygmy shrew has long been considered an illustrative model species, such that the uncertainty of the Irish colonization process has been dubbed ‘the pygmy shrew syndrome'. Here, we used new genetic data consisting of 218 cytochrome (cyt) b sequences, 153 control region sequences, 17 Y-intron sequences and 335 microsatellite multilocus genotypes to distinguish between four possible hypotheses for the colonization of the British Isles, formulated in the context of previously published data. Cyt b sequences from western Europe were basal to those found in Ireland, but also to those found in the periphery of Britain and several offshore islands. Although the central cyt b haplotype in Ireland was found in northern Spain, we argue that it most likely occurred in Britain also, from where the pygmy shrew colonized Ireland as a human introduction during the Holocene. Y-intron and microsatellite data are consistent with this hypothesis, and the biological traits and distributional data of pygmy shrews argue against long-distance colonization from Spain. The compact starburst of the Irish cyt b expansion and the low genetic diversity across all markers strongly suggests a recent colonization. This detailed molecular study of the pygmy shrew provides a new perspective on an old colonization question. PMID:21673740

  17. Dietary competition between the alien Asian Musk Shrew (Suncus murinus) and a re-introduced population of Telfair's Skink (Leiolopisma telfairii).

    Science.gov (United States)

    Brown, D S; Burger, R; Cole, N; Vencatasamy, D; Clare, E L; Montazam, A; Symondson, W O C

    2014-08-01

    Re-introduction of rare species to parts of their historical range is becoming increasingly important as a conservation strategy. Telfair's Skinks (Leiolopisma telfairii), once widespread on Mauritius, were until recently found only on Round Island. There it is vulnerable to stochastic events, including the introduction of alien predators that may either prey upon it or compete for food resources. Consequently, skinks have been introduced to Ile aux Aigrettes, another small Mauritian island that has been cleared of rats. However, the island has been invaded by Asian Musk Shrews (Suncus murinus), a commensal species spread by man well beyond its natural Asian range. Our aim was to use next-generation sequencing to analyse the diets of the shrews and skinks to look for niche competition. DNA was extracted from skink faeces and from the stomach contents of shrews. Application of shrew- and skink-specific primers revealed no mutual predation. The DNA was then amplified using general invertebrate primers with tags to identify individual predators, and then sequenced by 454 pyrosequencing. 119 prey MOTUs (molecular taxonomic units) were isolated, although none could be identified to species. Seeding of cladograms with known sequences allowed higher taxonomic assignments in some cases. Although most MOTUs were not shared by shrews and skinks, Pianka's niche overlap test showed significant prey overlap, suggesting potentially strong competition where food resources are limited. These results suggest that removal of the shrews from the island should remain a priority. © 2013 John Wiley & Sons Ltd.

  18. Mammals of South America, Volume 1, Marsupials, Xenarthrans, Shrews, and Bats

    Science.gov (United States)

    Gardner, A.L.

    2007-01-01

    The vast terrain between Panama and Tierra del Fuego contains some of the world?s richest mammalian fauna, but until now it has lacked a comprehensive systematic reference to the identification, distribution, and taxonomy of its mammals. The first such book of its kind and the inaugural volume in a three-part series, Mammals of South America both summarizes existing information and encourages further research of the mammals indigenous to the region. Containing identification keys and brief descriptions of each order, family, and genus, the first volume of Mammals of South America covers marsupials, shrews, armadillos, sloths, anteaters, and bats. Species accounts include taxonomic descriptions, synonymies, keys to identification, distributions with maps and a gazetteer of marginal localities, lists of recognized subspecies, brief summaries of natural history information, and discussions of issues related to taxonomic interpretations. Highly anticipated and much needed, this book will be a landmark contribution to mammalogy, zoology, tropical biology, and conservation biology.

  19. Solar radiation during rewarming from torpor in elephant shrews: supplementation or substitution of endogenous heat production?

    Science.gov (United States)

    Thompson, Michelle L; Mzilikazi, Nomakwezi; Bennett, Nigel C; McKechnie, Andrew E

    2015-01-01

    Many small mammals bask in the sun during rewarming from heterothermy, but the implications of this behaviour for their energy balance remain little understood. Specifically, it remains unclear whether solar radiation supplements endogenous metabolic thermogenesis (i.e., rewarming occurs through the additive effects of internally-produced and external heat), or whether solar radiation reduces the energy required to rewarm by substituting (i.e, replacing) metabolic heat production. To address this question, we examined patterns of torpor and rewarming rates in eastern rock elephant shrews (Elephantulus myurus) housed in outdoor cages with access to either natural levels of solar radiation or levels that were experimentally reduced by means of shade cloth. We also tested whether acclimation to solar radiation availability was manifested via phenotypic flexibility in basal metabolic rate (BMR), non-shivering thermogenesis (NST) capacity and/or summit metabolism (Msum). Rewarming rates varied significantly among treatments, with elephant shrews experiencing natural solar radiation levels rewarming faster than conspecifics experiencing solar radiation levels equivalent to approximately 20% or 40% of natural levels. BMR differed significantly between individuals experiencing natural levels of solar radiation and conspecifics experiencing approximately 20% of natural levels, but no between-treatment difference was evident for NST capacity or Msum. The positive relationship between solar radiation availability and rewarming rate, together with the absence of acclimation in maximum non-shivering and total heat production capacities, suggests that under the conditions of this study solar radiation supplemented rather than substituted metabolic thermogenesis as a source of heat during rewarming from heterothermy.

  20. Discovery of Natural Infection by Metagonimus hakubaensis Shimazu, 1999 (Trematoda: Heterophyidae) in Japanese Water Shrews (Chimarrogale platycephala) in Japan

    Science.gov (United States)

    KUDO, Noboru; SHIGETA, Kai; MATSUMOTO, Koji; OYAMADA, Takashi

    2014-01-01

    ABSTRACT ABSTRACT. A total of 611 preserved adult Metagonimus spp. specimens recovered from 32 of 53 Japanese water shrews (Chimarrogale platycephala) that had previously been collected in Aomori Prefecture between June 1994 and August 1996, were examined in this study. Morphological examination revealed that 603 of these flukes were identical to M. hakubaensis Shimazu, 1999, and that the others were M. takahashii Suzuki, 1930 (n=4), M. otsurui Saito et Shimizu, 1968 (n=2), and M. miyatai Saito et al., 1997 (n=2). Each of the 32 Japanese water shrews infected with M. hakubaensis contained between 1 and 83 flukes. This is the first record of the natural final host for M. hakubaensis, since this fluke species was described. PMID:25131808

  1. Computerized detection and analysis of cancer chemotherapy-induced emesis in a small animal model, musk shrew

    OpenAIRE

    Huang, Dong; Meyers, Kelly; Henry, Séverine; De la Torre, Fernando; Horn, Charles C.

    2011-01-01

    Vomiting is a common side effect of cancer chemotherapy and many drug treatments and diseases. In animal studies, the measurement of vomiting usually requires direct observation, which is time consuming and often lacks temporal precision. Musk shrews have been used to study the neurobiology of emesis and have a rapid emetic episode (~1 s for a sequence of retching and expulsion). The aims of the current study were to develop a method to automatically detect and characterize emetic episodes in...

  2. Study of the endoparasitic fauna of commensal rats and shrews caught in traditional wet markets in Taichung City, Taiwan.

    Science.gov (United States)

    Tung, Kwong-Chung; Hsiao, Fun-Chun; Wang, Kai-Sung; Yang, Cheng-Hsiung; Lai, Cheng-Hung

    2013-04-01

    Rats live in close proximity to human populations. Feral rodents are known to transmit diseases and act as reservoir hosts to many zoonotic parasites that pose health risks to humans. The aim of this study is to investigate endoparasitic infections in commensal rats and shrews caught in traditional wet markets in Taichung City, Taiwan. A total of 51 commensal wild rodents and shrews were caught in traditional wet markets in Taichung City, including 32 Rattus norvegicus, 11 R. rattus, and eight Suncus murinus. All tissues, organs, and intestinal contents were carefully examined after euthanasia for the detection of parasites. The overall prevalence of infection was 94.1%, and the infection rates in R. norvegicus, R. rattus, and S. murinus were 93.8%, 90.9%, and 100.0%, respectively. Four cestodes (Taenia taeniaeformis, Hymenolepis diminuta, H. nana, and Raillietina celebensis), seven nematodes (Angiostrongylus cantonensis, Capillaria hepatica, Heterakis spumosa, Nippostrongylus brasiliensis, Strongyloides ratti, Syphacia muris, and Trichosomoides crassicauda), and one protozoan (Sarcocystis spp.) were detected. Our findings indicate that commensal rodents and shrews found in the traditional wet markets of Taichung City are hosts to various zoonotic parasites and, therefore, pose a serious health risk to humans and domestic animals in Taiwan. Copyright © 2012. Published by Elsevier B.V.

  3. Carving out turf in a biodiversity hotspot: multiple, previously unrecognized shrew species co-occur on Java Island, Indonesia.

    Science.gov (United States)

    Esselstyn, Jacob A; Maharadatunkamsi; Achmadi, Anang S; Siler, Cameron D; Evans, Ben J

    2013-10-01

    In theory, competition among species in a shared habitat results in niche separation. In the case of small recondite mammals such as shrews, little is known about their autecologies, leaving open questions regarding the degree to which closely related species co-occur and how or whether ecological niches are partitioned. The extent to which species are able to coexist may depend on the degree to which they exploit different features of their habitat, which may in turn influence our ability to recognize them as species. We explored these issues in a biodiversity hotspot, by surveying shrew (genus Crocidura) diversity on the Indonesian island of Java. We sequenced portions of nine unlinked genes in 100-117 specimens of Javan shrews and incorporated homologous data from most known Crocidura species from other parts of island South-East Asia. Current taxonomy recognizes four Crocidura species on Java, including two endemics. However, our phylogenetic, population genetic and species delimitation analyses identify five species on the island, and all are endemic to Java. While the individual ranges of these species may not overlap in their entirety, we found up to four species living syntopically and all five species co-occurring on one mountain. Differences in species' body size, use of above ground-level habitats by one species and habitat partitioning along ecological gradients may have facilitated species diversification and coexistence. © 2013 John Wiley & Sons Ltd.

  4. A new species of small-eared shrew (Mammalia, Eulipotyphla, Cryptotis) from the Lacandona rain forest, Mexico

    Science.gov (United States)

    Guevara, Lázaro; Sánchez-Cordero, Víctor; León-Paniagua, Livia; Woodman, Neal

    2014-01-01

    The diversity and distribution of mammals in the American tropics remain incompletely known. We describe a new species of small-eared shrew (Soricidae, Cryptotis) from the Lacandona rain forest, Chiapas, southern Mexico. The new species is distinguished from other species of Cryptotis on the basis of a unique combination of pelage coloration, size, dental, cranial, postcranial, and external characters, and genetic distances. It appears most closely related to species in the Cryptotis nigrescens species group, which occurs from southern Mexico to montane regions of Colombia. This discovery is particularly remarkable because the new species is from a low-elevation habitat (approximately 90 m), whereas most shrews in the region are restricted to higher elevations, typically > 1,000 m. The only known locality for the new shrew is in one of the last areas in southern Mexico where relatively undisturbed tropical vegetation is still found. The type locality is protected by the Mexican government as part of the Yaxchilán Archaeological Site on the border between Mexico and Guatemala.

  5. Phylogeography of the Asian lesser white-toothed shrew, Crocidura shantungensis, in East Asia: role of the Korean Peninsula as refugium for small mammals.

    Science.gov (United States)

    Lee, Seo-Jin; Lee, Mu-Yeong; Lin, Liang-Kong; Lin, Y Kirk; Li, Yuchun; Shin, E-Hyun; Han, Sang-Hoon; Min, Mi-Sook; Lee, Hang; Kim, Kyung Seok

    2018-04-01

    Many peninsulas in the temperate zone played an important role as refugia of various flora and fauna, and the southern Korean Peninsula also served as a refugium for many small mammals in East Asia during the Pleistocene. The Asian lesser white-toothed shrew, Crocidura shantungensis, is a widely distributed species in East Asia, and is an appropriate model organism for exploring the role of the Korean Peninsula as a refugium of small mammals. Here, we investigated phylogenetic relationships and genetic diversity based on the entire sequence of the mitochondrial cytochrome b gene (1140 bp). A Bayesian tree for 98 haplotypes detected in 228 C. shantungensis specimens from East Asia revealed the presence of three major groups with at least 5 subgroups. Most haplotypes were distributed according to their geographic proximity. Pairwise F ST 's and analysis of molecular variance (AMOVA) revealed a high degree of genetic differentiation and variance among regions as well as among populations within region, implying little gene flow among local populations. Genetic evidence from South Korean islands, Jeju-do Island of South Korea, and Taiwan leads us to reject the hypothesis of recent population expansion. We observed unique island-type genetic characteristics consistent with geographic isolation and resultant genetic drift. Phylogeographic inference, together with estimates of genetic differentiation and diversity, suggest that the southern most part the Korean Peninsula, including offshore islands, played an important role as a refugium for C. shantungensis during the Pleistocene. However, the presence of several refugia on the mainland of northeast Asia is also proposed.

  6. Flowering Trees

    Indian Academy of Sciences (India)

    Dolichandrone atrovirens (Roth) K. Schum. (Spathe Trumpet Tree) of Bignoniaceae is a medium-sized handsome tree with a straight bole that branches at the top. Leaves are once pinnate, with two to three pairs of leaflets. Young parts of the tree are velvety. Inflorescence is a branched raceme borne at the branch ends.

  7. Flying lemurs – The 'flying tree shrews'? Molecular cytogenetic evidence for a Scandentia-Dermoptera sister clade

    Directory of Open Access Journals (Sweden)

    Volobouev Vitaly

    2008-05-01

    Full Text Available Abstract Background Flying lemurs or Colugos (order Dermoptera represent an ancient mammalian lineage that contains only two extant species. Although molecular evidence strongly supports that the orders Dermoptera, Scandentia, Lagomorpha, Rodentia and Primates form a superordinal clade called Supraprimates (or Euarchontoglires, the phylogenetic placement of Dermoptera within Supraprimates remains ambiguous. Results To search for cytogenetic signatures that could help to clarify the evolutionary affinities within this superordinal group, we have established a genome-wide comparative map between human and the Malayan flying lemur (Galeopterus variegatus by reciprocal chromosome painting using both human and G. variegatus chromosome-specific probes. The 22 human autosomal paints and the X chromosome paint defined 44 homologous segments in the G. variegatus genome. A putative inversion on GVA 11 was revealed by the hybridization patterns of human chromosome probes 16 and 19. Fifteen associations of human chromosome segments (HSA were detected in the G. variegatus genome: HSA1/3, 1/10, 2/21, 3/21, 4/8, 4/18, 7/15, 7/16, 7/19, 10/16, 12/22 (twice, 14/15, 16/19 (twice. Reverse painting of G. variegatus chromosome-specific paints onto human chromosomes confirmed the above results, and defined the origin of the homologous human chromosomal segments in these associations. In total, G. variegatus paints revealed 49 homologous chromosomal segments in the HSA genome. Conclusion Comparative analysis of our map with published maps from representative species of other placental orders, including Scandentia, Primates, Lagomorpha and Rodentia, suggests a signature rearrangement (HSA2q/21 association that links Scandentia and Dermoptera to one sister clade. Our results thus provide new evidence for the hypothesis that Scandentia and Dermoptera have a closer phylogenetic relationship to each other than either of them has to Primates.

  8. Tree compression with top trees

    DEFF Research Database (Denmark)

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

    2013-01-01

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

  9. Tree compression with top trees

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  10. Sticky snack for sengis: The Cape rock elephant-shrew, Elephantulus edwardii (Macroscelidea), as a pollinator of the Pagoda lily, Whiteheadia bifolia (Hyacinthaceae)

    Science.gov (United States)

    Wester, Petra

    2010-12-01

    Following the recent discovery of rodent pollination in the Pagoda lily, Whiteheadia bifolia (Hyacinthaceae) in South Africa, now the Cape rock elephant-shrew, Elephantulus edwardii (Macroscelidea, Afrotheria) is reported as an additional pollinator. Elephant-shrews, live-trapped near W. bifolia plants, were released in two terraria, containing the plants. The animals licked nectar with their long and slender tongues while being dusted with pollen and touching the stigmas of the flowers with their long and flexible noses. The captured elephant-shrews had W. bifolia pollen in their faeces, likely as a result of grooming their fur as they visited the flowers without eating or destroying them. The animals mostly preferred nectar over other food. This is the first record of pollination and nectar consumption in the primarily insectivorous E. edwardii, contributing to the very sparse knowledge about the behaviour of this unique clade of African mammals, as well as pollination by small mammals.

  11. Geographic isolation and elevational gradients promote diversification in an endemic shrew on Sulawesi.

    Science.gov (United States)

    Eldridge, Ryan A; Achmadi, Anang S; Giarla, Thomas C; Rowe, Kevin C; Esselstyn, Jacob A

    2018-01-01

    Phylogeographic research on endemic primates and amphibians inhabiting the Indonesian island of Sulawesi revealed the existence of seven areas of endemism (AoEs). Here, we use phylogenetic and population genetic analyses of one mitochondrial gene and 15 nuclear loci to assess geographic patterns of genetic partitioning in a shrew (Crocidura elongata) that is endemic to Sulawesi, but occurs across the island. We uncover substantial genetic diversity in this species both between and within AoEs, but we also identify close relationships between populations residing in different AoEs. One of the earliest divergences within C. elongata distinguishes a high-elevation clade from low-elevation clades. In addition, on one mountain, we observe three distinct genetic groups from low, middle, and high elevations, suggesting divergence along a single elevational gradient. In general, our results show that C. elongata, like several other Sulawesi endemic taxa, harbors extensive genetic diversity. This diversity is structured in part by known AoE boundaries, but also by elevational gradients and geographic isolation within AoEs. Copyright © 2017 Elsevier Inc. All rights reserved.

  12. Shrews, rats, and a polecat in "the pardoner’s tale": Chapter 3

    Science.gov (United States)

    Feinstein, Sandy; Woodman, Neal; Van Dyke, Carolynn

    2012-01-01

    While historically existing animals and literary animal characters inform allegorical and metaphorical characterization in The Canterbury Tales, figurative usage does not erase recognition of the material animal. "The Pardoner's Tale," for one, challenges the terms of conventional animal metaphors by refocusing attention on common animals as common animals and common human creatures as something worse than vermin. Most attention has been paid to the larger animals-goat, hare, and horse-that constitute the physical portrait of Chaucer's Pardoner in the "General Prologue" and in the prologue to his tale.! Like these animals, rats and a polecat, together with rhetorical shrews, appear in this tale as well as in other literature, including bestiaries and natural histories. Equally to the purpose, these animals could be physically observed as constituents of both urban and rural landscapes in fourteenth-century England.2 In the Middle Ages, animals were part of the environment as well as part of the culture: they lived inside as well as outside the city gates, priory walls, and even domestic spaces; a rat in the street or the garden might not be any less welcome or uncommon than encountering someone's horses and goats nibbling vegetation or blocking a passage. Not being out of the ordinary, though, such animals could (and can) be overlooked or dismissed as com­mon, too familiar to register. This chapter reveals why readers and listeners should pay close attention to the things they think they know and what they hear about what they think they know.

  13. RADIATION ECOLOGY ISSUES ASSOCIATED WITH MURINE RODENTS AND SHREWS IN THE CHERNOBYL EXCLUSION ZONE

    Energy Technology Data Exchange (ETDEWEB)

    Farfan, E.; Jannik, T.

    2011-10-01

    This article describes major studies performed by the Chernobyl Center's International Radioecology Laboratory (Slavutich, Ukraine) on radioecology of murine rodents and shrews inhabiting the Chernobyl Exclusion Zone. The article addresses the long-term (1986-2005) and seasonal dynamics of radioactive contamination of animals, and reviews interspecies differences in radionuclide accumulations and factors affecting the radionuclide accumulations. It is shown that bioavailability of radionuclides in the 'soil-to-plant' chain and a trophic specialization of animals play key roles in determining their actual contamination levels. The total absorbed dose rates in small mammals significantly reduced during the years following the Chernobyl Nuclear Power Plant accident. In 1986, the absorbed dose rate reached 1.3-6.0 Gy hr{sup -1} in the central areas of the Chernobyl Exclusion Zone (the 'Red Forest'). In 1988 and 1990, the total absorbed dose rates were 1.3 and 0.42 Gy hr{sup -1}, respectively. In 1995, 2000, and 2005, according to the present study, the total absorbed dose rates rarely exceeded 0.00023, 0.00018, and 0.00015 Gy hr{sup -1}, respectively. Contributions of individual radiation sources into the total absorbed dose are described.

  14. A climate for speciation: rapid spatial diversification within the Sorex cinereus complex of shrews

    Science.gov (United States)

    Hope, Andrew G.; Speer, Kelly A.; Demboski, John R.; Talbot, Sandra L.; Cook, Joseph A.

    2012-01-01

    The cyclic climate regime of the late Quaternary caused dramatic environmental change at high latitudes. Although these events may have been brief in periodicity from an evolutionary standpoint, multiple episodes of allopatry and divergence have been implicated in rapid radiations of a number of organisms. Shrews of the Sorex cinereus complex have long challenged taxonomists due to similar morphology and parapatric geographic ranges. Here, multi-locus phylogenetic and demographic assessments using a coalescent framework were combined to investigate spatiotemporal evolution of 13 nominal species with a widespread distribution throughout North America and across Beringia into Siberia. For these species, we first test a hypothesis of recent differentiation in response to Pleistocene climate versus more ancient divergence that would coincide with pre-Pleistocene perturbations. We then investigate the processes driving diversification over multiple continents. Our genetic analyses highlight novel diversity within these morphologically conserved mammals and clarify relationships between geographic distribution and evolutionary history. Demography within and among species indicates both regional stability and rapid expansion. Ancestral ecological differentiation coincident with early cladogenesis within the complex enabled alternating and repeated episodes of allopatry and expansion where successive glacial and interglacial phases each promoted divergence. The Sorex cinereus complex constitutes a valuable model for future comparative assessments of evolution in response to cyclic environmental change.

  15. Radiation ecology issues associated with murine rodents and shrews in the Chernobyl exclusion zone.

    Science.gov (United States)

    Gaschak, Sergey P; Maklyuk, Yulia A; Maksimenko, Andrey M; Bondarkov, Mikhail D; Jannik, G Timothy; Farfán, Eduardo B

    2011-10-01

    This article describes major studies performed by the Chernobyl Center's International Radioecology Laboratory (Slavutich, Ukraine) on radioecology of murine rodents and shrews inhabiting the Chernobyl Exclusion Zone. The article addresses the long-term (1986-2005) and seasonal dynamics of radioactive contamination of animals and reviews interspecies differences in radionuclide accumulations and factors affecting the radionuclide accumulations. It is shown that bioavailability of radionuclides in the "soil-to-plant" chain and a trophic specialization of animals play key roles in determining their actual contamination levels. The total absorbed dose rates in small mammals significantly reduced during the years following the Chernobyl Nuclear Power Plant accident. In 1986, the absorbed dose rate reached 1.3-6.0 Gy h(-1) in the central areas of the Chernobyl Exclusion Zone (the "Red Forest"). In 1988 and 1990, the total absorbed dose rates were 1.3 and 0.42 Gy h(-1), respectively. In 1995, 2000, and 2005, according to the present study, the total absorbed dose rates rarely exceeded 0.00023, 0.00018, and 0.00015 Gy h(-1), respectively. Contributions of individual radiation sources into the total absorbed dose are described.

  16. Action of Bacopa monnieri to antagonize cisplatin-induced emesis in Suncus murinus (house musk shrew

    Directory of Open Access Journals (Sweden)

    Ihsan Ullah

    2017-04-01

    Full Text Available Bacopa monnieri (BM, family Scrophulariaceae is used in several traditional systems of medicine for the management of epilepsy, depression, neuropathic pain, sleep disorders and memory deficits. The present study investigated the potential of BM methanol (BM-MetFr and BM n-butanol fractions (BM-ButFr to reduce chemotherapy-induced emesis in Suncus murinus (house musk shrew. Cisplatin (30 mg/kg, i.p. reliably induced retching and/or vomiting over a 2 day period. BM-MetFr (10–40 mg/kg, s.c. and BM-ButFr (5–20 mg/kg, s.c. antagonized the retching and/or vomiting response by ∼59.4% (p  0.05. In conclusion, the n-butanol fractions of BM have anti-emetic activity comparable with palonosetron and MPG. BM may be useful alone or in combination with other anti-emetic drugs for the treatment of chemotherapy-induced emesis in man.

  17. Invading and Expanding: Range Dynamics and Ecological Consequences of the Greater White-Toothed Shrew (Crocidura russula) Invasion in Ireland

    Science.gov (United States)

    McDevitt, Allan D.; Montgomery, W. Ian; Tosh, David G.; Lusby, John; Reid, Neil; White, Thomas A.; McDevitt, C. Damien; O'Halloran, John; Searle, Jeremy B.; Yearsley, Jon M.

    2014-01-01

    Establishing how invasive species impact upon pre-existing species is a fundamental question in ecology and conservation biology. The greater white-toothed shrew (Crocidura russula) is an invasive species in Ireland that was first recorded in 2007 and which, according to initial data, may be limiting the abundance/distribution of the pygmy shrew (Sorex minutus), previously Ireland's only shrew species. Because of these concerns, we undertook an intensive live-trapping survey (and used other data from live-trapping, sightings and bird of prey pellets/nest inspections collected between 2006 and 2013) to model the distribution and expansion of C. russula in Ireland and its impacts on Ireland's small mammal community. The main distribution range of C. russula was found to be approximately 7,600 km2 in 2013, with established outlier populations suggesting that the species is dispersing with human assistance within the island. The species is expanding rapidly for a small mammal, with a radial expansion rate of 5.5 km/yr overall (2008–2013), and independent estimates from live-trapping in 2012–2013 showing rates of 2.4–14.1 km/yr, 0.5–7.1 km/yr and 0–5.6 km/yr depending on the landscape features present. S. minutus is negatively associated with C. russula. S. minutus is completely absent at sites where C. russula is established and is only present at sites at the edge of and beyond the invasion range of C. russula. The speed of this invasion and the homogenous nature of the Irish landscape may mean that S. minutus has not had sufficient time to adapt to the sudden appearance of C. russula. This may mean the continued decline/disappearance of S. minutus as C. russula spreads throughout the island. PMID:24955824

  18. A study of commensal rodents and shrews with reference to the parasites of medical importance in Chanthaburi Province, Thailand.

    Science.gov (United States)

    Chenchittikul, M; Daengpium, S; Hasegawa, M; Itoh, T; Phanthumachinda, B

    1983-06-01

    A total of 622 and 110 commensal and forest rodents and shrews was examined in the urban and rural areas of Chanthaburi Province, Thailand. A higher density of commensal animals was found in urban than rural areas. Five enteropathogenic bacteria, and four helminth species of significant medical importance were collected. The Oriental rat-flea, X. cheopis was found prevalent among these animals. The findings of adult A. cantonensis worm in S. murinus the first reported case of the parasite developed into adult in an abnormal host.

  19. Flowering Trees

    Indian Academy of Sciences (India)

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

  20. Flowering Trees

    Indian Academy of Sciences (India)

    Brachichiton acerifolius F. Muell., commonly called as the Illawara flame tree is a member of Malvaceae family and is native to sub-tropical parts of Australia. Due to its spectacular flowers and tolerance to wide range of climates, it's now cultivated all over the world for its beauty. The tree produces flowers during the.

  1. Flowering Trees

    Indian Academy of Sciences (India)

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

  2. Flowering Trees

    Indian Academy of Sciences (India)

    Srimath

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

  3. Flowering Trees

    Indian Academy of Sciences (India)

    Baccaurea courtallensis Muell.-Arg. of Euphorbiaceae is an evergreen tree that is very attractive when in flower. Leaves are alternate. Male and female flowers are borne on separate trees. Inflorescences bearing several flowers arise in tufts on tubercles on the stem. Fruits are crimson red in colour. Seeds are covered.

  4. Prevalence of rabies virus and Hantaan virus infections in commensal rodents and shrews trapped in Bangkok.

    Science.gov (United States)

    Kantakamalakul, Wannee; Siritantikorn, Sontana; Thongcharoen, Prasert; Singchai, Chantra; Puthavathana, Pilaipan

    2003-11-01

    Five hundred rodents and shrews (Rattus norvegicus: 458, Rattus rattus: 28, Rattus exulans: 5, Mus musculus: 4 and Suncus murine: 5) trapped from the fresh food markets around Bangkok area were investigated for rabies virus and Hantaan virus infections. No rabies viral antigens in the animals' brains were detected by direct immunofluorescence. On the other hand, antibodies to Hantaan virus were demonstrated in the sera of 7 (1.53%) R. norvegicus caught in various markets using a particle agglutination technique. Further determination of the viral genome in rat lung tissue was performed by reverse transcriptase-polymerase chain reaction (RT-PCR) and nested PCR, 3 (0.66%) out of 7 were positive. HindIII and HifI restriction enzyme analyses showed the pattern of the Hantaan virus genome in 2 samples and that of the Seoul virus genome in the other. The results of the present study suggest that rodents from Bangkok's fresh food markets did not carry rabies. Thus, getting rid of rabies in dogs or cats in the Bangkok area may be easier than anticipated because there are no sources of asymptomatic reservoirs. This may result in the low incidence of rabies patients observed in Bangkok. On the contrary, the presence of antibodies and the Hantaan virus genome and Seoul virus genome in R. norvegicus will definitely provide evidence for physicians to be aware of hemorrhagic fever with renal syndrome (HFRS) and other clinical settings of Hantaan/Seoul virus disease in patients with a history of having contact with rats or their excreta.

  5. Behavioral patterns associated with chemotherapy-induced emesis: A potential signature for nausea in musk shrews

    Directory of Open Access Journals (Sweden)

    Charles Christopher Horn

    2011-07-01

    Full Text Available Nausea and vomiting are common symptoms in patients with many diseases, including cancer and its treatments. Although the neurological basis of vomiting is reasonably well known, an understanding of the physiology of nausea is lacking. The primary barrier to mechanistic research on the nausea system is the lack of an animal model. Indeed investigating the effects of anti-nausea drugs in preclinical models is difficult because the primary readout is often emesis. It is known that animals show a behavioral profile of sickness, associated with reduced feeding and movement, and possibly these general measures are signs of nausea. Studies attempting to relate the occurrence of additional behaviors to emesis have produced mixed results. Here we applied a statistical method, t-pattern (temporal pattern analysis, to determine patterns of behavior associated with emesis. Musk shrews were injected with the chemotherapy agent cisplatin (a gold standard in emesis research to induce acute (< 24 h and delayed (> 24 h emesis. Emesis and other behaviors were coded and tracked from video files. T-pattern analysis revealed hundreds of non-random patterns of behavior associated with emesis, including sniffing, changes in body contraction, and locomotion. There was little evidence that locomotion was inhibited by the occurrence of emesis. Eating and drinking, and other larger body movements including rearing, grooming, and body rotation, were significantly less common in emesis-related behavioral patterns in real versus randomized data. These results lend preliminary evidence for the expression of emesis-related behavioral patterns, including reduced ingestive behavior, grooming and exploratory behaviors. In summary, this statistical approach to behavioral analysis in a pre-clinical emesis research model could be used to assess the more global effects and limitations of drugs used to control nausea and its potential correlates, including reduced feeding and

  6. Influence of elevation and forest type on community assemblage and species distribution of shrews in the central and southern Appalachian mountains

    Science.gov (United States)

    W. Mark Ford; Timothy S. McCay; Michael A. Menzel; W. David Webster; Cathryn H. Greenberg; John F. Pagels; Joseph F. Merritt

    2005-01-01

    We analyzed shrew community data from 398,832 pitfall trapnights at 303 sites across the upper Piedmont, Blue ridge, northern Ridge and Valley, southern Ride and Valley, Cumberland Plateau and Allegheny Mountains and Plateau sections of the central and southern Appalachian Mountains from Alabama to Pennsylvania. The objectives of our research were to describe regional...

  7. How does the greater white-toothed shrew, Crocidura russula, responds to long-term heavy metal contamination? - A case study

    International Nuclear Information System (INIS)

    Marques, Carla Cristina; Sanchez-Chardi, Alejandro; Gabriel, Sofia Isabel; Nadal, Jacint; Viegas-Crespo, Ana Maria; Luz Mathias, Maria da

    2007-01-01

    Heavy metals accumulation in parallel with the evaluation of physiological and biochemical effects resulting from continued metal exposure were considered here using for the first time the great white-toothed shrew Crocidura russula as an in vivo model. Shrews were originated from an abandoned lead/zinc mining area and from a reference area, both in Alentejo, southern Portugal. Hepatic contents of nickel, copper, zinc, cadmium, mercury and lead were quantified by Inductively Coupled Plasma Mass Spectrometer (ICP-MS). Haematological parameters (white blood cells, red blood cells, haemoglobin and haematocrit) were obtained in a Coulter Counter Analyser and biochemical markers of the redox balance (glutathione S-transferase, glutathione peroxidase, and glutathione reductase) activities were measured spectrophotometrically using a Duo-50 spectrophotometer. Compared with control animals, significantly higher concentration of hepatic cadmium (9.29 vs. 1.18 μg/g dry weight) and nickel (1.56 vs. 0.343 μg/g dry weight) were detected in the shrews collected in the mining area. However, no significant changes were observed on haematological or enzymatic parameters in animals exposed to metal pollution. The obtained results show that shrews are good bioaccumulators of toxic heavy metals, but very tolerant to their effects, revealing an interesting long-term adaptation to polluted environments. In addition, this study provides reference values for haematological parameters and antioxidant enzymes levels in C. russula, which may be relevant for comparative purposes in further studies

  8. Emerging infectious disease implications of invasive mammalian species: the greater white-toothed shrew (Crocidura russula) is associated with a novel serovar of pathogenic Leptospira in Ireland

    Science.gov (United States)

    The greater white-toothed shrew (Crocidura russula) is an invasive mammalian species that was first recorded in Ireland in 2007. It currently occupies an area of approximately 7,600 km2 on the island. C. russula is normally distributed in Northern Africa and Western Europe, and was previously absent...

  9. Influence of elevation and forest type on community assemblage and species distribution of shrews in the central and southern Appalachian mountains

    Science.gov (United States)

    W. Mark Ford; Timothy S. McCay; Michael A. Menzel; W. David Webster; Cathryn H. Greenberg; John F. Pagels; Joseph F. Merritt; Joseph F. Merritt

    2005-01-01

    We analyzed shrew community data from 398,832 pitfall trapnights at 303 sites across the upper Piedmont, Blue Ridge, northern Ridge and Valley, southern Ridge and Valley, Cumberland Plateau and Allegheny Mountains and Plateau sections of the central and southern Appalachian Mountains from Alabama to Pennsylvania. The objectives of our research were to describe regional...

  10. The Asian house shrew Suncus murinus as a reservoir and source of human outbreaks of plague in Madagascar.

    Directory of Open Access Journals (Sweden)

    Soanandrasana Rahelinirina

    2017-11-01

    Full Text Available Identifying key reservoirs for zoonoses is crucial for understanding variation in incidence. Plague re-emerged in Mahajanga, Madagascar in the 1990s but there has been no confirmed case since 1999. Here we combine ecological and genetic data, from during and after the epidemics, with experimental infections to examine the role of the shrew Suncus murinus in the plague epidemiological cycle. The predominance of S. murinus captures during the epidemics, their carriage of the flea vector and their infection with Yersinia pestis suggest they played an important role in the maintenance and transmission of plague. S. murinus exhibit a high but variable resistance to experimental Y. pestis infections, providing evidence of its ability to act as a maintenance host. Genetic analyses of the strains isolated from various hosts were consistent with two partially-linked transmission cycles, with plague persisting within the S. murinus population, occasionally spilling over into the rat and human populations. The recent isolation from a rat in Mahajanga of a Y. pestis strain genetically close to shrew strains obtained during the epidemics reinforces this hypothesis and suggests circulation of plague continues. The observed decline in S. murinus and Xenopsylla cheopis since the epidemics appears to have decreased the frequency of spillover events to the more susceptible rats, which act as a source of infection for humans. Although this may explain the lack of confirmed human cases in recent years, the current circulation of plague within the city highlights the continuing health threat.

  11. The FAAH inhibitor URB-597 interferes with cisplatin- and nicotine-induced vomiting in the Suncus murinus (house musk shrew).

    Science.gov (United States)

    Parker, L A; Limebeer, C L; Rock, E M; Litt, D L; Kwiatkowska, M; Piomelli, D

    2009-04-20

    Considerable evidence implicates the endocannabinoid system as a neuromodulator of nausea and vomiting. The action of anandamide (AEA) can be prolonged by inhibiting its degradation, through the use of URB597 (URB), a Fatty Acid Amide Hydrolase (FAAH) enzyme inhibitor. Here we present evidence that the FAAH inhibitor, URB, interferes with cisplatin- and nicotine-induced vomiting in the Suncus murinus. In Experiment 1, shrews were injected with URB (0.9 mg/kg) or vehicle 120 min prior to the behavioral testing. They received a second injection of AEA (5 mg/kg) or vehicle 15 min prior to being injected with cisplatin (20 mg/kg) or saline and the number of vomiting episodes were counted for 60 min. In Experiment 2, shrews were injected with vehicle or URB (0.9 mg/kg) 120 min prior to receiving an injection of nicotine (5 mg/kg) or saline and the number of vomiting episodes were counted for 15 min. Experiment 3 evaluated the potential of the CB(1) antagonist, SR141716, to reverse the effect of URB on nicotine-induced vomiting. URB attenuated vomiting produced by cisplatin and nicotine and the combination of URB+AEA suppressed vomiting produced by cisplatin. The effect of URB on nicotine-induced vomiting was reversed by SR141716. These data suggest that the EC system plays a tonic role in the regulation of toxin-induced vomiting.

  12. Spermatozoa of the shrew, Suncus murinus, undergo the acrosome reaction and then selectively kill cells in penetrating the cumulus oophorus.

    Science.gov (United States)

    Kaneko, T; Iida, H; Bedford, J M; Mōri, T

    2001-08-01

    In the musk shrew, Suncus murinus (and other shrews), the cumulus oophorus is ovulated as a discrete, compact, matrix-free ball of cells linked by specialized junctions. In examining how they penetrate the cumulus, Suncus spermatozoa were observed to first bind consistently by the ventral face over the acrosomal region to the exposed smooth surface of a peripheral cumulus cell. This was apparently followed by point fusions between the plasma and outer acrosomal membranes. Thereafter, spermatozoa without acrosomes were observed within cumulus cells that displayed signs of necrosis, as did some radially neighboring cumulus cells linked by zona adherens and gap junctions. Eventually, penetration of spermatozoa as far as the perizonal space around the zona pellucida left linear tracks of locally necrotic cells flanked by normal cumulus cells. Based on these and previous observations, we conclude that the acrosome reaction in Suncus is always induced by cumulus cells, and that reacted spermatozoa penetrate the cumulus by selective invasion and killing of cumulus cells along a linear track. Loss of the acrosome also exposes an apical body/perforatorium that is covered with barbs that appear to assist reacted fertilizing spermatozoa in binding to the zona pellucida. Because fertilized eggs displayed no other spermatozoa within or bound to the zona, an efficient block to polyspermy must prevent such binding of additional spermatozoa.

  13. The Asian house shrew Suncus murinus as a reservoir and source of human outbreaks of plague in Madagascar.

    Science.gov (United States)

    Rahelinirina, Soanandrasana; Rajerison, Minoarisoa; Telfer, Sandra; Savin, Cyril; Carniel, Elisabeth; Duplantier, Jean-Marc

    2017-11-01

    Identifying key reservoirs for zoonoses is crucial for understanding variation in incidence. Plague re-emerged in Mahajanga, Madagascar in the 1990s but there has been no confirmed case since 1999. Here we combine ecological and genetic data, from during and after the epidemics, with experimental infections to examine the role of the shrew Suncus murinus in the plague epidemiological cycle. The predominance of S. murinus captures during the epidemics, their carriage of the flea vector and their infection with Yersinia pestis suggest they played an important role in the maintenance and transmission of plague. S. murinus exhibit a high but variable resistance to experimental Y. pestis infections, providing evidence of its ability to act as a maintenance host. Genetic analyses of the strains isolated from various hosts were consistent with two partially-linked transmission cycles, with plague persisting within the S. murinus population, occasionally spilling over into the rat and human populations. The recent isolation from a rat in Mahajanga of a Y. pestis strain genetically close to shrew strains obtained during the epidemics reinforces this hypothesis and suggests circulation of plague continues. The observed decline in S. murinus and Xenopsylla cheopis since the epidemics appears to have decreased the frequency of spillover events to the more susceptible rats, which act as a source of infection for humans. Although this may explain the lack of confirmed human cases in recent years, the current circulation of plague within the city highlights the continuing health threat.

  14. Helminth associations in white-toothed shrews Crocidura russula (Insectivora: Soricidae) from the Albufera Natural Park, Spain.

    Science.gov (United States)

    Portolés, Enrique; Granel, Pedro; Esteban, J Guillermo; Cabaret, Jacques

    2004-06-01

    The helminths of 218 white-toothed shrews from 29 sites in 2 biotopes in the Albufera Natural Park (Valencia, Spain) were examined from July 1990 to August 1991. An association analysis of helminths occurring at a prevalence of more than 4% was carried out for 4 species of cestodes located in the intestine (Hymenolepis pistillum, H. scalaris, H. tiara, and Pseudhymenolepis redonica) and 3 species of nematodes (Pseudophysaloptera sp. located in the stomach, Stammerinema rhopocephala larvae in the intestine and abdominal cavity, and Porrocaecum sp. in the thoracic and abdominal cavities). Bivariate (species pairs) versus multivariate analyses (associations within the entire set of species) were performed of presence-absence and of quantitative records (influence of intensity on associations). The associations were evaluated with respect to the sex and age of the host and to the sampling date and sites. The host and environment played a limited role, and the major determinant of species assemblage was phylogenetic. Positive associations were found among both the cestodes and the nematodes, whereas negative associations were found between cestodes and nematodes. The type of life cycle was probably the second greatest determinant of species associations. Nematodes using shrews as a paratenic host or as their definitive host were both positively associated.

  15. Flowering Trees

    Indian Academy of Sciences (India)

    Srimath

    shaped corolla. Fruit is large, ellipsoidal, green with a hard and smooth shell containing numerous flattened seeds, which are embedded in fleshy pulp. Calabash tree is commonly grown in the tropical gardens of the world as a botanical oddity.

  16. Electron Tree

    DEFF Research Database (Denmark)

    Appelt, Ane L; Rønde, Heidi S

    2013-01-01

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

  17. Flowering Trees

    Indian Academy of Sciences (India)

    branched evergreen shrub or small tree (6–7 m) with soft whitish-yellow wood. Branches are numerous and drooping. The leaves are elliptic-lanceolate and somewhat fleshy. Flowers are in loose axillary and terminal much-branched inflorescence, ...

  18. Flowering Trees

    Indian Academy of Sciences (India)

    narrow towards base. Flowers are large and attrac- tive, but emit unpleasant foetid smell. They appear in small numbers on erect terminal clusters and open at night. Stamens are numerous, pink or white. Style is slender and long, terminating in a small stigma. Fruit is green, ovoid and indistinctly lobed. Flowering Trees.

  19. ~{owering 'Trees

    Indian Academy of Sciences (India)

    Stamens are fused into a purple staminal tube that is toothed. Fruit is about 0.5 in. across, nearly globose, generally 5-seeded, green but yellow when ripe, quite smooth at first but wrinkled in drying, remaining long on the tree ajier ripening. The species is widely natural but occasionally cultivated for firewood as it grows very ...

  20. Flowering Trees

    Indian Academy of Sciences (India)

    Srimath

    quick-growing deciduous tree with a small crown. Branches are covered with dark conical prickles, which fall off after some time. The leaves are compound with three leaflets. Bright red or scarlet flowers which appear following leaf fall are in clusters at branch ends. Birds and bees visit flowers for nectar. Fruit is a cylindrical ...

  1. Flowering Trees

    Indian Academy of Sciences (India)

    deciduous tree with irregularly-shaped trunk, greyish-white scaly bark and milky latex. Leaves in opposite pairs are simple, oblong and whitish beneath. Flowers that occur in branched inflorescence are white, 2–. 3cm across and fragrant. Calyx is glandular inside. Petals bear numerous linear white scales, the corollary.

  2. Flowering Trees

    Indian Academy of Sciences (India)

    Muntingia calabura L. (Singapore cherry) of. Elaeocarpaceae is a medium size handsome ever- green tree. Leaves are simple and alternate with sticky hairs. Flowers are bisexual, bear numerous stamens, white in colour and arise in the leaf axils. Fruit is a berry, edible with several small seeds embedded in a fleshy pulp ...

  3. Flowering Trees

    Indian Academy of Sciences (India)

    Srimath

    . (6-10m high) evergreen tree with a straight trunk and broad open crown. Leaves are clustered at the end of twigs. They are dark green, broadest near the rounded apex and tapering towards the base with a short stalk. Flowers are greenish or ...

  4. ~{owering 'Trees

    Indian Academy of Sciences (India)

    size (upto 40 ft. high) deciduous tree with thick trunk, large crown of spreading branches and furrowed greenish-brown bark. (picture shows a young specimen). Leaves are 10-20 in. long, twice compound bearing numerous dark- green ...

  5. Flowering Trees

    Indian Academy of Sciences (India)

    Guaiacum officinale L. (LIGNUM-VITAE) of Zygophyllaceae is a dense-crowned, squat, knobbly, rough and twisted medium-sized ev- ergreen tree with mottled bark. The wood is very hard and resinous. Leaves are compound. The leaflets are smooth, leathery, ovate-ellipti- cal and appear in two pairs. Flowers (about 1.5.

  6. Flowering Trees

    Indian Academy of Sciences (India)

    IAS Admin

    Caesalpinia coriaria (Jacq.) Willd. (THE AMERICAN SUMACH, DIVI-DIVI) of. Caesalpiniaceae is a small unarmed tree reaching up to 10 m in height with a spreading crown. Leaves are alternate and twice compound. The flowers are small, about 0.6 cm (enlarged 5 times here), greenish-yellow, fragrant and appear in dense ...

  7. Flowering Trees

    Indian Academy of Sciences (India)

    Canthium parviflorum Lam. of Rubiaceae is a large shrub that often grows into a small tree with conspicuous spines. Leaves are simple, in pairs at each node and are shiny. Inflorescence is an axillary few-flowered cymose fascicle. Flowers are small (less than 1 cm across), 4-merous and greenish-white. Fruit is ellipsoid ...

  8. Flowering Trees

    Indian Academy of Sciences (India)

    Diospyros peregrina (Gaertn.) Guercke Syn. Diospyros embryopteris Pers., Diospyros malabarica Desr. (PALE MOON EBONY, RIBER EBONY) of Ebenaceae is a small or mid-sized slow-growing evergreen tree with spreading branches that form a dense crown. The bark is smooth, thick, dark and flakes off in large shreds.

  9. Flowering Trees

    Indian Academy of Sciences (India)

    Andira inermis (wright) DC. , Dog Almond of Fabaceae is a handsome lofty evergreen tree. Leaves are alternate and pinnately compound with 4–7 pairs of leaflets. Flowers are fragrant and are borne on compact branched inflorescences. Fruit is ellipsoidal one-seeded drupe that is peculiar to members of this family.

  10. :Ffowering 'Trees-

    Indian Academy of Sciences (India)

    The tree is a host of lac insects which secrete a resinous substance that yields shellac or lac. A ruby-coloured gum known as Bengal Kino is collected from the incisions made in the bark. The wood, resistant to water, is used in water-well work. The seeds are used as anthelmintic and as an antidote for snake-bite.

  11. Flowering Trees

    Indian Academy of Sciences (India)

    Trincomali Wood of Tiliaceae is a tall evergreen tree with straight trunk, smooth brownish-grey bark and simple broad leaves. Inflorescence is much branched with white flowers. Stamens are many with golden yellow anthers. Fruit is a capsule with six spreading wings. Seeds bear short stiff hairs that cause skin irritation.

  12. Tree Mortality

    Science.gov (United States)

    Mark J. Ambrose

    2012-01-01

    Tree mortality is a natural process in all forest ecosystems. However, extremely high mortality also can be an indicator of forest health issues. On a regional scale, high mortality levels may indicate widespread insect or disease problems. High mortality may also occur if a large proportion of the forest in a particular region is made up of older, senescent stands....

  13. Flowering Trees

    Indian Academy of Sciences (India)

    Sterculia foetida L. (INDIAN ALMOND,. JAVA OLIVE) of Sterculiaceae is a tall deciduous tree reaching a height of 20 m with faintly ridged grey bark. The bole reaches up to 2m in girth. Branches are reddish, usually horizontal. Leaves are large, palmately compound (5–7 leaflets) and clustered at the branch ends. Flowers ...

  14. Computerized detection and analysis of cancer chemotherapy-induced emesis in a small animal model, musk shrew.

    Science.gov (United States)

    Huang, Dong; Meyers, Kelly; Henry, Séverine; De la Torre, Fernando; Horn, Charles C

    2011-04-30

    Vomiting is a common side effect of cancer chemotherapy and many drug treatments and diseases. In animal studies, the measurement of vomiting usually requires direct observation, which is time consuming and often lacks temporal precision. Musk shrews have been used to study the neurobiology of emesis and have a rapid emetic episode (∼1 s for a sequence of retching and expulsion). The aim of the current study was to develop a method to automatically detect and characterize emetic episodes induced by the cancer chemotherapy agent cisplatin. The body contour in each video frame was tracked and normalized to a parameterized shape basis. The tracked shape was projected to a feature space that maximized the shape variations in the consecutive frames during retching. The resulting one dimensional projection was sufficient to detect most emetic episodes in the acute (peak at 2h) and delayed (peak at 54 h) phases after cisplatin treatment. Emetic episodes were relatively invariant in the number of retches (∼6.2), duration (∼1.2s), inter-retch interval (∼198 ms), and amplitude during the 72 h after cisplatin treatment. This approach should open a new vista into emesis research to permit tracking and analysis of emesis in a small animal model and facilitate the development of new antiemetic therapies. These results also yield a better understanding of the brain's central pattern generator for emesis and indicate that the retching response in the musk shrew (at ∼5.4 Hz) is the fastest ever recorded in a free-moving animal. Copyright © 2011 Elsevier B.V. All rights reserved.

  15. The unusual state of the cumulus oophorus and of sperm behaviour within it, in the musk shrew, Suncus murinus.

    Science.gov (United States)

    Bedford, J M; Mori, T; Oda, S

    1997-05-01

    In the musk shrew, Suncus murinus, the behaviour of the cumulus-egg complex and its interaction with spermatozoa were unusual in several respects. The cumulus oophorus was ovulated about 15.5 h after mating or treatment with hCG as a hyaluronidase-insensitive matrix-free ball of cells which remained for relatively long periods of about 14 h around fertilized, and for about 24 h around unfertilized eggs. As a probable function of the small number of up to about 10 or 20 spermatozoa that generally reached the oviduct ampulla from isthmic crypts, there was often a delay of up to 10 h after ovulation before most eggs were penetrated. Soon after ovulation, however, the corona radiata retreated progressively from the zona pellucida, creating a closed perizonal space within the cumulus oophorus. Usually, most spermatozoa that did reach the ampulla were found within a cumulus and generally within that perizonal space. However, whereas the acrosome was intact among the few free ampullary spermatozoa, and in those adhering to the zona of cumulus-free eggs after delayed mating, all spermatozoa seen moving within the cumulus or adhering to the zona of unfertilized eggs had shed the giant acrosome. In accord with current observations in other shrews, the cumulus in Suncus may therefore function not only to sequester spermatozoa, but also as an essential mediator of fertilization-probably by inducing the acrosome reaction. In the absence of the acrosomal carapace that expresses the zona receptors in most mammals, fertilizing Suncus spermatozoa could use an unusual array of barbs on the exposed perforatorium to attach to the zona pellucida.

  16. Distributional records of shrews (Mammalia, Soricomorpha, Soricidae) from Northern Central America with the first record of Sorex from Honduras

    Science.gov (United States)

    Woodman, Neal; Matson, John O.; McCarthy, Timothy J.; Eckerlin, Ralph P.; Bulmer, Walter; Ordonez-Garza, Nicte

    2012-01-01

    Short term surveys for small mammals in Guatemala and Honduras during 1992–2009 provided important new records for 12 taxa of shrews from 24 localities. These locality records expand the known geographic distributions for five species and for the genus Sorex Linnaeus, 1758: the geographic range of Cryptotis goodwini Jackson, 1933, now includes the Sierra de las Minas, Guatemala, and several isolated highlands in western Honduras; the known distribution of Cryptotis mayensis (Merriam, 1901) is increased with the first definite modern record for this shrew from Guatemala; Cryptotis merriami Choate, 1970, is now known to occur in the Sierra de las Minas and the Sierra del Merendon, Guatemala, as well as the isolated Sierra de Omoa and Montana de La Muralla in Honduras, and its documented elevational range (600–1720 m) is expanded; records of Sorex veraepacis Alston, 1877, expand the known distribution of this species to include the Sierra de Yalijux, Guatemala; and discovery of Sorex salvini Merriam, 1897, at Celaque, Honduras (1825–3110 m), represents a considerable extension of the geographic range of the species, and it is the first record of the genus Sorex from Honduras. In addition, the first record of potential syntopy among C. goodwini, C merriami, and Cryptotis orophilus (J.A. Allen, 1895), is reported at an elevation of 1430 m in the Sierra de Celaque, Honduras. Information associated with these records contributes substantially to knowledge of habitat use, elevational distributions, reproductive patterns, diet, and parasites of the species encountered. General patterns include the first evidence that Neotropical species of soricids have smaller litters than their temperate congeners.

  17. Surface tree languages and parallel derivation trees

    NARCIS (Netherlands)

    Engelfriet, Joost

    1976-01-01

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

  18. Trees are good, but…

    Science.gov (United States)

    E.G. McPherson; F. Ferrini

    2010-01-01

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

  19. Morphological and molecular characteristics of Malayfilaria sofiani Uni, Mat Udin & Takaoka n. g., n. sp. (Nematoda: Filarioidea) from the common treeshrew Tupaia glis Diard & Duvaucel (Mammalia: Scandentia) in Peninsular Malaysia.

    Science.gov (United States)

    Uni, Shigehiko; Mat Udin, Ahmad Syihan; Agatsuma, Takeshi; Saijuntha, Weerachai; Junker, Kerstin; Ramli, Rosli; Omar, Hasmahzaiti; Lim, Yvonne Ai-Lian; Sivanandam, Sinnadurai; Lefoulon, Emilie; Martin, Coralie; Belabut, Daicus Martin; Kasim, Saharul; Abdullah Halim, Muhammad Rasul; Zainuri, Nur Afiqah; Bhassu, Subha; Fukuda, Masako; Matsubayashi, Makoto; Harada, Masashi; Low, Van Lun; Chen, Chee Dhang; Suganuma, Narifumi; Hashim, Rosli; Takaoka, Hiroyuki; Azirun, Mohd Sofian

    2017-04-20

    The filarial nematodes Wuchereria bancrofti (Cobbold, 1877), Brugia malayi (Brug, 1927) and B. timori Partono, Purnomo, Dennis, Atmosoedjono, Oemijati & Cross, 1977 cause lymphatic diseases in humans in the tropics, while B. pahangi (Buckley & Edeson, 1956) infects carnivores and causes zoonotic diseases in humans in Malaysia. Wuchereria bancrofti, W. kalimantani Palmieri, Pulnomo, Dennis & Marwoto, 1980 and six out of ten Brugia spp. have been described from Australia, Southeast Asia, Sri Lanka and India. However, the origin and evolution of the species in the Wuchereria-Brugia clade remain unclear. While investigating the diversity of filarial parasites in Malaysia, we discovered an undescribed species in the common treeshrew Tupaia glis Diard & Duvaucel (Mammalia: Scandentia). We examined 81 common treeshrews from 14 areas in nine states and the Federal Territory of Peninsular Malaysia for filarial parasites. Once any filariae that were found had been isolated, we examined their morphological characteristics and determined the partial sequences of their mitochondrial cytochrome c oxidase subunit 1 (cox1) and 12S rRNA genes. Polymerase chain reaction (PCR) products of the internal transcribed spacer 1 (ITS1) region were then cloned into the pGEM-T vector, and the recombinant plasmids were used as templates for sequencing. Malayfilaria sofiani Uni, Mat Udin & Takaoka, n. g., n. sp. is described based on the morphological characteristics of adults and microfilariae found in common treeshrews from Jeram Pasu, Kelantan, Malaysia. The Kimura 2-parameter distance between the cox1 gene sequences of the new species and W. bancrofti was 11.8%. Based on the three gene sequences, the new species forms a monophyletic clade with W. bancrofti and Brugia spp. The adult parasites were found in tissues surrounding the lymph nodes of the neck of common treeshrews. The newly described species appears most closely related to Wuchereria spp. and Brugia spp., but differs from these in

  20. Simple street tree sampling

    Science.gov (United States)

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

    2015-01-01

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

  1. Programming macro tree transducers

    DEFF Research Database (Denmark)

    Bahr, Patrick; Day, Laurence E.

    2013-01-01

    A tree transducer is a set of mutually recursive functions transforming an input tree into an output tree. Macro tree transducers extend this recursion scheme by allowing each function to be defined in terms of an arbitrary number of accumulation parameters. In this paper, we show how macro tree ...

  2. Modular tree automata

    DEFF Research Database (Denmark)

    Bahr, Patrick

    2012-01-01

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

  3. City of Pittsburgh Trees

    Data.gov (United States)

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

  4. Can they dig it? Functional morphology and semifossoriality among small-eared shrews, genus Cryptotis (Mammalia, Soricidae).

    Science.gov (United States)

    Woodman, Neal; Gaffney, Sarah A

    2014-07-01

    Small-eared shrews (Mammalia: Soricidae: Cryptotis), exhibit modifications of the forelimb skeleton that have been interpreted as adaptations for semifossoriality. Most species inhabit remote regions, however, and their locomotory and foraging behaviors remain mostly speculative. To better understand the morphological modifications in the absence of direct observations, we quantified variation in these species by measuring 151 individuals representing 18 species and populations of Cryptotis and two species of moles (Talpidae) for comparison. From our measurements, we calculated 22 indices, most of which have been used previously to characterize substrate use among rodents and other taxa. We analyzed the indices using 1) average percentile ranks, 2) principal components analysis, and 3) cluster analysis. From these analyses, we determined that three basic modes of substrate adaptation are present within Cryptotis: 1) a primarily terrestrial mode, with species that are capable of burrowing, but lack adaptations to increase digging efficiency, 2) a semifossorial mode, with species whose forelimbs bones show strong muscle attachment areas and increased mechanical advantage, and 3) an intermediate mode. In addition to identifying new morphological characters and contributing to our understanding of the functional morphology of soricids, these analyses provide additional insight into the ecology of the species of interest. © 2014 Wiley Periodicals, Inc.

  5. Tissue, age, and sex distribution of thallium in shrews from Doñana, a protected area in SW Spain.

    Science.gov (United States)

    Sánchez-Chardi, Alejandro

    2007-09-20

    In 1998, the protected area of Doñana, an important natural region in SW Europe, was affected with great amount of acidic waters and sludge from a pyrite mine loaded with toxic metals such as thallium (Tl). Since this ecological catastrophe, several studies have addressed the effects of this pollution on the flora and fauna in this protected area. However, in contrast to other non-essential metals, scarce information on Tl was available after this disaster, especially in terrestrial environments. This study reported a 3- and 10-fold increase in Tl in liver and kidneys, respectively, of the greater white-toothed shrew, Crocidura russula, in the polluted site in comparison with reference animals. Kidneys showed the highest concentrations of this metal in the polluted site, whereas both organs analysed have similar concentrations in the reference site. Although no significant age-dependent variation was found, adults had higher concentrations than juveniles. Moreover, females showed higher concentrations than males. These results demonstrate the high entrance and transfer of Tl in terrestrial food-chains. To the best of my knowledge, these data constitute the first measurements of Tl in mammals from the protected area of Doñana and are among the few available for insectivorous mammals.

  6. The Book of Ruth and Song of Songs in the First Hebrew Translation of The Taming of the Shrew

    Directory of Open Access Journals (Sweden)

    Kahn Lily

    2017-12-01

    Full Text Available This article investigates the earliest Hebrew rendition of a Shakespearean comedy, Judah Elkind’s מוסר סוררה musar sorera ‘The Education of the Rebellious Woman’ (The Taming of the Shrew, which was translated directly from the English source text and published in Berditchev in 1892. Elkind’s translation is the only comedy among a small group of pioneering Shakespeare renditions conducted in late nineteenth-century Eastern Europe by adherents of the Jewish Enlightenment movement. It was rooted in a strongly ideological initiative to establish a modern European-style literature in Hebrew and reflecting Jewish cultural values at a time when the language was still primarily a written medium on the cusp of its large-scale revernacularisation in Palestine. The article examines the ways in which Elkind’s employment of a Judaising translation technique drawing heavily on romantic imagery from prominent biblical intertexts, particularly the Book of Ruth and the Song of Songs, affects the Petruchio and Katherine plotline in the target text. Elkind’s use of carefully selected biblical names for the main characters and his conscious insertion of biblical verses well known in Jewish tradition for their romantic connotations serve to transform Petruchio and Katherine into Peretz and Hoglah, the heroes of a distinctly Jewish love story which offers a unique and intriguing perspective on the translation of Shakespearean comedy.

  7. Estimating species trees from unrooted gene trees.

    Science.gov (United States)

    Liu, Liang; Yu, Lili

    2011-10-01

    In this study, we develop a distance method for inferring unrooted species trees from a collection of unrooted gene trees. The species tree is estimated by the neighbor joining (NJ) tree built from a distance matrix in which the distance between two species is defined as the average number of internodes between two species across gene trees, that is, average gene-tree internode distance. The distance method is named NJ(st) to distinguish it from the original NJ method. Under the coalescent model, we show that if gene trees are known or estimated correctly, the NJ(st) method is statistically consistent in estimating unrooted species trees. The simulation results suggest that NJ(st) and STAR (another coalescence-based method for inferring species trees) perform almost equally well in estimating topologies of species trees, whereas the Bayesian coalescence-based method, BEST, outperforms both NJ(st) and STAR. Unlike BEST and STAR, the NJ(st) method can take unrooted gene trees to infer species trees without using an outgroup. In addition, the NJ(st) method can handle missing data and is thus useful in phylogenomic studies in which data sets often contain missing loci for some individuals.

  8. Full-length genome sequence of Mossman virus, a novel paramyxovirus isolated from rodents in Australia

    International Nuclear Information System (INIS)

    Miller, Philippa J.; Boyle, David B.; Eaton, Bryan T.; Wang Linfa

    2003-01-01

    Mossman virus (MoV) was isolated on two occasions from wild rats trapped in Queensland, Australia, during the early 1970s. Together with Nariva virus and J-virus MoV belongs to a group of novel paramyxoviruses isolated from rodents during the last 40 years, none of which had been characterized at the molecular level until now. cDNA subtraction strategies used to isolate virus-specific cDNA derived from both MoV-infected cells and crude MoV pellets were pivotal steps in rapid characterization of the complete genome sequence. Analysis of the full-length genome and its encoded proteins confirmed that MoV is a novel member of the subfamily Paramyxovirinae which cannot be assigned to an existing genus. MoV appears to be more closely related to another unclassified paramyxovirus Tupaia paramyxovirus (TPMV), isolated from the tree shrew Tupaia belangeri. Together with Salem virus (SalV), a further unclassified paramyxovirus that was isolated from a horse, MoV and TPMV make up a new collection of paramyxoviruses situated evolutionally between the genus Morbillivirus and the newly established genus Henipavirus

  9. Chromosome localization of the loci for PEPA, PEPB, PEPS, IDH1, GSR, MPI, PGM1, NP, SOD1, and ME1 in the common shrew (Sorex araneus).

    Science.gov (United States)

    Matyakhina, L D; Colonin, M G; Pack, S D; Borodin, P M; Searle, J B; Serov, O L

    1996-04-01

    This report extends the genetic map of the common shrew (Sorex araneus) by adding chromosome assignments for ten genes to the seven already mapped (Pack et al. 1995). A somatic cell hybrid panel was used for the mapping. The genes for peptidase A (PEPA) and isocitrate dehydrogenase-1 (IDH1) map to chromosome de; the genes for phosphoglucomutase-1 (PGM1), superoxide dismutase-1 (SOD1), and mannosephosphate isomerase (MPI) are located on chromosome af; the genes for nucleoside phosphorylase (NP) and glutathione reductase (GSR) are on chromosome ik; and the genes for peptidase S (PEPS), malic enzyme-1 (ME1), peptidase B (PEPB) are found on chromosomes jl, go, and mp respectively.

  10. Nomenclatural notes and identification of small-eared shrews (Mammalia: genus Cryptotis) from Cobán, Guatemala, in The Natural History Museum, London

    Science.gov (United States)

    Woodman, Neal

    2011-01-01

    A small series of shrews collected in Guatemala and registered in the British Museum between 1843 and 1907 includes parts of type series for three species: Corsira tropicalis Gray (1843), Sorex micrurus Tomes (1862), and Blarina tropicalis Merriam (1895). These three names are now considered equivalent, but my recent review of the specimens comprising the series indicates that they include three distinct species: Cryptotis merriami Choate (1970), Cryptotis oreoryctes Woodman (2011), and Cryptotis tropicalis (Merriam 1895). I review the taxonomic history of these specimens, provide current identifications tied directly to museum register numbers, describe how to distinguish the three species, and provide revised synonymies for these species.

  11. Urban tree growth modeling

    Science.gov (United States)

    E. Gregory McPherson; Paula J. Peper

    2012-01-01

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

  12. Keeping trees as assets

    Science.gov (United States)

    Kevin T. Smith

    2009-01-01

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

  13. Classification and regression trees

    CERN Document Server

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

    1984-01-01

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

  14. A wide hybrid zone of chromosome races of the common shrew, Sorex araneus Linnaeus, 1758 (Mammalia, between the Dnieper and Berezina Rivers (Belarus

    Directory of Open Access Journals (Sweden)

    Yu Borisov

    2010-12-01

    Full Text Available Karyological study of 75 specimens of the common shrew, Sorex araneus Linnaeus, 1758, from 8 localities in the Berezina River basin (eastern Belarus was carried out. A wide hybrid zone (not less than 100 km between the northern West Dvina chromosome race (XX / XYY, af, bc, gm, hk, ip, jl, no, qr, tu and the southern Turov race (XX / XYY, af, bc, g, h/k, i, jl, m, n, o, p, q, r, tu was revealed in this region. Frequencies of fused-unfused arms comprising four diagnostic metacentrics of the West Dvina race (g/m, h/k, n/o, q/r were calculated in all capture sites. Taking into consideration the absence of metacentric ip in specimens from six northern localities, the Borisov (Bs race (XX / XYY, af, bc, g/m, h/k, i, jl, n/o, p, q/r, tu (Orlov, Borisov, 2009 was distinguished in these sites. Common shrews from two southern localities on the right and left banks of the Berezina River (Berezino vicinity were referred to the Turov race. The presence of four metacentrics descended from the West Dvina race in the Bs race testifies to the hypothesis expressed earlier that the polymorphic populations of the S. araneus between the Dnieper and Berezina Rivers originated as a result of the West Dvina race spreading from the north and of hybridization between this race and local populations with acrocentric chromosomes.

  15. Accumulation of Methylmercury in Invertebrates and Masked Shrews (Sorex cinereus) at an Upland Forest-Peatland Interface in Northern Minnesota, USA.

    Science.gov (United States)

    Tavshunsky, Ilana; Eggert, Susan L; Mitchell, Carl P J

    2017-12-01

    Mercury (Hg) methylation is often elevated at the terrestrial-peatland interface, but methylmercury (MeHg) production at this "hot spot" has not been linked with in situ biotic accumulation. We examined total Hg and MeHg levels in peat, invertebrates and tissues of the insectivore Sorex cinereus (masked shrew), inhabiting a terrestrial-peatland ecotone in northern Minnesota, USA. Mean MeHg concentrations in S. cinereus (71 ng g -1 ) fell between concentrations measured in spiders (mean 70-140 ng g -1 ), and ground beetles and millipedes (mean 29-42 ng g -1 ). Methylmercury concentrations in S. cinereus increased with age and differed among tissues, with highest concentrations in kidneys and muscle, followed by liver and brain. Nearly all Hg in S. cinereus was in the methylated form. Overall, the high proportional accumulation of MeHg in peat at the site (3.5% total Hg as MeHg) did not lead to particularly elevated concentrations in invertebrates or shrews, which are below values considered a toxicological risk.

  16. Fault tree handbook

    International Nuclear Information System (INIS)

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

    1981-01-01

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

  17. Covering tree with stars

    DEFF Research Database (Denmark)

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

    2013-01-01

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

  18. Covering tree with stars

    DEFF Research Database (Denmark)

    Baumbach, Jan; Guo, Jiong; Ibragimov, Rashid

    2015-01-01

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

  19. Fault-Tree Compiler

    Science.gov (United States)

    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.

  20. Trees and highway safety.

    Science.gov (United States)

    2011-03-01

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

  1. Decision-Tree Program

    Science.gov (United States)

    Buntine, Wray

    1994-01-01

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

  2. Winter Birch Trees

    Science.gov (United States)

    Sweeney, Debra; Rounds, Judy

    2011-01-01

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

  3. Total well dominated trees

    DEFF Research Database (Denmark)

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

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

  4. Macro tree transducers

    NARCIS (Netherlands)

    Engelfriet, Joost; Vogler, Heiko

    1985-01-01

    Macro tree transducers are a combination of top-down tree transducers and macro grammars. They serve as a model for syntax-directed semantics in which context information can be handled. In this paper the formal model of macro tree transducers is studied by investigating typical automata theoretical

  5. TreePics: visualizing trees with pictures

    Directory of Open Access Journals (Sweden)

    Nicolas Puillandre

    2017-09-01

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

  6. Delta-9-tetrahydrocannabinol differentially suppresses cisplatin-induced emesis and indices of motor function via cannabinoid CB(1) receptors in the least shrew.

    Science.gov (United States)

    Darmani, N A

    2001-01-01

    We have recently shown that the cannabinoid CB(1) receptor antagonist, SR 141716A, produces emesis in the least shrew (Cryptotis parva) in a dose- and route-dependent manner. This effect was blocked by delta-9-tetrahydrocannabinol (Delta(9)-THC). The present study investigates the cannabinoid receptor mechanisms by which Delta(9)-THC produces its antiemetic effects against cisplatin (20 mg/kg, i.p.)-induced emesis as well as its cannabimimetic activity profile (motor reduction) in the least shrew. Intraperitoneal administration of Delta(9)-THC (1, 2.5, 5 and 10 mg/kg) dose-dependently reduced both the percentage of animals vomiting (ID(50)=1.8+/-1.6 mg/kg) and the frequency of vomits (ID(50)=0.36+/-1.18 mg/kg) in a potent manner. The lowest significantly effective antiemetic dose of Delta(9)-THC for the latter emesis parameters was 2.5 mg/kg. Although Delta(9)-THC reduced the frequency of vomits up to 98%, it failed to completely protect all tested shrews from vomiting (80% protection). The cannabinoid CB(1) antagonist (SR 141716A) and not the CB(2) antagonist (SR 144528), reversed the antiemetic effects of Delta(9)-THC in a dose-dependent fashion. Delta(9)-THC (1, 5, 10 and 20 mg/kg, ip) suppressed locomotor parameters (spontaneous locomotor activity, duration of movement and rearing frequency) in a biphasic manner and only the 20-mg/kg dose simultaneously suppressed the triad of locomotor parameters to a significant degree. Subcutaneous (1-10 mg/kg) and intraperitoneal (0.05-40 mg/kg) injection of some doses of SR 141716A caused significant reductions in one or more components of the triad of locomotor parameters but these reductions were not dose dependent. Subcutaneous injection of SR 141716A (0.2, 1, 5 and 10 mg/kg) reversed the motor suppressant effects of a 20-mg/kg dose of Delta(9)-THC (ip) in a dose-dependent manner. Relative to its motor suppressant effects, Delta(9)-THC is a more potent antiemetic agent. Both effects are probably mediated via CB(1

  7. Karyotypic evolution and organization of the highly repetitive DNA sequences in the Japanese shrew-moles, Dymecodon pilirostris and Urotrichus talpoides.

    Science.gov (United States)

    Nakata, A; Yoshimura, A; Kuro-o, M; Obara, Y

    2005-01-01

    The karyological relationship and organization of highly repetitive DNA sequences in Japanese shrew-moles were studied by zoo-blot hybridization and fluorescence in situ hybridization (FISH). When the genomic DNA of the eastern race of Urotrichus talpoides was digested with PstI, three fragments of highly repetitive DNA sequences, approximately 0.7, 0.9, and 1.4 kb in length, were observed as distinct bands. The results of FISH in the eastern race of U. talpoides using these three fragments separately as probes showed that the 0.7-kb PstI fragment was distributed in the centromeric regions of most chromosomes, and that the 0.9- and 1.4-kb fragments were predominantly located in the C-heterochromatin region of chromosome 13p. Although the western race of U. talpoides also had three PstI fragments, 0.9- and 1.4-kb PstI fragments were more ambiguous than those of the eastern race. The PstI- digested genomic DNA in Dymecodonpilirostris produced only a faint 0.9-kb band, and its signal patterns obtained by zoo-blot hybridization were clearly different from those of U. talpoides. The 0.7-kb fragment of U. talpoides hybridized strongly with the 0.9-kb fragment of D. pilirostris. In a FISH analysis, the 0.9-kb fragment of D. pilirostris hybridized with highly repetitive DNA in the centromeric regions of most chromosomes from both D. pilirostris and U. talpoides. Zoo-blot hybridization and FISH analyses suggest that the 0.9- and 1.4-kb PstI fragments were generated specifically in the genome of U. talpoides after the common ancestor differentiated into two extant shrew-mole species. A difference in the length of the centromeric elements between U. talpoides and D. pilirostris might be observed due to certain modifications of the repeating unit.

  8. The anti-asthmatic drug pranlukast suppresses the delayed-phase vomiting and reverses intracellular indices of emesis evoked by cisplatin in the least shrew (Cryptotis parva).

    Science.gov (United States)

    Darmani, Nissar A; Chebolu, Seetha; Zhong, Weixia; Kim, William D; Narlesky, Matthew; Adams, Joia; Dong, Fanglong

    2017-08-15

    The introduction of second generation serotonin 5-HT 3 receptor (5-HT 3 ) antagonist palonosetron combined with long-acting substance P neurokinin NK 1 receptor (NK 1 ) antagonists (e.g. netupitant) has substantially improved antiemetic therapy against early- and delayed-phases of emesis caused by highly emetogenic chemotherapeutics such as cisplatin. However, the improved efficacy comes at a cost that many patients cannot afford. We introduce a new class of antiemetic, the antiasthmatic leukotriene CysLT1 receptor antagonist pranlukast for the suppression of cisplatin-evoked vomiting. Pranlukast (10mg/kg) by itself significantly reduced the mean frequency of vomits (70%) and fully protected least shrews from vomiting (46%) during the delayed-phase of cisplatin (10mg/kg)-evoked vomiting. Although, pranlukast tended to substantially reduce both the mean frequency of vomits and the number of shrews vomiting during the early-phase, these reductions failed to attain significance. When combined with a first (tropisetron)- or a second (palonosetron)-generation 5-HT 3 receptor antagonist, pranlukast potentiated their antiemetic efficacy during both phases of vomiting. In addition, pranlukast by itself prevented several intracellular signal markers of cisplatin-evoked delayed-vomiting such as phosphorylation of ERK1/2 and PKA. When pranlukast was combined with either palonosetron or tropisetron, these combinations suppressed the evoked phosphorylation of: i) ERK1/2 during both acute- and delayed-phase, ii) PKCα/β at the peak acute-phase, and iii) PKA at the peak delayed-phase. The current and our published findings suggest that overall behavioral and intracellular signaling effects of pranlukast via blockade of CysLT1 receptors generally appear to be similar to the NK 1 receptor antagonist netupitant with some differences. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. The valuative tree

    CERN Document Server

    Favre, Charles

    2004-01-01

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

  10. A theory of game trees, based on solution trees

    NARCIS (Netherlands)

    W.H.L.M. Pijls (Wim); A. de Bruin (Arie); A. Plaat (Aske)

    1996-01-01

    textabstractIn this paper a complete theory of game tree algorithms is presented, entirely based upon the notion of a solution tree. Two types of solution trees are distinguished: max and min solution trees respectively. We show that most game tree algorithms construct a superposition of a max and a

  11. D2-tree

    DEFF Research Database (Denmark)

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

    2015-01-01

    We present a new overlay, called the Deterministic Decentralized tree (D2-tree). The D2-tree compares favorably to other overlays for the following reasons: (a) it provides matching and better complexities, which are deterministic for the supported operations; (b) the management of nodes (peers......-balancing scheme of elements into nodes is deterministic and general enough to be applied to other hierarchical tree-based overlays. This load-balancing mechanism is based on an innovative lazy weight-balancing mechanism, which is interesting in its own right....

  12. Morocco - Fruit Tree Productivity

    Data.gov (United States)

    Millennium Challenge Corporation — Date Tree Irrigation Project: The specific objectives of this evaluation are threefold: - Performance evaluation of project activities, like the mid-term evaluation,...

  13. Are trees long-lived?

    Science.gov (United States)

    Kevin T. Smith

    2009-01-01

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

  14. shrew, Croeidura bieolor

    African Journals Online (AJOL)

    'n Wyfie wat in die Nasionale Krugerwildtuin gevang is, is waargeneem terwyl sy geboorte geskenk het aan twee kleintjies. Die na·geboortelike ontwikkeling van die kleintjies waarvan hier verslag gedoen word, was stadiger as twee vorige gepubliseerde gevalle. Voorgestelde redes vir die teenstrydighede is die onderskeie ...

  15. Decision Tree Phytoremediation

    Science.gov (United States)

    1999-12-01

    8 2.4 Irrigation, Agronomic Inputs, and...documents will provide the reader in-depth background on the science and engineering mechanisms of phytoremediation. Using the decision tree and the...ITRC – Phytoremediation Decision Tree December 1999 8 • Contaminant levels • Plant selection • Treatability • Irrigation, agronomic

  16. Tree biology and dendrochemistry

    Science.gov (United States)

    Kevin T. Smith; Walter C. Shortle

    1996-01-01

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

  17. Structural Equation Model Trees

    Science.gov (United States)

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

    2013-01-01

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

  18. Uncovering dynamic fault trees

    NARCIS (Netherlands)

    Junges, Sebastian; Guck, Dennis; Katoen, Joost P.; Stoelinga, Mariëlle Ida Antoinette

    Fault tree analysis is a widespread industry standard for assessing system reliability. Standard (static) fault trees model the failure behaviour of systems in dependence of their component failures. To overcome their limited expressive power, common dependability patterns, such as spare management,

  19. Matching Subsequences in Trees

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li

    2009-01-01

    Given two rooted, labeled trees P and T the tree path subsequence problem is to determine which paths in P are subsequences of which paths in T. Here a path begins at the root and ends at a leaf. In this paper we propose this problem as a useful query primitive for XML data, and provide new...

  20. Trees Are Terrific!

    Science.gov (United States)

    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…

  1. Individual tree control

    Science.gov (United States)

    Harvey A. Holt

    1989-01-01

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

  2. Trees and Climate Change

    OpenAIRE

    Dettenmaier, Megan; Kuhns, Michael; Unger, Bethany; McAvoy, Darren

    2017-01-01

    This fact sheet describes the complex relationship between forests and climate change based on current research. It explains ways that trees can mitigate some of the risks associated with climate change. It details the impacts that forests are having on the changing climate and discuss specific ways that trees can be used to reduce or counter carbon emissions directly and indirectly.

  3. The tree BVOC index

    Science.gov (United States)

    J.R. Simpson; E.G. McPherson

    2011-01-01

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

  4. Environmental tritium in trees

    International Nuclear Information System (INIS)

    Brown, R.M.

    1979-01-01

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

  5. Coded Splitting Tree Protocols

    DEFF Research Database (Denmark)

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

    2013-01-01

    This paper presents a novel approach to multiple access control called coded splitting tree protocol. The approach builds on the known tree splitting protocols, code structure and successive interference cancellation (SIC). Several instances of the tree splitting protocol are initiated, each...... instance is terminated prematurely and subsequently iterated. The combined set of leaves from all the tree instances can then be viewed as a graph code, which is decodable using belief propagation. The main design problem is determining the order of splitting, which enables successful decoding as early...... as possible. Evaluations show that the proposed protocol provides considerable gains over the standard tree splitting protocol applying SIC. The improvement comes at the expense of an increased feedback and receiver complexity....

  6. Language trees not equal gene trees.

    Science.gov (United States)

    Steele, James; Kandler, Anne

    2010-09-01

    Darwin saw similarities between the evolution of species and the evolution of languages, and it is now widely accepted that similarities between related languages can often be interpreted in terms of a bifurcating descent history ('phylogenesis'). Such interpretations are supported when the distributions of shared and unshared traits (for example, in terms of etymological roots for elements of basic vocabulary) are analysed using tree-building techniques and found to be well-explained by a phylogenetic model. In this article, we question the demographic assumption which is sometimes made when a tree-building approach has been taken to a set of cultures or languages, namely that the resulting tree is also representative of a bifurcating population history. Using historical census data relating to Gaelic- and English-speaking inhabitants of Sutherland (Highland Scotland), we have explored the dynamics of language death due to language shift, representing the extreme case of lack of congruence between the genetic and the culture-historical processes. Such cases highlight the important role of selective cultural migration (or shifting between branches) in determining the extinction rates of different languages on such trees.

  7. Skewed Binary Search Trees

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Moruz, Gabriel

    2006-01-01

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

  8. Phylogenetic trees in bioinformatics

    Energy Technology Data Exchange (ETDEWEB)

    Burr, Tom L [Los Alamos National Laboratory

    2008-01-01

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

  9. Appropriate fossil calibrations and tree constraints uphold the Mesozoic divergence of solenodons from other extant mammals.

    Science.gov (United States)

    Springer, Mark S; Murphy, William J; Roca, Alfred L

    2018-04-01

    The mammalian order Eulipotyphla includes four extant families of insectivorans: Solenodontidae (solenodons); Talpidae (moles); Soricidae (shrews); and Erinaceidae (hedgehogs). Of these, Solenodontidae includes only two extant species, which are endemic to the largest islands of the Greater Antilles: Cuba and Hispaniola. Most molecular studies suggest that eulipotyphlan families diverged from each other across several million years, with the basal split between Solenodontidae and other families occurring in the Late Cretaceous. By contrast, Sato et al. (2016) suggest that eulipotyphlan families diverged from each other in a polytomy ∼58.6 million years ago (Mya). This more recent divergence estimate for Solenodontidae versus other extant eulipotyphlans suggests that solenodons must have arrived in the Greater Antilles via overwater dispersal rather than vicariance. Here, we show that the young timetree estimates for eulipotyphlan families and the polytomy are due to an inverted ingroup-outgroup arrangement of the tree, the result of using Tracer rather than TreeAnnotator to compile interfamilial divergence times, and of not enforcing the monophly of well-established clades such as Laurasiatheria and Eulipotyphla. Finally, Sato et al.'s (2016) timetree includes several zombie lineages where estimated divergence times are much younger than minimum ages that are implied by the fossil record. We reanalyzed Sato et al.'s (2016) original data with enforced monophyly for well-established clades and updated fossil calibrations that eliminate the inference of zombie lineages. Our resulting timetrees, which were compiled with TreeAnnotator rather than Tracer, produce dates that are in good agreement with other recent studies and place the basal split between Solenodontidae and other eulipotyphlans in the Late Cretaceous. Copyright © 2018 Elsevier Inc. All rights reserved.

  10. Clock Tree Power Analysis

    OpenAIRE

    Austbø, Knut

    2016-01-01

    The buffered clock tree structure is commonly used to distribute the clock signal to the memory elements in digital circuits. Since the clock signal is used as a temporal reference, it has to be distributed to the registers with decent timing characteristics and low skew. In order to achieve this, buffers and inverters are inserted in the clock tree, typically by a synthesis tool. The clock tree is a major contributor to the power consumption. This is a result of a combination of high swit...

  11. Generalising tree traversals and tree transformations to DAGs

    DEFF Research Database (Denmark)

    Bahr, Patrick; Axelsson, Emil

    2017-01-01

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

  12. Big trees, old trees, and growth factor tables

    Science.gov (United States)

    Kevin T. Smith

    2018-01-01

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

  13. Structural Equation Model Trees

    Science.gov (United States)

    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

  14. Tea Tree Oil

    Science.gov (United States)

    ... of Grants and Contracts General Award Mechanisms Small Business Research Grant Program (SBIR) Funding for: Natural Product ... cuts and wounds by the aboriginal people of Australia. Today, tea tree oil is often used externally ...

  15. A parallel buffer tree

    DEFF Research Database (Denmark)

    Sitchinava, Nodar; Zeh, Norbert

    2012-01-01

    We present the parallel buffer tree, a parallel external memory (PEM) data structure for batched search problems. This data structure is a non-trivial extension of Arge's sequential buffer tree to a private-cache multiprocessor environment and reduces the number of I/O operations by the number...... of available processor cores compared to its sequential counterpart, thereby taking full advantage of multicore parallelism. The parallel buffer tree is a search tree data structure that supports the batched parallel processing of a sequence of N insertions, deletions, membership queries, and range queries...... in the optimal OhOf(psortN + K/PB) parallel I/O complexity, where K is the size of the output reported in the process and psortN is the parallel I/O complexity of sorting N elements using P processors....

  16. NLCD 2001 - Tree Canopy

    Data.gov (United States)

    Minnesota Department of Natural Resources — The National Land Cover Database 2001 tree canopy layer for Minnesota (mapping zones 39-42, 50-51) was produced through a cooperative project conducted by the...

  17. Value tree analysis

    International Nuclear Information System (INIS)

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

    1985-01-01

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

  18. Adaptive Context Tree Weighting

    OpenAIRE

    O'Neill, Alexander; Hutter, Marcus; Shao, Wen; Sunehag, Peter

    2012-01-01

    We describe an adaptive context tree weighting (ACTW) algorithm, as an extension to the standard context tree weighting (CTW) algorithm. Unlike the standard CTW algorithm, which weights all observations equally regardless of the depth, ACTW gives increasing weight to more recent observations, aiming to improve performance in cases where the input sequence is from a non-stationary distribution. Data compression results show ACTW variants improving over CTW on merged files from standard compres...

  19. Type extension trees

    DEFF Research Database (Denmark)

    Jaeger, Manfred

    2006-01-01

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

  20. Multiscale singularity trees

    DEFF Research Database (Denmark)

    Somchaipeng, Kerawit; Sporring, Jon; Johansen, Peter

    2007-01-01

    We propose MultiScale Singularity Trees (MSSTs) as a structure to represent images, and we propose an algorithm for image comparison based on comparing MSSTs. The algorithm is tested on 3 public image databases and compared to 2 state-of-theart methods. We conclude that the computational complexity...... of our algorithm only allows for the comparison of small trees, and that the results of our method are comparable with state-of-the-art using much fewer parameters for image representation....

  1. Tree Improvement Glossary

    DEFF Research Database (Denmark)

    Schmidt, Lars Holger

    Forest tree improvement encompasses a number of scientific and technical areas like floral-, reproductive- and micro-biology, genetics breeding methods and strategies, propagation, gene conservation, data analysis and statistics, each area with a comprehensive terminology. The terms selected...... for definition here are those most frequently used in tree improvement literature. Clonal propagation is included in the view of the great expansion of that field as a means of mass multiplication of improved material....

  2. Dependency Tree Annotation Software

    Science.gov (United States)

    2015-11-01

    between words. DTE supports the widely used Conference on Computational Natural Language Learning (CoNLL)-X format as well as several other file...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...software application called Dependency Tree Editor (DTE) that can read files in Computational Natural Language Learning (CoNLL)-X format and use them

  3. Tree felling 2014

    CERN Multimedia

    2014-01-01

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

  4. Anatomy of the Pythagoras' Tree

    Science.gov (United States)

    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…

  5. Attack Trees with Sequential Conjunction

    NARCIS (Netherlands)

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

    2015-01-01

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

  6. Tree manipulation experiment

    Science.gov (United States)

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

    2012-12-01

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

  7. At the foot of the shrew: Manus morphology distinguishes closely-related Cryptotis goodwini and Cryptotis griseoventris (Mammalia: Soricidae) in Central America

    Science.gov (United States)

    Woodman, Neal; Stephens, Ryan B.

    2010-01-01

    Small-eared shrews (Mammalia, Soricidae) of the New World genus Cryptotis are distributed from eastern North America to the northern Andes of South America. One well-defined clade in this genus is the Central American Cryptotis mexicana group, whose members are set off from other species in the genus by their variably broader fore feet and more elongate and broadened fore claws. Two species in the C. mexicana group, Cryptotis goodwini Jackson and Cryptotis griseoventris Jackson, inhabit highlands in Guatemala and southern Mexico and are presumed to be sister species whose primary distinguishing feature is the larger body size of C. goodwini. To better characterize these species and confirm the identification of recently-collected specimens, we obtained digital X-ray images of the manus from large series of dried skins of both species. Measurements of the metacarpals and phalanges successfully separated most specimens of C. goodwini and C. griseoventris. These measurements also show that the fore feet of C. griseoventris from Chiapas, Mexico, are morphologically distinct from those of members of the species inhabiting Guatemala. Univariate, bivariate, and multivariate analyses indicate that fore foot characters are more conservative within species of the C. mexicana group than are cranio-mandibular characters. Patterns of evolution of fore foot characters that superficially appear to be linear gradations are actually more complex, illustrating individual evolutionary trajectories.

  8. Steiner trees in industry

    CERN Document Server

    Du, Ding-Zhu

    2001-01-01

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

  9. Visualization of Uncertain Contour Trees

    DEFF Research Database (Denmark)

    Kraus, Martin

    2010-01-01

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

  10. TreeFam: 2008 Update

    DEFF Research Database (Denmark)

    Ruan, Jue; Li, Heng; Chen, Zhongzhong

    2008-01-01

    TreeFam (http://www.treefam.org) was developed to provide curated phylogenetic trees for all animal gene families, as well as orthologue and paralogue assignments. Release 4.0 of TreeFam contains curated trees for 1314 families and automatically generated trees for another 14,351 families. We have...... expanded TreeFam to include 25 fully sequenced animal genomes, as well as four genomes from plant and fungal outgroup species. We have also introduced more accurate approaches for automatically grouping genes into families, for building phylogenetic trees, and for inferring orthologues and paralogues....... The user interface for viewing phylogenetic trees and family information has been improved. Furthermore, a new perl API lets users easily extract data from the TreeFam mysql database....

  11. Generic Ising trees

    DEFF Research Database (Denmark)

    Durhuus, Bergfinnur Jøgvan; Napolitano, George Maria

    2012-01-01

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

  12. Life cycle of Renylaima capensis, a brachylaimid trematode of shrews and slugs in South Africa: two-host and three-host transmission modalities suggested by epizootiology and DNA sequencing

    Directory of Open Access Journals (Sweden)

    Sirgel Wilhelm F

    2012-08-01

    Full Text Available Abstract Background The life cycle of the brachylaimid trematode species Renylaima capensis, infecting the urinary system of the shrew Myosorex varius (Mammalia: Soricidae: Crocidosoricinae in the Hottentots Holland Nature Reserve, South Africa, has been elucidated by a study of its larval stages, epizootiological data in local snails and mammals during a 34-year period, and its verification with mtDNA sequencing. Methods Parasites obtained from dissected animals were mounted in microscope slides for the parasitological study and measured according to standardized methods. The mitochondrial DNA cox1 gene was sequenced by the dideoxy chain-termination method. Results The slugs Ariostralis nebulosa and Ariopelta capensis (Gastropoda: Arionidae act as specific first and second intermediate hosts, respectively. Branched sporocysts massively develop in A. nebulosa. Intrasporocystic mature cercariae show differentiated gonads, male terminal duct, ventral genital pore, and usually no tail, opposite to Brachylaimidae in which mature cercariae show a germinal primordium and small tail. Unencysted metacercariae, usually brevicaudate, infect the kidney of A. capensis and differ from mature cercariae by only a slightly greater size. The final microhabitats are the kidneys and ureters of the shrews, kidney pelvis and calyces in light infections and also kidney medulla and cortex in heavy infections. Sporocysts, cercariae, metacercariae and adults proved to belong to R. capensis by analysis of a 437-bp-long cox1 fragment, which was identical except for three mutations in metacercariae, of which only one silent. Epizootiological studies showed usual sporocyst infection in A. nebulosa and very rare metacercarial infection in A. capensis, which does not agree with high prevalences and intensities in the shrews. Conclusions The presence of monotesticular adult forms and larval prevalences and intensities observed suggest that R. capensis may use two transmission

  13. Portraits of Tree Families

    NARCIS (Netherlands)

    Balgooy, van M.M.J.

    1998-01-01

    With the publication of the second volume of the series ‘Malesian Seed Plants’, entitled ‘Portraits of Tree Families’, I would like to refer to the Introduction of the first volume, ‘Spot-characters’ for a historical background and an explanation of the aims of this series. The present book treats

  14. Oak Tree Planting Project

    Science.gov (United States)

    Sherryl L. Nives; William D. Tietje; William H. Weitkamp

    1991-01-01

    An Oak Tree Planting Project was conducted during 1989/90 in San Luis Obispo County by the Integrated Hardwood Range Management Program (IHRMP)/Central Coast. The local media and an IHRMP workshop were used to publicize the Planting Project and give information on the status of oaks (Quercus spp.) in California and oak planting techniques. Outreach...

  15. P{owering 'Trees

    Indian Academy of Sciences (India)

    Melia dubia Cav. of Meliaceae is a large deciduous tree. Leaves are compound with toothed leaflets. Flowers are small, greenish-yellow in much-branched inflorescences. Fruits are green, ellipsoidal with a single seed covered by hard portion ( as in a mango fruit) and surrounded by fleshy pulp outside. The bark is bitter ...

  16. Base tree property

    Czech Academy of Sciences Publication Activity Database

    Balcar, B.; Doucha, Michal; Hrušák, M.

    2015-01-01

    Roč. 32, č. 1 (2015), s. 69-81 ISSN 0167-8094 R&D Projects: GA AV ČR IAA100190902 Institutional support: RVO:67985840 Keywords : forcing * Boolean algebras * base tree Subject RIV: BA - General Mathematics Impact factor: 0.614, year: 2015 http://link.springer.com/article/10.1007/s11083-013-9316-2

  17. How to Prune Trees

    Science.gov (United States)

    Peter Bedker; Joseph O' Brien; Manfred Mielke

    2012-01-01

    The objective of pruning is to produce strong, healthy, attractive plants. By understanding how, when and why to prune, and by following a few simple principles, this objective can be achievedHow to Prune Trees (Revised 2012) Agency Publisher: Agriculture Dept., Forest Service, Northeastern Area State and Price forestry USA List Price:$4.00 Sale...

  18. Multiquarks and Steiner trees

    International Nuclear Information System (INIS)

    Richard, Jean-Marc

    2010-01-01

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

  19. Christmas Tree Category Manual.

    Science.gov (United States)

    Bowman, James S.; Turmel, Jon P.

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

  20. Chapter 5 - Tree Mortality

    Science.gov (United States)

    Mark J. Ambrose

    2014-01-01

    Tree mortality is a natural process in all forest ecosystems. Extremely high mortality, however, can also be an indicator of forest health issues. On a regional scale, high mortality levels may indicate widespread insect or disease problems. High mortality may also occur if a large proportion of the forest in a particular region is made up of older, senescent stands....

  1. The TS-Tree

    DEFF Research Database (Denmark)

    Assent, Ira; Krieger, Ralph; Afschari, Farzad

    2008-01-01

    Continuous growth in sensor data and other temporal data increases the importance of retrieval and similarity search in time series data. Efficient time series query processing is crucial for interactive applications. Existing multidimensional indexes like the R-tree provide efficient querying fo...

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

    African Journals Online (AJOL)

    PROF HORSFALL

    ABSTRACT: The importance of trees in urban environment is now widely recognized as they cleanse the ... urban environment prevent solar radiation from ..... In urban areas, tree height is an important consideration in deciding what species to plant and/or where to plant them. Considering that many urban tree. Fig. 7.

  3. Solution trees as a basis for game tree search

    NARCIS (Netherlands)

    A. de Bruin (Arie); W.H.L.M. Pijls (Wim); A. Plaat (Aske)

    1994-01-01

    textabstractA game tree algorithm is an algorithm computing the minimax value of the root of a game tree. Many algorithms use the notion of establishing proofs that this value lies above or below some boundary value. We show that this amounts to the construction of a solution tree. We discuss the

  4. A suffix tree or not a suffix tree?

    DEFF Research Database (Denmark)

    Starikovskaya, Tatiana; Vildhøj, Hjalte Wedel

    2015-01-01

    , in particular we do not require that S ends with a unique symbol. This corresponds to considering the more general definition of implicit or extended suffix trees. Such general suffix trees have many applications and are for example needed to allow efficient updates when suffix trees are built online. Deciding...

  5. Tree Transduction Tools for Cdec

    Directory of Open Access Journals (Sweden)

    Austin Matthews

    2014-09-01

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

  6. Selecting Landscape Plants: Shade Trees

    OpenAIRE

    Relf, Diane; Appleton, Bonnie Lee, 1948-2012; Close, David

    2015-01-01

    Because of the permanency of trees and their importance in the landscape, care must be taken to select the best species for each situation. This publication goes over how to choose landscape trees that are shade tolerant.

  7. Emerging Infectious Disease Implications of Invasive Mammalian Species: The Greater White-Toothed Shrew (Crocidura russula) Is Associated With a Novel Serovar of Pathogenic Leptospira in Ireland.

    Science.gov (United States)

    Nally, Jarlath E; Arent, Zbigniew; Bayles, Darrell O; Hornsby, Richard L; Gilmore, Colm; Regan, Siobhan; McDevitt, Allan D; Yearsley, Jon; Fanning, Séamus; McMahon, Barry J

    2016-12-01

    The greater white-toothed shrew (Crocidura russula) is an invasive mammalian species that was first recorded in Ireland in 2007. It currently occupies an area of approximately 7,600 km2 on the island. C. russula is normally distributed in Northern Africa and Western Europe, and was previously absent from the British Isles. Whilst invasive species can have dramatic and rapid impacts on faunal and floral communities, they may also be carriers of pathogens facilitating disease transmission in potentially naive populations. Pathogenic leptospires are endemic in Ireland and a significant cause of human and animal disease. From 18 trapped C. russula, 3 isolates of Leptospira were cultured. However, typing of these isolates by standard serological reference methods was negative, and suggested an, as yet, unidentified serovar. Sequence analysis of 16S ribosomal RNA and secY indicated that these novel isolates belong to Leptospira alstonii, a unique pathogenic species of which only 7 isolates have been described to date. Earlier isolations were limited geographically to China, Japan and Malaysia, and this leptospiral species had not previously been cultured from mammals. Restriction enzyme analysis (REA) further confirms the novelty of these strains since no similar patterns were observed with a reference database of leptospires. As with other pathogenic Leptospira species, these isolates contain lipL32 and do not grow in the presence of 8-azagunaine; however no evidence of disease was apparent after experimental infection of hamsters. These isolates are genetically related to L. alstonii but have a novel REA pattern; they represent a new serovar which we designate as serovar Room22. This study demonstrates that invasive mammalian species act as bridge vectors of novel zoonotic pathogens such as Leptospira.

  8. Mercury in soil, earthworms and organs of voles Myodes glareolus and shrew Sorex araneus in the vicinity of an industrial complex in Northwest Russia (Cherepovets).

    Science.gov (United States)

    Komov, V T; Ivanova, E S; Poddubnaya, N Y; Gremyachikh, V A

    2017-03-01

    The characteristic properties of uptake and distribution of mercury in terrestrial ecosystems have received much lesser attention compared to aquatic particularly in Russia. Terrestrial ecosystems adjacent to large industrial manufactures-potential sources of mercury inflow into the environment frequently remain unstudied. This is the first report on mercury (Hg) levels in the basic elements of terrestrial ecosystems situated close to a large metallurgical complex.Mean values of mercury concentration (mg Hg/kg dry weight) in the vicinity of city of Cherepovets were the following: 0.056 ± 0.033-in the humus layer of soil; 0.556 ± 0.159-in earthworms; in the organs of voles Myodes glareolus (kidneys-0.021 ± 0.001; liver-0.014 ± 0.003; muscle-0.014 ± 0.001; brain-0.008 ± 0.002); in the organs of shrew Sorex araneus (kidneys-0.191 ± 0.016; liver-0.124 ± 0.011; muscle-0.108 ± 0.009; brain-0.065 ± 0.000). Correlation dependences between Hg content in soil and earthworms (r s  = 0.85, p mercury content in the studied objects was significantly lower than values of corresponding parameters in the soils and biota from industrial (polluted) areas of Great Britain, the USA, and China.

  9. Selecting Landscape Plants: Flowering Trees

    OpenAIRE

    Relf, Diane; Appleton, Bonnie Lee, 1948-2012

    2009-01-01

    This publication helps the reader to select wisely among the many species and varieties of flowering trees available. The following are considerations that should be taken into account when choosing flowering trees for the home landscape: selections factors, environmental responses, availability and adaptability, and flowering tree descriptions.

  10. Inferences from growing trees backwards

    Science.gov (United States)

    David W. Green; Kent A. McDonald

    1997-01-01

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

  11. Generalising tree traversals to DAGs

    DEFF Research Database (Denmark)

    Bahr, Patrick; Axelsson, Emil

    2015-01-01

    We present a recursion scheme based on attribute grammars that can be transparently applied to trees and acyclic graphs. Our recursion scheme allows the programmer to implement a tree traversal and then apply it to compact graph representations of trees instead. The resulting graph traversals avoid...

  12. Our Air: Unfit for Trees.

    Science.gov (United States)

    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,…

  13. The Hopi Fruit Tree Book.

    Science.gov (United States)

    Nyhuis, Jane

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

  14. Rectilinear Full Steiner Tree Generation

    DEFF Research Database (Denmark)

    Zachariasen, Martin

    1999-01-01

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

  15. DensiTree: making sense of sets of phylogenetic trees.

    Science.gov (United States)

    Bouckaert, Remco R

    2010-05-15

    Bayesian analysis through programs like BEAST (Drummond and Rumbaut, 2007) and MrBayes (Huelsenbeck et al., 2001) provides a powerful method for reconstruction of evolutionary relationships. One of the benefits of Bayesian methods is that well-founded estimates of uncertainty in models can be made available. So, for example, not only the mean time of a most recent common ancestor (tMRCA) is estimated, but also the spread. This distribution over model space is represented by a set of trees, which can be rather large and difficult to interpret. DensiTree is a tool that helps navigating these sets of trees. The main idea behind DensiTree is to draw all trees in the set transparently. As a result, areas where a lot of the trees agree in topology and branch lengths show up as highly colored areas, while areas with little agreement show up as webs. This makes it possible to quickly get an impression of properties of the tree set such as well-supported clades, distribution of tMRCA and areas of topological uncertainty. Thus, DensiTree provides a quick method for qualitative analysis of tree sets. DensiTree is freely available from http://compevol.auckland.ac.nz/software/DensiTree/. The program is licensed under GPL and source code is available. remco@cs.auckland.ac.nz

  16. Tree Colors: Color Schemes for Tree-Structured Data.

    Science.gov (United States)

    Tennekes, Martijn; de Jonge, Edwin

    2014-12-01

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

  17. 75 FR 25103 - Tree Assistance Program

    Science.gov (United States)

    2010-05-07

    ... produced for commercial purposes, such as a maple tree for syrup, papaya tree, or orchard tree. Trees used... tomato plants, biennials such as the plants that produce strawberries, and annuals such as pumpkins...

  18. The Stephen H. Long Expedition (1819?1820), Titian R. Peale?s field illustrations, and the lost holotypes of the North American shrews Sorex brevicaudus Say and Sorex parvus Say (Mammalia: Soricidae) from the Philadelphia Museum

    Science.gov (United States)

    Woodman, N.

    2009-01-01

    While encamped for the winter of 1819?1820 at Engineer Cantonment along the Missouri River in present-day eastern Nebraska, members of Major Stephen Harriman Long?s Expedition to the Rocky Mountains collected a number of animals that were previously unknown. Among the mammals were two soricids that were subsequently described by Thomas Say as Sorex brevicaudus (Northern Short-tailed Shrew, Blarina brevicauda) and Sorex parvus (Least Shrew, Cryptotis parvus). The holotypes of these species were deposited and placed on public exhibit in the Philadelphia Museum, the predominant North American systematic collection of the early nineteenth century. Like most private museums of that era, the Philadelphia Museum eventually went out of business, and its collections were dispersed and, for the most part, lost. Fortunately, Titian R. Peale made a detailed field sketch of the two specimens soon after their capture and subsequently executed a watercolor based on that sketch. In addition, an engraving of the holotypes was published in the decade following the discovery of the two species. Illustrations of holotypes are taxonomically useful when they depict diagnostic characters of species. They take on added taxonomic significance in the absence of the holotypes. In the cases of Sorex brevicaudus and Sorex parvus, pictures provide strong confirmation of the taxonomic identities of these two species, as well as recording the early history of the specimens.

  19. System for Rapid, Precise Modulation of Intraocular Pressure, toward Minimally-Invasive In Vivo Measurement of Intracranial Pressure.

    Directory of Open Access Journals (Sweden)

    Max A Stockslager

    Full Text Available Pathologic changes in intracranial pressure (ICP are commonly observed in a variety of medical conditions, including traumatic brain injury, stroke, brain tumors, and glaucoma. However, current ICP measurement techniques are invasive, requiring a lumbar puncture or surgical insertion of a cannula into the cerebrospinal fluid (CSF-filled ventricles of the brain. A potential alternative approach to ICP measurement leverages the unique anatomy of the central retinal vein, which is exposed to both intraocular pressure (IOP and ICP as it travels inside the eye and through the optic nerve; manipulating IOP while observing changes in the natural pulsations of the central retinal vein could potentially provide an accurate, indirect measure of ICP. As a step toward implementing this technique, we describe the design, fabrication, and characterization of a system that is capable of manipulating IOP in vivo with <0.1 mmHg resolution and settling times less than 2 seconds. In vitro tests were carried out to characterize system performance. Then, as a proof of concept, we used the system to manipulate IOP in tree shrews (Tupaia belangeri while video of the retinal vessels was recorded and the caliber of a selected vein was quantified. Modulating IOP using our system elicited a rapid change in the appearance of the retinal vein of interest: IOP was lowered from 10 to 3 mmHg, and retinal vein caliber sharply increased as IOP decreased from 7 to 5 mmHg. Another important feature of this technology is its capability to measure ocular compliance and outflow facility in vivo, as demonstrated in tree shrews. Collectively, these proof-of-concept demonstrations support the utility of this system to manipulate IOP for a variety of useful applications in ocular biomechanics, and provide a framework for further study of the mechanisms of retinal venous pulsation.

  20. Fault-Tree Compiler Program

    Science.gov (United States)

    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.

  1. Making CSB + -Trees Processor Conscious

    DEFF Research Database (Denmark)

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

    2005-01-01

    Cache-conscious indexes, such as CSB+-tree, are sensitive to the underlying processor architecture. In this paper, we focus on how to adapt the CSB+-tree so that it performs well on a range of different processor architectures. Previous work has focused on the impact of node size on the performance...... of the CSB+-tree. We argue that it is necessary to consider a larger group of parameters in order to adapt CSB+-tree to processor architectures as different as Pentium and Itanium. We identify this group of parameters and study how it impacts the performance of CSB+-tree on Itanium 2. Finally, we propose...

  2. Molecular identification of blood meal sources of ticks (Acari, Ixodidae using cytochrome b gene as a genetic marker

    Directory of Open Access Journals (Sweden)

    Ernieenor Faraliana Che Lah

    2015-01-01

    Full Text Available Blood meal analysis (BMA from ticks allows for the identification of natural hosts of ticks (Acari: Ixodidae. The aim of this study is to identify the blood meal sources of field collected on-host ticks using PCR analysis. DNA of four genera of ticks was isolated and their cytochrome b (Cyt b gene was amplified to identify host blood meals. A phylogenetic tree was constructed based on data of Cyt b sequences using Neighbor Joining (NJ and Maximum Parsimony (MP analysis using MEGA 5.05 for the clustering of hosts of tick species. Twenty out of 27 samples showed maximum similarity (99% with GenBank sequences through a Basic Local Alignment Search Tool (BLAST while 7 samples only showed a similarity range of between 91–98%. The phylogenetic trees showed that the blood meal samples were derived from small rodents (Leopoldamys sabanus, Rattus tiomanicus and Sundamys muelleri, shrews (Tupaia glis and mammals (Tapirus indicus and Prionailurus bengalensis, supported by 82–88% bootstrap values. In this study, Cyt b gene as a molecular target produced reliable results and was very significant for the effective identification of ticks’ blood meal. The assay can be used as a tool for identifying unknown blood meals of field collected on-host ticks.

  3. Trees for future forests

    DEFF Research Database (Denmark)

    Lobo, Albin

    Climate change creates new challenges in forest management. The increase in temperature may in the long run be beneficial for the forests in the northern latitudes, but the high rate at which climate change is predicted to proceed will make adaptation difficult because trees are long living sessile...... of precipitation. Adaptive traits such as phenology which is sensitive to changes in temperature and drought resistance as a response to water scarcity are studied. Quantitative genetics is extensively used in field phenotyping to identify the availability of sufficient genetic variation within species. Other...... as a faster mechanism in aiding climate change adaptation in trees. Drought resistance varied among the different species belonging to a single genus showing the inherent capacity of native species to overcome water scarcity in severely drought prone regions of the world. More research into the important...

  4. Wood for the trees

    Directory of Open Access Journals (Sweden)

    Rob Garbutt

    2013-10-01

    Full Text Available Our paper focuses on the materiality, cultural history and cultural relations of selected artworks in the exhibition Wood for the trees (Lismore Regional Gallery, New South Wales, Australia, 10 June – 17 July 2011. The title of the exhibition, intentionally misreading the aphorism “Can’t see the wood for the trees”, by reading the wood for the resource rather than the collective wood[s], implies conservation, preservation, and the need for sustaining the originating resource. These ideas have particular resonance on the NSW far north coast, a region once rich in rainforest. While the Indigenous population had sustainable practices of forest and land management, the colonists deployed felling and harvesting in order to convert the value of the local, abundant rainforest trees into high-value timber. By the late twentieth century, however, a new wave of settlers launched a protest movements against the proposed logging of remnant rainforest at Terania Creek and elsewhere in the region. Wood for the trees, curated by Gallery Director Brett Adlington, plays on this dynamic relationship between wood, trees and people. We discuss the way selected artworks give expression to the themes or concepts of productive labour, nature and culture, conservation and sustainability, and memory. The artworks include Watjinbuy Marrawilil’s (1980 Carved ancestral figure ceremonial pole, Elizabeth Stops’ (2009/10 Explorations into colonisation, Hossein Valamanesh’s (2008 Memory stick, and AñA Wojak’s (2008 Unread book (in a forgotten language. Our art writing on the works, a practice informed by Bal (2002, Muecke (2008 and Papastergiadis (2004, becomes a conversation between the works and the themes or concepts. As a form of material excess of the most productive kind (Grosz, 2008, p. 7, art seeds a response to that which is in the air waiting to be said of the past, present and future.

  5. Pushdown machines for the macro tree transducer

    NARCIS (Netherlands)

    Engelfriet, Joost; Vogler, Heiko

    1986-01-01

    The macro tree transducer can be considered as a system of recursive function procedures with parameters, where the recursion is on a tree (e.g., the syntax tree of a program). We investigate characterizations of the class of tree (tree-to-string) translations which is induced by macro tree

  6. Recursive Trees for Practical ORAM

    Directory of Open Access Journals (Sweden)

    Moataz Tarik

    2015-06-01

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

  7. Mathematical foundations of event trees

    International Nuclear Information System (INIS)

    Papazoglou, Ioannis A.

    1998-01-01

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

  8. (Almost) practical tree codes

    KAUST Repository

    Khina, Anatoly

    2016-08-15

    We consider the problem of stabilizing an unstable plant driven by bounded noise over a digital noisy communication link, a scenario at the heart of networked control. To stabilize such a plant, one needs real-time encoding and decoding with an error probability profile that decays exponentially with the decoding delay. The works of Schulman and Sahai over the past two decades have developed the notions of tree codes and anytime capacity, and provided the theoretical framework for studying such problems. Nonetheless, there has been little practical progress in this area due to the absence of explicit constructions of tree codes with efficient encoding and decoding algorithms. Recently, linear time-invariant tree codes were proposed to achieve the desired result under maximum-likelihood decoding. In this work, we take one more step towards practicality, by showing that these codes can be efficiently decoded using sequential decoding algorithms, up to some loss in performance (and with some practical complexity caveats). We supplement our theoretical results with numerical simulations that demonstrate the effectiveness of the decoder in a control system setting.

  9. Submodular unsplittable flow on trees

    DEFF Research Database (Denmark)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2014-01-01

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

  11. TREE SYMBOLISM IN SLAVIC FOLK CULTURE: APPLE TREE

    Directory of Open Access Journals (Sweden)

    Tatyana A. Agapkina

    2017-03-01

    Full Text Available The essay focuses on the mythopoetic image of the apple tree and its ritual use in traditional culture and folklore of the Slavic nations. The work employs folklore material alongside ethnographic and linguistic data that accentuates and develops the folklore symbolism of the apple tree. I argue that this image is comprised of a number of relatively autonomous fragments. The apple tree and its apples are a family metaphor of a kind symbolizing a mother and a child. In wedding folklore, the apple tree stands for a bride as the wedding ritual testifies; apple tree branches are widely used in the ritual itself (as a ritual tree or as material used in the making of a wedding banner, wedding wreaths, decorations for a wedding loaf [karavai], etc.. Another manifestation of the apple tree in folklore is the tree of knowledge; it relates the image to a large number of legendary etiological plots such as: Eve’s temptation by the Serpent, fall of Eve and Adam, the origin of Adam’s Apple (adam, prohibition to eat apples before the church holiday of Transfiguration and some others. At the same time, their autonomy regardless, the fragments of the mythopoetic image of the apple tree form part of the solid folklore universe and counteract with each other within this framework.

  12. Profile of Antiemetic Activity of Netupitant Alone or in Combination with Palonosetron and Dexamethasone in Ferrets and Suncus murinus (House Musk Shrew).

    Science.gov (United States)

    Rudd, John A; Ngan, Man P; Lu, Zengbing; Higgins, Guy A; Giuliano, Claudio; Lovati, Emanuela; Pietra, Claudio

    2016-01-01

    Chemotherapy-induced acute and delayed emesis involves the activation of multiple pathways, with 5-hydroxytryptamine (5-HT; serotonin) playing a major role in the initial response. Substance P tachykinin NK1 receptor antagonists can reduce emesis induced by disparate emetic challenges and therefore have a clinical utility as broad inhibitory anti-emetic drugs. In the present studies, we investigate the broad inhibitory anti-emetic profile of a relatively new NK1 receptor antagonist, netupitant, alone or in combination with the long acting 5-HT3 receptor antagonist, palonosetron, for a potential to reduce emesis in ferrets and shrews. Ferrets were pretreated with netupitant and/or palonosetron, and then administered apomorphine (0.125 mg/kg, s.c.), morphine (0.5 mg/kg, s.c.), ipecacuanha (1.2 mg/kg, p.o.), copper sulfate (100 mg/kg, intragastric), or cisplatin (5-10 mg/kg, i.p.); in other studies netupitant was administered to Suncus murinus before motion (4 cm horizontal displacement, 2 Hz for 10 min). Netupitant (3 mg/kg, p.o.) abolished apomorphine-, morphine-, ipecacuanha- and copper sulfate-induced emesis. Lower doses of netupitant (0.03-0.3 mg/kg, p.o.) dose-dependently reduced cisplatin (10 mg/kg, i.p.)-induced emesis in an acute (8 h) model, and motion-induced emesis in S. murinus. In a ferret cisplatin (5 mg/kg, i.p.)-induced acute and delayed emesis model, netupitant administered once at 3 mg/kg, p.o., abolished the first 24 h response and reduced the 24-72 h response by 94.6%; the reduction was markedly superior to the effect of a three times per day administration of ondansetron (1 mg/kg, i.p.). A single administration of netupitant (1 mg/kg, p.o.) plus palonosetron (0.1 mg/kg, p.o.) combined with dexamethasone (1 mg/kg, i.p., once per day), also significantly antagonized cisplatin-induced acute and delayed emesis and was comparable with a once-daily regimen of ondansetron (1 mg/kg, p.o.) plus aprepitant (1 mg/kg, p.o.) in combination with dexamethasone

  13. Tree plastic bark

    OpenAIRE

    Casado Arroyo, Carlos

    2016-01-01

    Tree plastic bark" consiste en la realización de una intervención artística en un entorno natural concreto, generando de esta manera un Site Specific(1). Como hace alusión Rosalind Krauss en sus reflexiones “La escultura en el campo expandido”(2), comenta que su origen esta claramente ligado con el concepto de monumentalidad. La escultura es un monumento, se crea para conmemorar algún hecho o personaje relevante y está realizada para una ubicación concreta. La investigación parte de la id...

  14. The fault-tree compiler

    Science.gov (United States)

    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.

  15. Large Deviations for Random Trees.

    Science.gov (United States)

    Bakhtin, Yuri; Heitsch, Christine

    2008-08-01

    We consider large random trees under Gibbs distributions and prove a Large Deviation Principle (LDP) for the distribution of degrees of vertices of the tree. The LDP rate function is given explicitly. An immediate consequence is a Law of Large Numbers for the distribution of vertex degrees in a large random tree. Our motivation for this study comes from the analysis of RNA secondary structures.

  16. Tree felling: a necessary evil

    CERN Multimedia

    CERN Bulletin

    2013-01-01

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

  17. Human decision error (HUMDEE) trees

    International Nuclear Information System (INIS)

    Ostrom, L.T.

    1993-01-01

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

  18. Making CSB + -Trees Processor Conscious

    DEFF Research Database (Denmark)

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

    2005-01-01

    Cache-conscious indexes, such as CSB+-tree, are sensitive to the underlying processor architecture. In this paper, we focus on how to adapt the CSB+-tree so that it performs well on a range of different processor architectures. Previous work has focused on the impact of node size on the performan...... a systematic method for adapting CSB+-tree to new platforms. This work is a first step towards integrating CSB+-tree in MySQL’s heap storage manager....

  19. The Steiner tree problem

    CERN Document Server

    Hwang, FK; Winter, P

    1992-01-01

    The Steiner problem asks for a shortest network which spans a given set of points. Minimum spanning networks have been well-studied when all connections are required to be between the given points. The novelty of the Steiner tree problem is that new auxiliary points can be introduced between the original points so that a spanning network of all the points will be shorter than otherwise possible. These new points are called Steiner points - locating them has proved problematic and research has diverged along many different avenues. This volume is devoted to the assimilation of the rich field of intriguing analyses and the consolidation of the fragments. A section has been given to each of the three major areas of interest which have emerged. The first concerns the Euclidean Steiner Problem, historically the original Steiner tree problem proposed by Jarník and Kössler in 1934. The second deals with the Steiner Problem in Networks, which was propounded independently by Hakimi and Levin and has enjoyed the most...

  20. Genealogy and gene trees.

    Science.gov (United States)

    Rasmuson, Marianne

    2008-02-01

    Heredity can be followed in persons or in genes. Persons can be identified only a few generations back, but simplified models indicate that universal ancestors to all now living persons have occurred in the past. Genetic variability can be characterized as variants of DNA sequences. Data are available only from living persons, but from the pattern of variation gene trees can be inferred by means of coalescence models. The merging of lines backwards in time leads to a MRCA (most recent common ancestor). The time and place of living for this inferred person can give insights in human evolutionary history. Demographic processes are incorporated in the model, but since culture and customs are known to influence demography the models used ought to be tested against available genealogy. The Icelandic data base offers a possibility to do so and points to some discrepancies. Mitochondrial DNA and Y chromosome patterns give a rather consistent view of human evolutionary history during the latest 100 000 years but the earlier epochs of human evolution demand gene trees with longer branches. The results of such studies reveal as yet unsolved problems about the sources of our genome.

  1. Distributed Merge Trees

    Energy Technology Data Exchange (ETDEWEB)

    Morozov, Dmitriy; Weber, Gunther

    2013-01-08

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

  2. Occurrence of leguminous trees

    Energy Technology Data Exchange (ETDEWEB)

    Kirkbride, J.H.; Arkcoll, D.B.A.; Turnbull, J.W.; Magalhaes, L.M.S.; Fernandes, N.P.

    1984-01-01

    Five papers from the symposium are presented. Kirkbride, J.H. Jr.; Legumes of the cerrado. pp 23-46 (Refs. 55) A review is given. Some 548 legume species in 59 genera are listed that have been reported from cerrado vegetation. Felker, P.; Legume trees in semi-arid and arid areas. pp 47-59 (Refs. 41) A review is given of worldwide research activities. Arkcoll, D.B.; A comparison of some fast growing species suitable for woodlots in the wet tropics. pp 61-68 (Refs. 9) Studies are described near Manaus on intensive silviculture (for fuelwood production) of Eucalyptus deglupta, Cedrelinga catanaeformis (catenaeformis), Jacaranda copaia, and Inga edulis. Turnbull, J.W.; Six phyllodinous Acacia species for planting in the humid tropical lowlands. pp 69-73 (Refs. 14) Distribution, ecology, growth, and utilization are described for A. auriculiformis, A. mangium, A. aulacocarpa, A. crassicarpa, A. cincinnata, and A. polystachya. Magalhaes, L.M.S., Fernandes, N.P.; Experimental stands of leguminous trees in the Manaus region. pp 75-79 (Refs. 8) Performance up to age 20 yr of Cedrelinga catenaeformis, Dalbergia nigra, Dinizia excelsa, Dipteryx odorata, Dipteryx sp., Diplotropis sp., Eperua bijuga, Pithecellobium racemosum, Vouacapoua pallidior, and Hymenaea sp. is described.

  3. Visualizing Individual Tree Differences in Tree-Ring Studies

    Directory of Open Access Journals (Sweden)

    Mario Trouillier

    2018-04-01

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

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

    Science.gov (United States)

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

    2013-11-01

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

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

    Directory of Open Access Journals (Sweden)

    Ralph Pethica

    2010-01-01

    Full Text Available 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.

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

    African Journals Online (AJOL)

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

  7. Urban tree database and allometric equations

    Science.gov (United States)

    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...

  8. Genetic transformation of forest trees

    African Journals Online (AJOL)

    Admin

    the stress from the regeneration process. We hope that the great progress achieved in the biology of. Agrobacterium and the expression of the genes playing key role in plant development will be helpful in solving the constraint linked to the genetic transformation of forest trees. Genetic transformation of forest trees offers a ...

  9. Chain-Constrained Spanning Trees

    NARCIS (Netherlands)

    Olver, N.K.; Zenklusen, R.

    2013-01-01

    We consider the problem of finding a spanning tree satisfying a family of additional constraints. Several settings have been considered previously, the most famous being the problem of finding a spanning tree with degree constraints. Since the problem is hard, the goal is typically to find a

  10. Tree Hydraulics: How Sap Rises

    Science.gov (United States)

    Denny, Mark

    2012-01-01

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

  11. Using farm trees for fuelwood

    Energy Technology Data Exchange (ETDEWEB)

    Poulsen, G.

    1983-01-01

    In the tropics, a significant proportion of wood supplies is obtained from trees on farmland rather than from forest. Reliable estimates of wood fuel resources are difficult to obtain by conventional mensuration techniques since such trees are often subjected to regular heavy pruning and pollarding. Productive potential of hedgerows and other small scrub vegetation used for fuel is also difficult to measure.

  12. Genome Trees from Conservation Profiles.

    Directory of Open Access Journals (Sweden)

    2005-12-01

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

  13. Tree physiology and bark beetles

    Science.gov (United States)

    Michael G. Ryan; Gerard Sapes; Anna Sala; Sharon Hood

    2015-01-01

    Irruptive bark beetles usually co-occur with their co-evolved tree hosts at very low (endemic) population densities. However, recent droughts and higher temperatures have promoted widespread tree mortality with consequences for forest carbon, fire and ecosystem services (Kurz et al., 2008; Raffa et al., 2008; Jenkins et al., 2012). In this issue of New Phytologist,...

  14. Who pays for tree improvement?

    Science.gov (United States)

    Tom D. Byram; E. M. Raley

    2011-01-01

    Tree improvement has been one of the most successful collaborative research efforts in history, eliciting participation from a wide variety of players. This effort has included state forestry agencies, research universities, integrated forest industries, and the USDA Forest Service. Tree improvement was organized through cooperatives whose objectives were to distribute...

  15. Automated Generation of Attack Trees

    DEFF Research Database (Denmark)

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

    2014-01-01

    -prone and impracticable for large systems. Nonetheless, the automated generation of attack trees has only been explored in connection to computer networks and levering rich models, whose analysis typically leads to an exponential blow-up of the state space. We propose a static analysis approach where attack trees...

  16. Adjustable chain trees for proteins

    DEFF Research Database (Denmark)

    Winter, Pawel; Fonseca, Rasmus

    2012-01-01

    A chain tree is a data structure for changing protein conformations. It enables very fast detection of clashes and free energy potential calculations. A modified version of chain trees that adjust themselves to the changing conformations of folding proteins is introduced. This results in much...

  17. Visualizing Contour Trees within Histograms

    DEFF Research Database (Denmark)

    Kraus, Martin

    2010-01-01

    Many of the topological features of the isosurfaces of a scalar volume field can be compactly represented by its contour tree. Unfortunately, the contour trees of most real-world volume data sets are too complex to be visualized by dot-and-line diagrams. Therefore, we propose a new visualization ...

  18. Modelling tree biomasses in Finland

    Energy Technology Data Exchange (ETDEWEB)

    Repola, J.

    2013-06-01

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

  19. Tree Coding of Bilevel Images

    DEFF Research Database (Denmark)

    Martins, Bo; Forchhammer, Søren

    1998-01-01

    Presently, sequential tree coders are the best general purpose bilevel image coders and the best coders of halftoned images. The current ISO standard, Joint Bilevel Image Experts Group (JBIG), is a good example. A sequential tree coder encodes the data by feeding estimates of conditional...... probabilities to an arithmetic coder. The conditional probabilities are estimated from co-occurrence statistics of past pixels, the statistics are stored in a tree. By organizing the code length calculations properly, a vast number of possible models (trees) reflecting different pixel orderings can...... is one order of magnitude slower than JBIG, obtains excellent and highly robust compression performance. A multipass free tree coding scheme produces superior compression results for all test images. A multipass free template coding scheme produces significantly better results than JBIG for difficult...

  20. Decision trees in epidemiological research

    Directory of Open Access Journals (Sweden)

    Ashwini Venkatasubramaniam

    2017-09-01

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

  1. Decision trees in epidemiological research.

    Science.gov (United States)

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

    2017-01-01

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

  2. Schoolyard Trees: Planning and Planting for Survival.

    Science.gov (United States)

    Coffey, Ann

    2001-01-01

    Considers factors that affect the fate of schoolyard trees and focuses on the importance of what is considered during tree selection. Includes of list of characteristics of tree projects that have a low survival rate. (DDR)

  3. Modeling hippocampal neurogenesis across the lifespan in seven species.

    Science.gov (United States)

    Lazic, Stanley E

    2012-08-01

    The aim of this study was to estimate the number of new cells and neurons added to the dentate gyrus across the lifespan, and to compare the rate of age-associated decline in neurogenesis across species. Data from mice (Mus musculus), rats (Rattus norvegicus), lesser hedgehog tenrecs (Echinops telfairi), macaques (Macaca mulatta), marmosets (Callithrix jacchus), tree shrews (Tupaia belangeri), and humans (Homo sapiens) were extracted from 21 data sets published in 14 different reports. Analysis of variance (ANOVA), exponential, Weibull, and power models were fit to the data to determine which best described the relationship between age and neurogenesis. Exponential models provided a suitable fit and were used to estimate the relevant parameters. The rate of decrease of neurogenesis correlated with species longevity (r = 0.769, p = 0.043), but not body mass or basal metabolic rate. Of all the cells added postnatally to the mouse dentate gyrus, only 8.5% (95% confidence interval [CI], 1.0% to 14.7%) of these will be added after middle age. In addition, only 5.7% (95% CI 0.7% to 9.9%) of the existing cell population turns over from middle age and onward. Thus, relatively few new cells are added for much of an animal's life, and only a proportion of these will mature into functional neurons. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. Profile of Antiemetic Activity of Netupitant Alone or in Combination with Palonosetron and Dexamethasone in Ferrets and Suncus murinus (house musk shrew

    Directory of Open Access Journals (Sweden)

    John A Rudd

    2016-08-01

    Full Text Available Background and Aims: Chemotherapy-induced acute and delayed emesis involves the activation of multiple pathways, with 5-hydroxytryptamine (5-HT; serotonin playing a major role in the initial response. Substance P tachykinin NK1 receptor antagonists can reduce emesis induced by disparate emetic challenges and therefore have a clinical utility as broad inhibitory anti-emetic drugs. In the present studies, we investigate the broad inhibitory anti-emetic profile of a relatively new NK1 receptor antagonist, netupitant, alone or in combination with the long acting 5-HT3 receptor antagonist, palonosetron, for a potential to reduce emesis in ferrets and shrews.Materials and Methods: Ferrets were pretreated with netupitant and/or palonosetron, or their combination, and then administered apomorphine (0.125 mg/kg, s.c., morphine (0.5 mg/kg, s.c., ipecacuanha (1.2 mg/kg, p.o., copper sulphate (100 mg/kg, intragastric, or cisplatin (5-10 mg/kg, i.p.; in other studies netupitant was administered to Suncus murinus before motion (4 cm horizontal displacement, 2 Hz for 10 min.Results: Netupitant (3 mg/kg, p.o. abolished apomorphine-, morphine-, ipecacuanha- and copper sulphate-induced emesis. Lower doses of netupitant (0.03-0.3 mg/kg, p.o. dose-dependently reduced cisplatin (10 mg/kg, i.p.-induced emesis in an acute (8 h model, and motion-induced emesis in Suncus murinus. In a ferret cisplatin (5 mg/kg, i.p.-induced acute and delayed emesis model, netupitant administered once at 3 mg/kg, p.o., abolished the first 24 h response and reduced the 24-72 h response by 94.6 %; the reduction was markedly superior to the effect of a three times per day administration of ondansetron (1 mg/kg, i.p.. A single administration of netupitant (1 mg/kg, p.o. plus palonosetron (0.1 mg/kg, p.o. combined with dexamethasone (1 mg/kg, i.p., once per day, also significantly antagonized cisplatin-induced acute and delayed emesis and was comparable with a once-daily regimen of

  5. Thapsigargin-induced activation of Ca(2+)-CaMKII-ERK in brainstem contributes to substance P release and induction of emesis in the least shrew.

    Science.gov (United States)

    Zhong, Weixia; Chebolu, Seetha; Darmani, Nissar A

    2016-04-01

    Cytoplasmic calcium (Ca(2+)) mobilization has been proposed to be an important factor in the induction of emesis. The selective sarcoplasmic/endoplasmic reticulum Ca(2+)-ATPase (SERCA) inhibitor thapsigargin, is known to deplete intracellular Ca(2+) stores, which consequently evokes extracellular Ca(2+) entry through cell membrane-associated channels, accompanied by a prominent rise in cytosolic Ca(2+). A pro-drug form of thapsigargin is currently under clinical trial as a targeted cancer chemotherapeutic. We envisioned that the intracellular effects of thapsigargin could cause emesis and planned to investigate its mechanisms of emetic action. Indeed, thapsigargin did induce vomiting in the least shrew in a dose-dependent and bell-shaped manner, with maximal efficacy (100%) at 0.5 mg/kg (i.p.). Thapsigargin (0.5 mg/kg) also caused increases in c-Fos immunoreactivity in the brainstem emetic nuclei including the area postrema (AP), nucleus tractus solitarius (NTS) and dorsal motor nucleus of the vagus (DMNX), as well as enhancement of substance P (SP) immunoreactivity in DMNX. In addition, thapsigargin (0.5 mg/kg, i.p.) led to vomit-associated and time-dependent increases in phosphorylation of Ca(2+)/calmodulin kinase IIα (CaMKIIα) and extracellular signal-regulated protein kinase 1/2 (ERK1/2) in the brainstem. We then explored the suppressive potential of diverse chemicals against thapsigargin-evoked emesis including antagonists of: i) neurokinin-1 receptors (netupitant), ii) the type 3 serotonin receptors (palonosetron), iii) store-operated Ca(2+) entry (YM-58483), iv) L-type Ca(2+) channels (nifedipine), and v) SER Ca(2+)-release channels inositol trisphosphate (IP3Rs) (2-APB)-, and ryanodine (RyRs) (dantrolene)-receptors. In addition, the antiemetic potential of inhibitors of CaMKII (KN93) and ERK1/2 (PD98059) were investigated. All tested antagonists/blockers attenuated emetic parameters to varying degrees except palonosetron, however a combination of non

  6. The Heritage of Nature: Heritage Trees

    Directory of Open Access Journals (Sweden)

    Zöhre Polat

    2017-08-01

    Full Text Available Heritage trees are naturel heritages. Heritage trees are typically a large, individual tree with unique value, which is considered irreplaceable. The major criteria for heritage tree designation are age, rarity, and size, as well as aesthetic, botanical, ecological, and historical value. Today many researcher’s focus on recording,, protection and management strategies of heritage trees. Counties have different strategies about heritage trees. The aims of the study are; (1 Preserving the characteristics of being heritage trees, (2 Present suggestions for record, protection and management strategies of heritage trees in Turkey.

  7. Maximum Gene-Support Tree

    Directory of Open Access Journals (Sweden)

    Yunfeng Shan

    2008-01-01

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

  8. Tree Ordination as Invented Tradition

    Directory of Open Access Journals (Sweden)

    Avery Morrow

    2012-01-01

    Full Text Available The symbolic ordination of trees as monks in Thailand is widely perceived in Western scholarship to be proof of the power of Buddhism to spur ecological thought. However, a closer analysis of tree ordination demonstrates that it is not primarily about Buddhist teaching, but rather is an invented tradition based on the sanctity of Thai Buddhist symbols as well as those of spirit worship and the monarchy. Tree ordinations performed by non-Buddhist minorities in Thailand do not demonstrate a religious commitment but rather a political one.

  9. TreeCluster: Massively scalable transmission clustering using phylogenetic trees

    OpenAIRE

    Moshiri, Alexander

    2018-01-01

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

  10. Moose?tree interactions: rebrowsing is common across tree species

    OpenAIRE

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

    2017-01-01

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

  11. Random ancestor trees

    International Nuclear Information System (INIS)

    Ben-Naim, E; Krapivsky, P L

    2010-01-01

    We investigate a network growth model in which the genealogy controls the evolution. In this model, a new node selects a random target node and links either to this target node, or to its parent, or to its grandparent, etc; all nodes from the target node to its most ancient ancestor are equiprobable destinations. The emerging random ancestor tree is very shallow: the fraction g n of nodes at distance n from the root decreases super-exponentially with n, g n = e −1 /(n − 1)!. We find that a macroscopic hub at the root coexists with highly connected nodes at higher generations. The maximal degree of a node at the nth generation grows algebraically as N 1/β n , where N is the system size. We obtain the series of nontrivial exponents which are roots of transcendental equations: β 1 ≅1.351 746, β 2 ≅1.682 201, etc. As a consequence, the fraction p k of nodes with degree k has an algebraic tail, p k ∼ k −γ , with γ = β 1 + 1 = 2.351 746

  12. Resummed tree heptagon

    Science.gov (United States)

    Belitsky, A. V.

    2018-04-01

    The form factor program for the regularized space-time S-matrix in planar maximally supersymmetric gauge theory, known as the pentagon operator product expansion, is formulated in terms of flux-tube excitations propagating on a dual two-dimensional world-sheet, whose dynamics is known exactly as a function of 't Hooft coupling. Both MHV and non-MHV amplitudes are described in a uniform, systematic fashion within this framework, with the difference between the two encoded in coupling-dependent helicity form factors expressed via Zhukowski variables. The nontrivial SU(4) tensor structure of flux-tube transitions is coupling independent and is known for any number of charged excitations from solutions of a system of Watson and Mirror equations. This description allows one to resum the infinite series of form factors and recover the space-time S-matrix exactly in kinematical variables at a given order of perturbation series. Recently, this was done for the hexagon. Presently, we successfully perform resummation for the seven-leg tree NMHV amplitude. To this end, we construct the flux-tube integrands of the fifteen independent Grassmann component of the heptagon with an infinite number of small fermion-antifermion pairs accounted for in NMHV two-channel conformal blocks.

  13. Distance labeling schemes for trees

    DEFF Research Database (Denmark)

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

    2016-01-01

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

  14. Spanning Tree Based Attribute Clustering

    DEFF Research Database (Denmark)

    Zeng, Yifeng; Jorge, Cordero Hernandez

    2009-01-01

    inconsistent edges from a maximum spanning tree by starting appropriate initial modes, therefore generating stable clusters. It discovers sound clusters through simple graph operations and achieves significant computational savings. We compare the Star Discovery algorithm against earlier attribute clustering...

  15. Decision tree modeling using R.

    Science.gov (United States)

    Zhang, Zhongheng

    2016-08-01

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

  16. Algorithms for Decision Tree Construction

    KAUST Repository

    Chikalov, Igor

    2011-01-01

    The study of algorithms for decision tree construction was initiated in 1960s. The first algorithms are based on the separation heuristic [13, 31] that at each step tries dividing the set of objects as evenly as possible. Later Garey and Graham [28] showed that such algorithm may construct decision trees whose average depth is arbitrarily far from the minimum. Hyafil and Rivest in [35] proved NP-hardness of DT problem that is constructing a tree with the minimum average depth for a diagnostic problem over 2-valued information system and uniform probability distribution. Cox et al. in [22] showed that for a two-class problem over information system, even finding the root node attribute for an optimal tree is an NP-hard problem. © Springer-Verlag Berlin Heidelberg 2011.

  17. Generic physical protection logic trees

    Energy Technology Data Exchange (ETDEWEB)

    Paulus, W.K.

    1981-10-01

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

  18. Longest Common Extensions in Trees

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  19. Longest common extensions in trees

    DEFF Research Database (Denmark)

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

    2016-01-01

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

  20. Objective consensus from decision trees.

    Science.gov (United States)

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

    2014-12-05

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

  1. Generic physical protection logic trees

    International Nuclear Information System (INIS)

    Paulus, W.K.

    1981-10-01

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

  2. Microwave sensing of tree trunks

    Science.gov (United States)

    Jezova, Jana; Mertens, Laurence; Lambot, Sebastien

    2015-04-01

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

  3. Tight bounds for top tree compression

    DEFF Research Database (Denmark)

    Bille, Philip; Fernstrøm, Finn; Gørtz, Inge Li

    2017-01-01

    We consider compressing labeled, ordered and rooted trees using DAG compression and top tree compression. We show that there exists a family of trees such that the size of the DAG compression is always a logarithmic factor smaller than the size of the top tree compression (even for an alphabet...

  4. Factors that influence Christmas tree sales

    Science.gov (United States)

    Thomas H. Pendleton; Lawrence D. Garrett

    1970-01-01

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

  5. Critical wind speed at which trees break

    Science.gov (United States)

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

    2016-02-01

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

  6. TreeGenes: A forest tree genome database.

    Science.gov (United States)

    Wegrzyn, Jill L; Lee, Jennifer M; Tearse, Brandon R; Neale, David B

    2008-01-01

    The Dendrome Project and associated TreeGenes database serve the forest genetics research community through a curated and integrated web-based relational database. The research community is composed of approximately 2 000 members representing over 730 organizations worldwide. The database itself is composed of a wide range of genetic data from many forest trees with focused efforts on commercially important members of the Pinaceae family. The primary data types curated include species, publications, tree and DNA extraction information, genetic maps, molecular markers, ESTs, genotypic, and phenotypic data. There are currently ten main search modules or user access points within this PostgreSQL database. These access points allow users to navigate logically through the related data types. The goals of the Dendrome Project are to (1) provide a comprehensive resource for forest tree genomics data to facilitate gene discovery in related species, (2) develop interfaces that encourage the submission and integration of all genomic data, and to (3) centralize and distribute existing and novel online tools for the research community that both support and ease analysis. Recent developments have focused on increasing data content, functional annotations, data retrieval, and visualization tools. TreeGenes was developed to provide a centralized web resource with analysis and visualization tools to support data storage and exchange.

  7. A bicriterion Steiner tree problem on graph

    Directory of Open Access Journals (Sweden)

    Vujošević Mirko B.

    2003-01-01

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

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

    Science.gov (United States)

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

    2015-11-01

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

  9. Utilization of nitrogen fixing trees

    Energy Technology Data Exchange (ETDEWEB)

    Brewbaker, J.L.; Beldt, R. van den; MacDicken, K.; Budowski, G.; Kass, D.C.L.; Russo, R.O.; Escalante, G.; Herrera, R.; Aranguren, J.; Arkcoll, D.B.; Doebereinger, J. (cord.)

    1983-01-01

    Six papers from the symposium are noted. Brewbaker, J.L., Beldt, R. van den, MacDicken, K. Fuelwood uses and properties of nitrogen-fixing trees, pp 193-204, (Refs. 15). Includes a list of 35 nitrogen-fixing trees of high fuelwood value. Budowski, G.; Kass, D.C.L.; Russo, R.O. Leguminous trees for shade, pp 205-222, (Refs. 68). Escalante, G., Herrera, R., Aranguren, J.; Nitrogen fixation in shade trees (Erythrina poeppigiana) in cocoa plantations in northern Venezuela, pp 223-230, (Refs. 13). Arkcoll, D.B.; Some leguminous trees providing useful fruits in the North of Brazil, pp 235-239, (Refs. 13). This paper deals with Parkia platycephala, Pentaclethra macroloba, Swartzia sp., Cassia leiandra, Hymenaea courbaril, dipteryz odorata, Inga edulis, I. macrophylla, and I. cinnamonea. Baggio, A.J.; Possibilities of the use of Gliricidia sepium in agroforestry systems in Brazil, pp 241-243; (Refs. 15). Seiffert, N.F.; Biological nitrogen and protein production of Leucaena cultivars grown to supplement the nutrition of ruminants, pp 245-249, (Refs. 14). Leucaena leucocephala cv. Peru, L. campina grande (L. leucocephala), and L. cunningham (L. leucocephalae) were promising for use as browse by beef cattle in central Brazil.

  10. Totally optimal decision trees for Boolean functions

    KAUST Repository

    Chikalov, Igor

    2016-07-28

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

  11. Mapping tree density at a global scale.

    Science.gov (United States)

    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.

  12. Drawing Contour Trees in the Plane.

    Science.gov (United States)

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

    2011-11-01

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

  13. Integrated fault tree development environment

    International Nuclear Information System (INIS)

    Dixon, B.W.

    1986-01-01

    Probabilistic Risk Assessment (PRA) techniques are utilized in the nuclear industry to perform safety analyses of complex defense-in-depth systems. A major effort in PRA development is fault tree construction. The Integrated Fault Tree Environment (IFTREE) is an interactive, graphics-based tool for fault tree design. IFTREE provides integrated building, editing, and analysis features on a personal workstation. The design philosophy of IFTREE is presented, and the interface is described. IFTREE utilizes a unique rule-based solution algorithm founded in artificial intelligence (AI) techniques. The impact of the AI approach on the program design is stressed. IFTREE has been developed to handle the design and maintenance of full-size living PRAs and is currently in use

  14. Construction of an α-labeled tree from a given set of α-labeled trees

    Directory of Open Access Journals (Sweden)

    G. Sethuraman

    2017-08-01

    Full Text Available Inspired by the method of Koh et al. (1979 of combining known graceful trees to construct bigger graceful trees, a new class of graceful trees is constructed from a set of k known graceful trees, k≥2 in a specific way. In fact, each member of this new class of trees admits α-labeling, a stronger version of graceful labeling. Consequently, each member of this family of trees decomposes complete graphs and complete bipartite graphs.

  15. The tree gangs of Glittertown

    International Nuclear Information System (INIS)

    Boerner-Ein, D.

    1991-01-01

    This article describes the activities of four groups in Los Angeles as part of The Global ReLeaf challenge to plant trees for environmental improvement and to combat global warming. The activities include: training of 'citizen foresters' in selection of tree species, planting sites, maintenance, and fund-raising; education of school children about recycling, organic gardening, water conservation and composting. By working with civic groups, school children, public works, housing developers and the forestry division these groups hope to cool their communities and reduce energy consumption

  16. A Distributed Spanning Tree Algorithm

    DEFF Research Database (Denmark)

    Johansen, Karl Erik; Jørgensen, Ulla Lundin; Nielsen, Sven Hauge

    We present a distributed algorithm for constructing a spanning tree for connected undirected graphs. Nodes correspond to processors and edges correspond to two-way channels. Each processor has initially a distinct identity and all processors perform the same algorithm. Computation as well...... as communication is asynchronous. The total number of messages sent during a construction of a spanning tree is at most 2E+3NlogN. The maximal message size is loglogN+log(maxid)+3, where maxid is the maximal processor identity....

  17. A distributed spanning tree algorithm

    DEFF Research Database (Denmark)

    Johansen, Karl Erik; Jørgensen, Ulla Lundin; Nielsen, Svend Hauge

    1988-01-01

    We present a distributed algorithm for constructing a spanning tree for connected undirected graphs. Nodes correspond to processors and edges correspond to two way channels. Each processor has initially a distinct identity and all processors perform the same algorithm. Computation as well...... as communication is asyncronous. The total number of messages sent during a construction of a spanning tree is at most 2E+3NlogN. The maximal message size is loglogN+log(maxid)+3, where maxid is the maximal processor identity....

  18. Interpreting CNNs via Decision Trees

    OpenAIRE

    Zhang, Quanshi; Yang, Yu; Wu, Ying Nian; Zhu, Song-Chun

    2018-01-01

    This paper presents a method to learn a decision tree to quantitatively explain the logic of each prediction of a pre-trained convolutional neural networks (CNNs). Our method boosts the following two aspects of network interpretability. 1) In the CNN, each filter in a high conv-layer must represent a specific object part, instead of describing mixed patterns without clear meanings. 2) People can explain each specific prediction made by the CNN at the semantic level using a decision tree, i.e....

  19. Tree size comparison of some important street trees growing at ...

    African Journals Online (AJOL)

    The importance of trees in urban environment is now widely recognized as they cleanse the particulate air pollution and help to make cities and towns more agreeable places to dwell upon. A detailed survey was conducted to study the size of Alstonia scholaris, Azadirachta indica, Bombax ceiba, Cassia fistula, Eucalyptus ...

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

    Science.gov (United States)

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

    2011-01-01

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

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

    Science.gov (United States)

    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.

  2. Usefulness of problem tree, objective tree and logical framework ...

    African Journals Online (AJOL)

    The discussion has led to the conclusion that higher learning institutions are not adequately preparing graduates to face the increasing labor market demands in terms of skills and competitiveness. Having outlined the roots of the problem through the problem tree, the researchers proposed potential strategies to handle the ...

  3. Human action analysis with randomized trees

    CERN Document Server

    Yu, Gang; Liu, Zicheng

    2014-01-01

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

  4. Integrating cyber attacks within fault trees

    International Nuclear Information System (INIS)

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

    2009-01-01

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

  5. Edge-Disjoint Fibonacci Trees in Hypercube

    Directory of Open Access Journals (Sweden)

    Indhumathi Raman

    2014-01-01

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

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

    Science.gov (United States)

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

    2018-01-01

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

  7. Mycotoxins in edible tree nuts.

    Science.gov (United States)

    Molyneux, Russell J; Mahoney, Noreen; Kim, Jong H; Campbell, Bruce C

    2007-10-20

    Tree nuts (almonds, pistachios, and walnuts) are an exceptionally valuable crop, especially in California, with an aggregate value approaching $3.5 billion. Much of this economic value comes from overseas markets, with up to 60% of the crop being exported. The product can be contaminated with aflatoxins or ochratoxins, with the former being of special concern because of the strict regulatory levels (4 ppb total aflatoxins) applied by the European Community (EC). Natural, consumer-acceptable control methods are therefore required to conform to such limits. Research has shown that aflatoxin production is markedly decreased by the presence of natural antioxidants that occur in tree nuts, including hydrolysable tannins, flavonoids and phenolic acids. In vitro testing of individual compounds showed that the antiaflatoxigenic effect correlated with the structure and concentration of such compounds in individual nut varieties and species. This lead to the hypothesis that aflatoxin biosynthesis is stimulated by oxidative stress on the fungus and that compounds capable of relieving oxidative stress should therefore suppress or eliminate aflatoxin biosynthesis. Oxidative stress induced in A. flavus by addition of tert-butyl hydroperoxide to the media stimulated peak aflatoxin production and maintained high levels over time. However, aflatoxin formation was significantly inhibited by incorporation into the media of the antioxidant, tannic acid. Measures to increase natural products with antioxidant properties in tree nuts may thereby reduce or eliminate the ability of A. flavus to biosynthesize aflatoxins, thus ensuring levels at or below regulatory limits and maintaining export markets for U.S. tree nuts.

  8. Reclamation with trees in Illinois

    Science.gov (United States)

    Brad Evilsizer

    1980-01-01

    Thru private initiative, Illinois citizens historically have invented and conducted large-scale tree planting programs, starting with hedgerow fences and farmstead windbreaks and continuing with surface mine reclamation and farm woodlands. With invaluable help from public and private scientific personnel, the old and new programs hold promise of enlargement and...

  9. Trees of Our National Forests.

    Science.gov (United States)

    Forest Service (USDA), Washington, DC.

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

  10. Protected Vertices in Motzkin trees

    OpenAIRE

    Van Duzer, Anthony

    2017-01-01

    In this paper we find recurrence relations for the asymptotic probability a vertex is $k$ protected in all Motzkin trees. We use a similar technique to calculate the probabilities for balanced vertices of rank $k$. From this we calculate upper and lower bounds for the probability a vertex is balanced and upper and lower bounds for the expected rank of balanced vertices.

  11. storey and canopy tree species

    African Journals Online (AJOL)

    different tree species. The data presented here would therefore help in the planning and management of tropical forest reserves and development of management inteiventions to enhance forest productivity and ecological balance. Materials and methods. Study site. Kalinzu Forest Reserve is a tropical rain forest locate<.! in.

  12. Tree value conversion standards revisited

    Science.gov (United States)

    Paul S. DeBald; Martin E. Dale; Martin E. Dale

    1991-01-01

    Updated tree value conversion standards (TVCS) are presented for 12 important hardwood species of the oak-hickory forest. These updated standards-developed for each species by butt-log grade, merchantable height, and diameter at breast height-reflect the changes in lumber prices and in conversion costs which have occurred since 1976 when the original TVCS were...

  13. Trends in game tree search

    NARCIS (Netherlands)

    A. de Bruin (Arie); W.H.L.M. Pijls (Wim)

    2003-01-01

    textabstractThis paper deals with algorithms searching trees generated by two-person, zero-sum games with perfect information. The standard algorithm in this field is alpha-beta. We will discuss this algorithm as well as extensions, like transposition tables, iterative deepening and NegaScout.

  14. Tree improvement and environmental forestry

    Science.gov (United States)

    Warren T. Doolittle

    1971-01-01

    I was invited to talk to you about some of the things tree improvement can do to help our forest environment. Now I do not claim to have a corner on the market for ideas that geneticists can use in our environment, and I know that a number of scholarly papers have been presented previously on this subject.

  15. The Tree of Animal Life

    Science.gov (United States)

    Braude, Stan

    2007-01-01

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

  16. Linguistics, Logic, and Finite Trees

    NARCIS (Netherlands)

    Blackburn, P.; Meyer-Viol, W.

    1993-01-01

    A modal logic is developed to deal with finite ordered binary trees as they are used in (computational) linguistics. A modal language is introduced with operators for the 'mother of', 'first daughter of' and 'second daughter of' relations together with their transitive reflexive closures.

  17. Are there tides within trees?

    Science.gov (United States)

    Fisahn, Joachim

    2018-01-24

    Tree stem diameters and electrical stem potentials exhibit rhythmic variations with periodicities of 24-25 h. Under free-running conditions of constant light or darkness these rhythms were suggested to be mediated by the lunisolar gravitational force. To further unravel the regulation of tree stem diameter dilatations, many of the published time courses of diameter variations were re-evaluated in conjunction with the contemporaneous time courses of the lunisolar tidal acceleration. This was accomplished by application of the Etide program, which estimates, with high temporal resolution, local gravitational changes as a consequence of the diurnal variations of the lunisolar gravitational force due to the orbits and relative positions of Earth, Moon and Sun. In all instances investigated, it was evident that a synchronism exists between the times of the turning points of both the lunisolar tide and stem diameter variations when the direction of extension changes. This finding of synchrony documents that the lunisolar tide is a regulator of the tree stem diameter dilatations. Under the described experimental conditions, rhythms in tree stem diameter dilations and electrical stem potentials are controlled by the lunisolar gravitational acceleration. © The Author(s) 2018. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  18. GumTree: Data reduction

    International Nuclear Information System (INIS)

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

    2006-01-01

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

  19. Ecology: Drought and dead trees

    Science.gov (United States)

    Richard Birdsey; Yude. Pan

    2011-01-01

    Drought has emerged as a major threat to the world's forests. A study shows that tree mortality in Canada's boreal forests has increased by nearly 5% per year—much higher than expected—owing to water stress from regional warming.

  20. Ice Nuclei from Birch Trees

    Science.gov (United States)

    Felgitsch, Laura; Seifried, Teresa; Winkler, Philipp; Schmale, David, III; Grothe, Hinrich

    2017-04-01

    While the importance of heterogeneous ice nucleation in the atmosphere is known, we still know very little about the substances triggering these freezing events. Recent findings support the theory that biological ice nuclei (IN) exhibit the ability to play an important role in these processes. Huffman et al. (2013) showed a burst of biological IN over woodlands triggered by rain events. Birch pollen are known to release a high number of efficient IN if incubated in water (Pummer et al. 2012). Therefore birches are of interest in our research on this topic. Plants native to the timberline, such as birch trees, have to cope with very cold climatic conditions, rendering freezing avoidance impossible. These plants trigger freezing in their extracellular spaces to control the freezing process and avoid intracellular freezing, which would have lethal consequences. The plants hereby try to freeze at a temperature well above homogeneous freezing temperatures but still at temperatures low enough to not be effected by brief night frosts. To achieve this, IN are an important tool. The specific objective of our work was to study the potential sources and distribution of IN in birch trees. We collected leaves, fruit, bark, and trunk cores from a series of mature birch trees in Tyrol, Austria at different altitudes and sampling sites. We also collected samples from a birch tree in an urban park in Vienna, Austria. Our data show a sampling site dependence and the distribution of IN throughout the tree. Our data suggest that leaves, bark, and wood of birch can function as a source of IN, which are easily extracted with water. The IN are therefore not restricted to pollen. Hence, the amount of IN, which can be released from birch trees, is tremendous and has been underrated so far. Future work aims to elucidate the nature, contribution, and potential ecological roles of IN from birch trees in different habitats. Huffman, J.A., Prenni, A.J., DeMott, P.J., Pöhlker, C., Mason, R

  1. Tree rings and radiocarbon calibration

    International Nuclear Information System (INIS)

    Barbetti, M.

    1999-01-01

    Only a few kinds of trees in Australia and Southeast Asia are known to have growth rings that are both distinct and annual. Those that do are therefore extremely important to climatic and isotope studies. In western Tasmania, extensive work with Huon pine (Lagarostrobos franklinii) has shown that many living trees are more than 1,000 years old, and that their ring widths are sensitive to temperature, rainfall and cloud cover (Buckley et al. 1997). At the Stanley River there is a forest of living (and recently felled) trees which we have sampled and measured. There are also thousands of subfossil Huon pine logs, buried at depths less than 5 metres in an area of floodplain extending over a distance of more than a kilometre with a width of tens of metres. Some of these logs have been buried for 50,000 years or more, but most of them belong to the period between 15,000 years and the present. In previous expeditions in the 1980s and 1990s, we excavated and sampled about 350 logs (Barbetti et al. 1995; Nanson et al. 1995). By measuring the ring-width patterns, and matching them between logs and living trees, we have constructed a tree-ring dated chronology from 571 BC to AD 1992. We have also built a 4254-ring floating chronology (placed by radiocarbon at ca. 3580 to 7830 years ago), and an earlier 1268-ring chronology (ca. 7,580 to 8,850 years ago). There are many individuals, or pairs of logs which match and together span several centuries, at 9,000 years ago and beyond

  2. International Tree Ring Data Bank (ITRDB)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Tree ring data from the International Tree Ring Data Bank and World Data Center for Paleoclimatology archives. Data include raw treering measurements (most are...

  3. Understanding search trees via statistical physics

    Indian Academy of Sciences (India)

    ary search tree model (where stands for the number of branches of the search tree), an important problem for data storage in computer science, using a variety of statistical physics techniques that allow us to obtain exact asymptotic results.

  4. Animals and trees: food for thought

    Energy Technology Data Exchange (ETDEWEB)

    Openshaw, K.

    1979-01-01

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

  5. Africa's highest mountain harbours Africa's tallest trees

    OpenAIRE

    Hemp Andreas; Zimmermann Reiner; Remmele Sabine; Pommer Ulf; Berauer Bernd; Hemp Claudia; Fischer Markus

    2017-01-01

    While world records of tree heights were set by American, Australian and Asian tree species, Africa seemed to play no role here. In our study we show that Entandrophragma excelsum (Meliaceae) found in a remote valley at Kilimanjaro has to be included in the list of the world’s superlative trees. Estimating tree age from growth rates monitored by high resolution dendrometry indicates that tall individuals may reach more than 470 years of age. A unique combination of anatomical peculiarities an...

  6. Old trees: Extraction, Conservation Can Coexist

    OpenAIRE

    Aerts, Raf

    2013-01-01

    Letters Because large old trees are essential for forest ecosystem integrity and biodiversity, timber extraction in managed forests should preferentially be concentrated where large old trees are least likely to develop ("Global decline in large old trees," D. B. Lindenmayer et al., Perspectives, 7 December 2012, p. 1305). However, timber extraction and the conservation of large old trees are not necessarily mutually exclusive. Current forest policy and management practices in Flanders...

  7. A Durable Flash Memory Search Tree

    OpenAIRE

    Clay III, James; Wortman, Kevin

    2012-01-01

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

  8. Using tree diversity to compare phylogenetic heuristics.

    Science.gov (United States)

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

    2009-04-29

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

  9. A Multipurpose Tree for Puerto Rico

    Science.gov (United States)

    Martin Chudnoff; C. B. Briscoe

    1965-01-01

    Cadam (Anthocaephalus cadamba Miq.) grows very rapidly on a wide variety of sited in Puerto Rico. Tree form is excellent, seed is produced in abundance every year by mature trees, planting is easy and cheap, and relatively little care is required after planting. No important attacks of insects of disease have occurred on trees grown in Puerto Rico for 35 years. The...

  10. A practical alternative to single tree selection?

    Science.gov (United States)

    Gary W. Miller; H. Clay Smith

    1993-01-01

    When landowners want to develop and maintain an uneven-aged tree structure in eastern hardwood stands, single-tree selection often is suggested as the only advisable, long-term partial regeneration harvest method. Single-tree selection is preferred because it provides a means for improving quality and controlling stocking of the residual stand necessary for sustained...

  11. Street tree structural differences and associated stormwater ...

    Science.gov (United States)

    Green infrastructure approaches leverage vegetation and soil to improve environmental quality. Municipal street trees are crucial components of urban green infrastructure because they provide stormwater interception benefits and other ecosystem services. Thus, it is important to understand the patterns and drivers of structural heterogeneity in urban street tree assemblages. In this study, we compared the forest structure of street trees across nine communities along both geographic and demographic gradients in metropolitan Cincinnati, Ohio, USA. Specifically, we used a two-part statistical model to compare both the proportion of sampled street segments containing zero trees, and basal area magnitude for street segments with trees. We made community-scale comparisons based on street tree management, socioeconomics, and geographic setting. Then, using modeled stormwater interception estimates from i-Tree Streets, we investigated the implications of heterogeneity in street tree assemblages for stormwater interception benefits. The forest structure of street trees varied across communities in relation to management practices, namely participation in the Tree City USA program. As a consequence of this structural difference, we observed a stark discrepancy in estimated stormwater interception between Tree City USA participants (128.7 m3/km street length) and non-participants (59.2 m3/km street length). While street tree assemblages did not vary by community poverty s

  12. New tree puller increases yield 20%

    Science.gov (United States)

    E. Kerr

    1977-01-01

    A new tree harvester that extracts both taproot and stem makes a pine tree 20 percent more useful. The machine shears the lateral roots close to the taprrot and then plucks the entire tree from the ground like a carrot. The concept was developed by Dr. Peter Koch at the U.S. Forest Service's Southern Forest Experiment Station in Pineville, La. The shearing...

  13. On Tree-Constrained Matchings and Generalizations

    NARCIS (Netherlands)

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

    2011-01-01

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

  14. Mapping tree density at a global scale

    NARCIS (Netherlands)

    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.; Hengeveld, G.M.; Nabuurs, G.J.

    2015-01-01

    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

  15. Community assessment of tropical tree biomass

    DEFF Research Database (Denmark)

    Theilade, Ida; Rutishauser, Ervan; Poulsen, Michael K.

    2015-01-01

    previous experience. Indeed, only experienced monitors were able to discriminate trees with low wood densities. Local ecological knowledge did not allow consistent tree identification across monitors. Conclusion Future REDD+ programmes may benefit from the systematic training of local monitors in tree DBH...

  16. The smallest Randic index for trees

    Indian Academy of Sciences (India)

    Randic indices among trees are determined, and the corresponding extremal trees are characterized. Keywords. Extremal graph; tree; the general Randic index. 1. Introduction. In 1975, Randic [6] introduced the branching index as the sum of d(u)d(v). −1/2 over all edges uv of a (molecular) graph G = (V, E), i.e.. R(G) = ∑.

  17. Aspects of insertion in random trees

    NARCIS (Netherlands)

    Bagchi, Arunabha; Reingold, E.M.

    1982-01-01

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

  18. QDist—Quartet Distance Between Evolutionary Trees

    DEFF Research Database (Denmark)

    Mailund; Pedersen, Christian N. Storm

    2004-01-01

    QDist is a program for computing the quartet distance between two unrooted evolutionary trees, i.e. the number of quartet topology differences between the two trees, where a quartet topology is the topological subtree induced by four species. The implementation is based on an algorithm with running...... time O(n log² n), which makes it practical to compare large trees....

  19. INDIGENOUS WOODLAND TREE SPECIES OF ETHIOPIA

    African Journals Online (AJOL)

    area, Abijata Shalla and Awash National Parks. At each site a total of 15 study trees were selected from 50 x 50 m releves. From each tree, data on tree height, diameter at breast height (DBH), canopy depth and canopy diameter were collected. Effect of treeson undercanopy vegetation diversity was assessed by estimating ...

  20. Maintenance of carbohydrate transport in tall trees

    DEFF Research Database (Denmark)

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

    2017-01-01

    Trees present a critical challenge to long-distance transport because as a tree grows in height and the transport pathway increases in length, the hydraulic resistance of the vascular tissue should increase. This has led many to question whether trees can rely on a passive transport mechanism...

  1. A composition theorem for decision tree complexity

    OpenAIRE

    Montanaro, Ashley

    2013-01-01

    We completely characterise the complexity in the decision tree model of computing composite relations of the form h = g(f^1,...,f^n), where each relation f^i is boolean-valued. Immediate corollaries include a direct sum theorem for decision tree complexity and a tight characterisation of the decision tree complexity of iterated boolean functions.

  2. Tree planting: not a simple solution

    Science.gov (United States)

    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...

  3. Tree biomass in the North Central Region.

    Science.gov (United States)

    Gerhard K. Raile; Pamela J. Jakes

    1982-01-01

    Methods for calculating tree biomass are outlined, and the biomass on commercial forest land is estimated for 11 north-central states. Tree biomass in the North Central Region totals 3.6 billion tons, or 50 tons per commercial forest acre. For all species, total tree biomass is concentrated in growing-stock boles.

  4. Do you believe in palm trees?

    Science.gov (United States)

    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...

  5. Evaluating realized genetic gains from tree improvement.

    Science.gov (United States)

    J.B. St. Clair

    1993-01-01

    Tree improvement has become an essential part of the management of forest lands for wood production, and predicting yields and realized gains from forests planted with genetically-improved trees will become increasingly important. This paper discusses concepts of tree improvement and genetic gain important to growth and yield modeling, and reviews previous studies of...

  6. Which trees should be removed in thinning?

    Directory of Open Access Journals (Sweden)

    Timo Pukkala

    2015-12-01

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

  7. THE CONTRIBUTION OF AGROFORESTRY TREE PRODUCTS TO ...

    African Journals Online (AJOL)

    philiph

    A study to evaluate the contributions and economic benefits of agro-forestry tree products to rural farmers in Karim-Lamido Local ... derivable from this practice and its contributions and economic benefit to farmers' livelihood should be intensified ..... and fast growing tree species, and replacement for every tree felled. Gideon ...

  8. Tree Rings in the Tropics: Insights into the Ecology and Climate Sensitivity of Tropical Trees

    NARCIS (Netherlands)

    Brienen, R.J.W.; Schöngart, J.; Zuidema, P.A.

    2016-01-01

    Tree-ring studies provide important contributions to understanding the climate sensitivity of tropical trees and the effects of global change on tropical forests. This chapter reviews recent advances in tropical tree-ring research. In tropical lowlands, tree ring formation is mainly driven by

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

    DEFF Research Database (Denmark)

    Feragen, Aasa; Owen, Megan; Petersen, Jens

    2013-01-01

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

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

    NARCIS (Netherlands)

    Soliz Gamboa, C.C.|info:eu-repo/dai/nl/30484053X

    2010-01-01

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

  11. Implementing municipal tree planting: Los Angeles million tree initiative

    Science.gov (United States)

    S. Pincetl

    2010-01-01

    Urban forests are increasingly being seen as an important infrastructure that can help cities remediate their environmental impacts. This work reports on the first steps in implementing a million tree program in Los Angeles and the ways such a biogenic—living—infrastructure has been approached. Numbers of studies have been done to quantify the benefits of urban forests...

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

    DEFF Research Database (Denmark)

    Feragen, Aasa; Owen, Megan; Petersen, Jens

    2013-01-01

    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...... (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...... 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...

  13. Household Tree Planting in Tigrai, Northern Ethiopia: Tree Species, Purposes, and Determinants

    OpenAIRE

    Gebreegziabher, Zenebe; Mekonnen, Alemu; Kassie, Menale; Köhlin, Gunnar

    2010-01-01

    Trees have multiple purposes in rural Ethiopia, providing significant economic and ecological benefits. Planting trees supplies rural households with wood products for their own consumption, as well for sale, and decreases soil degradation. We used cross-sectional household-level data to analyze the determinants of household tree planting and explored the most important tree attributes or purpose(s) that enhance the propensity to plant trees. We set up a sample selection framework that simult...

  14. Inducibility of d-ary trees

    OpenAIRE

    Czabarka, Éva; Dossou-Olory, Audace A. V.; Székely, László A.; Wagner, Stephan

    2018-01-01

    Imitating a recently introduced invariant of trees, we initiate the study of the inducibility of $d$-ary trees (rooted trees whose vertex outdegrees are bounded from above by $d\\geq 2$) with a given number of leaves. We determine the exact inducibility for stars and binary caterpillars. For $T$ in the family of strictly $d$-ary trees (every vertex has $0$ or $d$ children), we prove that the difference between the maximum density of a $d$-ary tree $D$ in $T$ and the inducibility of $D$ is of o...

  15. Making CSB+-Tree Processor Conscious

    DEFF Research Database (Denmark)

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

    2005-01-01

    Cache-conscious indexes, such as CSB+-tree, are sensitive to the underlying processor architecture. In this paper, we focus on how to adapt the CSB+-tree so that it performs well on a range of different processor architectures. Previous work has focused on the impact of node size on the performance...... of the CSB+-tree. We argue that it is necessary to consider a larger group of parameters in order to adapt CSB+-tree to processor architectures as different as Pentium and Itanium. We identify this group of parameters and study how it impacts the performance of CSB+-tree on Itanium 2. Finally, we propose...

  16. Computing Refined Buneman Trees in Cubic Time

    DEFF Research Database (Denmark)

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

    2003-01-01

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

  17. Phosphorus nutrition of mycorrhizal trees.

    Science.gov (United States)

    Plassard, C; Dell, B

    2010-09-01

    Globally, phosphorus (P) limits productivity of trees in many forests and plantations especially in highly weathered, acidic or calcareous profiles. Most trees form mycorrhizal associations which are prevalent in the organic and mineral soil horizons. This review critically examines mechanisms that enhance the acquisition of P by tree roots. Mycorrhizal roots have a greater capacity to take up phosphate (Pi) from the soil solution than non-mycorrhizal root tips. Factors that contribute to this include the extent of extraradical hyphal penetration of soil and the physiology and biochemistry of the fungal/soil and fungal/plant interfaces. Ectomycorrhizal (ECM) trees are likely to benefit from association with basidiomycetes that possess several high-affinity Pi transporters that are expressed in extraradical hyphae and whose expression is enhanced by P deficiency. To understand fully the role of these putative transporters in the symbiosis, data regarding their localization, Pi transport capacities and regulation are required. Some ECM fungi are able to effect release of Pi from insoluble mineral P through excretion of low-molecular-weight organic anions such as oxalate, but the relative contribution of insoluble P dissolution in situ remains to be quantified. How the production of oxalate is regulated by nitrogen remains a key question to be answered. Lastly, phosphatase release from mycorrhizas is likely to play a significant role in the acquisition of Pi from labile organic forms of P (Po). As labile forms of Po can constitute the major fraction of the total P in some tropical and temperate soils, a greater understanding of the forms of Po available to the phosphatases is warranted.

  18. Relationships between stem diameter at breast height (DBH), tree ...

    African Journals Online (AJOL)

    buba

    amount of light that the tree intercepts for photosynthesis. The tree stem size has its own adaptive significance to a tree. It must be strong ... the amount of solar radiation intercepted by a tree. (Tanka, 2006). Stem dbh is also an important tree characteristics and an accurate prediction of tree dimensions. It has become ...

  19. Anatomical modeling of the bronchial tree

    Science.gov (United States)

    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.

  20. Rooted triple consensus and anomalous gene trees

    Directory of Open Access Journals (Sweden)

    Schmidt Heiko A

    2008-04-01

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

  1. Meta-learning in decision tree induction

    CERN Document Server

    Grąbczewski, Krzysztof

    2014-01-01

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

  2. On finding minimum-diameter clique trees

    Energy Technology Data Exchange (ETDEWEB)

    Blair, J.R.S. (Tennessee Univ., Knoxville, TN (United States). Dept. of Computer Science); Peyton, B.W. (Oak Ridge National Lab., TN (United States))

    1991-08-01

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

  3. Inferring rooted species trees from unrooted gene trees using approximate Bayesian computation.

    Science.gov (United States)

    Alanzi, Ayed R A; Degnan, James H

    2017-11-01

    Methods for inferring species trees from gene trees motivated by incomplete lineage sorting typically use either rooted gene trees to infer a rooted species tree, or use unrooted gene trees to infer an unrooted species tree, which is then typically rooted using one or more outgroups. Theoretically, however, it has been known since 2011 that it is possible to consistently infer the root of the species tree directly from unrooted gene trees without assuming an outgroup. Here, we use approximate Bayesian computation to infer the root of the species tree from unrooted gene trees assuming the multispecies coalescent model. It is hoped that this approach will be useful in cases where an appropriate outgroup is difficult to find and gene trees do not follow a molecular clock. We use approximate Bayesian computation to infer the root of the species tree from unrooted gene trees. This approach could also be useful when there is prior information that makes a small number of root locations plausible in an unrooted species tree. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Shu-Chuan Chen

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

  5. Public Reactions to New Street Tree Planting

    Directory of Open Access Journals (Sweden)

    Ruth A. Rae

    2010-01-01

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

  6. Broad-spectrum antiemetic potential of the L-type calcium channel antagonist nifedipine and evidence for its additive antiemetic interaction with the 5-HT(3) receptor antagonist palonosetron in the least shrew (Cryptotis parva).

    Science.gov (United States)

    Darmani, Nissar A; Zhong, Weixia; Chebolu, Seetha; Vaezi, Mariam; Alkam, Tursun

    2014-01-05

    Cisplatin-like chemotherapeutics cause vomiting via release of multiple neurotransmitters (dopamine, serotonin (5-HT), or substance P (SP)) from the gastrointestinal enterochromaffin cells and/or the brainstem via a calcium dependent process. Diverse channels in the plasma membrane allow extracellular Ca(2+) entry into cells for the transmitter release process. Agonists of 5-HT3 receptors increase calcium influx through both 5-HT3 receptors and L-type Ca(2+) channels. We envisaged that L-type calcium agonists such as FPL 64176 should cause vomiting and corresponding antagonists such as nifedipine would behave as broad-spectrum antiemetics. Administration of FPL 64176 did cause vomiting in the least shrew in a dose-dependent fashion. Nifedipine and the 5-HT3 receptor antagonist palonosetron, potently suppressed FPL 64176-induced vomiting, while a combination of ineffective doses of these antagonists was more efficacious. Subsequently, we investigated the broad-spectrum antiemetic potential of nifedipine against diverse emetogens including agonists of serotonergic 5-HT3- (e.g. 5-HT or 2-Me-5-HT), SP tachykinin NK1- (GR73632), dopamine D2- (apomorphine or quinpirole), and cholinergic M1- (McN-A-343) receptors, as well as the non-specific emetogen, cisplatin. Nifedipine by itself suppressed vomiting in a potent and dose-dependent manner caused by the above emetogens except cisplatin. Moreover, low doses of nifedipine potentiated the antiemetic efficacy of non-effective or semi-effective doses of palonosetron against vomiting caused by either 2-Me-5-HT or cisplatin. Thus, our findings demonstrate that activation of L-type calcium channels causes vomiting, whereas blockade of these ion channels by nifedipine-like antagonists not only provides broad-spectrum antiemetic activity but can also potentiate the antiemetic efficacy of well-established antiemetics such as palonosetron. L-type calcium channel antagonists should also provide antiemetic activity against drug

  7. Interaction between non-psychotropic cannabinoids in marihuana: effect of cannabigerol (CBG) on the anti-nausea or anti-emetic effects of cannabidiol (CBD) in rats and shrews.

    Science.gov (United States)

    Rock, Erin M; Goodwin, Jennifer M; Limebeer, Cheryl L; Breuer, Aviva; Pertwee, Roger G; Mechoulam, Raphael; Parker, Linda A

    2011-06-01

    The interaction between two non-psychotropic cannabinoids, cannabidiol (CBD) and cannabigerol (CBG), which have been reported to act as a 5-hydroxytryptamine 1A (5-HT(1A)) agonist and antagonist, respectively, was evaluated. To evaluate the potential of CBG to reverse the anti-nausea, anti-emetic effects of CBD. In experiment 1, rats were pre-treated with CBG (0.0, 1, 5, and 10 mg/kg, ip), 15 min prior to being treated with CBD (experiment 1a: VEH or 5 mg/kg, ip) or 8-OH-DPAT (experiment 1b: VEH or 0.01 mg/kg, ip). Thirty minutes later, all rats received a pairing of 0.1% saccharin solution and LiCl (20 ml/kg of 0.15 M, ip). Seventy-two hours later, the rats received a drug-free taste reactivity test with saccharin to evaluate the effects of the treatments on the establishment of conditioned gaping reactions (a model of nausea). As well, conditioned saccharin avoidance was measured. In experiment 2, Suncus murinus were injected with CBG (5 mg/kg, ip) or VEH 15 min prior to CBD (5 mg/kg) or VEH and 30 min later were injected with LiCl (60 ml/kg of 0.15 M, i.p.), and the number of vomiting episodes were measured. CBD (5 mg/kg) suppressed conditioned gaping in rats and vomiting in shrews, which were reversed by pre-treatment with all doses of CBG. CBG also prevented the anti-nausea effects of 8-OH-DPAT. Interactions between moderate doses of CBG and CBD may oppose one another at the 5-HT(1A) receptor in the regulation of nausea and vomiting.

  8. Bijective Diameters of Gene Tree Parsimony Costs.

    Science.gov (United States)

    Gorecki, Pawel; Eulenstein, Oliver

    2017-08-04

    Synthesizing median trees from a collection of gene trees under the biologically motivated gene tree parsimony (GTP) costs has provided credible species tree estimates. GTP costs are defined for each of the classic evolutionary processes. These costs count the minimum number of events necessary to reconcile the gene tree with the species tree where the leaf-genes are mapped to the leaf-species through a function called labeling. To better understand the synthesis of median trees under these costs there is an increased interest in analyzing their diameters. The diameters of a GTP cost between a gene tree and a species tree are the maximum values of this cost of one or both topologies of the trees involved. We are concerned about the diameters of the GTP costs under bijective labelings. While these diameters are linear time computable for the gene duplication and deep coalescence costs, this has been unknown for the classic gene duplication and loss, and for the loss cost. For the first time, we show how to compute these diameters and proof that this can be achieved in linear time, and thus, completing the computational time analysis for all of the bijective diameters under the GTP costs.

  9. ETE: a python Environment for Tree Exploration.

    Science.gov (United States)

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

    2010-01-13

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

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

    DEFF Research Database (Denmark)

    Li, Heng; Coghlan, Avril; Ruan, Jue

    2006-01-01

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

  11. Helping to increase tree crops

    International Nuclear Information System (INIS)

    1970-01-01

    Tree crops such as coffee, coconuts, palm oil, citrus fruits and cocoa are of major importance to the economies of countries in Africa, Asia and Latin America, and may be a prime source of foreign exchange earnings. The search for ways to improve efficiently the yields of crops like these - now being aided by the Division of Atomic Energy in Food and Agriculture operated jointly with the Food and Agriculture Organization - thus has a clearly defined practical goal. D. Nethsinghe deals here with some of the work. (author)

  12. VC-dimension of univariate decision trees.

    Science.gov (United States)

    Yildiz, Olcay Taner

    2015-02-01

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

  13. Maximum Bounded Rooted-Tree Packing Problem

    OpenAIRE

    Kerivin, Herve; Leblet, Jimmy; Simon, Gwendal; Zhou, Fen

    2011-01-01

    Given a graph and a root, the Maximum Bounded Rooted-Tree Packing (MBRTP) problem aims at finding K rooted-trees that span the largest subset of vertices, when each vertex has a limited outdegree. This problem is motivated by peer-to-peer streaming overlays in under-provisioned systems. We prove that the MBRTP problem is NP-complete. We present two polynomial-time algorithms that computes an optimal solution on complete graphs and trees respectively.

  14. Tank waste remediation system architecture tree; TOPICAL

    International Nuclear Information System (INIS)

    PECK, L.G.

    1999-01-01

    The TWRS Architecture Tree presented in this document is a hierarchical breakdown to support the TWRS systems engineering analysis of the TWRS physical system, including facilities, hardware and software. The purpose for this systems engineering architecture tree is to describe and communicate the system's selected and existing architecture, to provide a common structure to improve the integration of work and resulting products, and to provide a framework as a basis for TWRS Specification Tree development

  15. Dead Trees Bring Life to Forest Critters

    Science.gov (United States)

    Thomas Nicholls; Mike Ostry

    2003-01-01

    What good is a dying or dead tree in a forest? Dead and dying trees don't awe us with their beauty; they just stand or lie there on the forest floor, offering no promise of lumber or other wood products we need. But if we look more closely at such trees, we may see lots of life in them: a raccoon family huddled in a burrow, a downy woodpecker excavating another...

  16. Behavior Trees for UAV Mission Management

    OpenAIRE

    Klöckner, Andreas

    2013-01-01

    Behavior trees are a recent development in artificial intelligence for computer games. Their application has been proposed to increase modularity of an unmanned aerial vehicle's control system. This paper first describes advantages of behavior trees for use in mission management. The paper then points out research towards their deployment. Finally, newly developed transient tasks are introduced to behavior trees. These allow for finite-state-machine-like initialization and interruption of tas...

  17. Tank waste remediation system architecture tree

    International Nuclear Information System (INIS)

    PECK, L.G.

    1999-01-01

    The TWRS Architecture Tree presented in this document is a hierarchical breakdown to support the TWRS systems engineering analysis of the TWRS physical system, including facilities, hardware and software. The purpose for this systems engineering architecture tree is to describe and communicate the system's selected and existing architecture, to provide a common structure to improve the integration of work and resulting products, and to provide a framework as a basis for TWRS Specification Tree development

  18. On Tree-Constrained Matchings and Generalizations

    OpenAIRE

    Canzar, Stefan; Elbassioni, Khaled; Klau, Gunnar W.; Mestre, Julián

    2015-01-01

    htmlabstractWe consider the following \\textsc{Tree-Constrained Bipartite Matching} problem: Given two rooted trees $T_1=(V_1,E_1)$, $T_2=(V_2,E_2)$ and a weight function $w: V_1\\times V_2 \\mapsto \\mathbb{R}_+$, find a maximum weight matching $\\mathcal{M}$ between nodes of the two trees, such that none of the matched nodes is an ancestor of another matched node in either of the trees. This generalization of the classical bipartite matching problem appears, for example, in the computational ana...

  19. On the centroid of increasing trees

    OpenAIRE

    Durant, Kevin; Wagner, Stephan

    2018-01-01

    A centroid node in a tree is a node for which the sum of the distances to all other nodes attains its minimum, or equivalently a node with the property that none of its branches contains more than half of the other nodes. We generalise some known results regarding the behaviour of centroid nodes in random recursive trees (due to Moon) to the class of very simple increasing trees, which also includes the families of plane-oriented and $d$-ary increasing trees. In particular, we derive limits o...

  20. Vessel tree extraction using locally optimal paths

    DEFF Research Database (Denmark)

    Lo, Pechin Chien Pau; van Ginneken, Bram; de Bruijne, Marleen

    2010-01-01

    This paper proposes a method to extract vessel trees by continually extending detected branches with locally optimal paths. Our approach uses a cost function from a multi scale vessel enhancement filter. Optimal paths are selected based on rules that take into account the geometric characteristics...... of the vessel tree. Experiments were performed on 10 low dose chest CT scans for which the pulmonary vessel trees were extracted. The proposed method is shown to extract a better connected vessel tree and extract more of the small peripheral vessels in comparison to applying a threshold on the output...

  1. Computer aided fault tree synthesis

    International Nuclear Information System (INIS)

    Poucet, A.

    1983-01-01

    Nuclear as well as non-nuclear organisations are showing during the past few years a growing interest in the field of reliability analysis. This urges for the development of powerful, state of the art methods and computer codes for performing such analysis on complex systems. In this report an interactive, computer aided approach is discussed, based on the well known fault tree technique. The time consuming and difficut task of manually constructing a system model (one or more fault trees) is replaced by an efficient interactive procedure in which the flexibility and the learning process inherent to the manual approach are combined with the accuracy in the modelling and the speed of the fully automatical approach. The method presented is based upon the use of a library containing component models. The possibility of setting up a standard library of models of general use and the link with a data collection system are discussed. The method has been implemented in the CAFTS-SALP software package which is described shortly in the report

  2. Tree asymmetry--a sensitive and practical measure for binary topological trees.

    Science.gov (United States)

    Van Pelt, J; Uylings, H B; Verwer, R W; Pentney, R J; Woldenberg, M J

    1992-09-01

    The topological structure of a binary tree is characterized by a measure called tree asymmetry, defined as the mean value of the asymmetry of its partitions. The statistical properties of this tree-asymmetry measure have been studied using a growth model for binary trees. The tree-asymmetry measure appears to be sensitive for topological differences and the tree-asymmetry expectation for the growth model that we used appears to be almost independent of the size of the trees. These properties and the simple definition make the measure suitable for practical use, for instance for characterizing, comparing and interpreting sets of branching patterns. Examples are given of the analysis of three sets of neuronal branching patterns. It is shown that the variance in tree-asymmetry values for these observed branching patterns corresponds perfectly with the variance predicted by the used growth model.

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

    NARCIS (Netherlands)

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

    2011-01-01

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

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

    Science.gov (United States)

    Mai, Uyen; Sayyari, Erfan; Mirarab, Siavash

    2017-01-01

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

  5. Evaluating a non-destructive method for calibrating tree biomass equations derived from tree branching architecture

    NARCIS (Netherlands)

    MacFarlane, D.W.; Kuyah, S.; Mulia, R.; Dietz, J.; Muthuri, C.; Noordwijk, van M.

    2014-01-01

    Functional branch analysis (FBA) is a promising non-destructive alternative to the standard destructive method of tree biomass equation development. In FBA, a theoretical model of tree branching architecture is calibrated with measurements of tree stems and branches to estimate the coefficients of

  6. The history of Newton's apple tree

    Science.gov (United States)

    Keesing, R. G.

    1998-05-01

    This article contains a brief introduction to Newton's early life to put into context the subsequent events in this narrative. It is followed by a summary of accounts of Newton's famous story of his discovery of universal gravitation which was occasioned by the fall of an apple in the year 1665/6. Evidence of Newton's friendship with a prosperous Yorkshire family who planted an apple tree arbour in the early years of the eighteenth century to celebrate his discovery is presented. A considerable amount of new and unpublished pictorial and documentary material is included relating to a particular apple tree which grew in the garden of Woolsthorpe Manor (Newton's birthplace) and which blew down in a storm before the year 1816. Evidence is then presented which describes how this tree was chosen to be the focus of Newton's account. Details of the propagation of the apple tree growing in the garden at Woolsthorpe in the early part of the last century are then discussed, and the results of a dendrochronological study of two of these trees is presented. It is then pointed out that there is considerable evidence to show that the apple tree presently growing at Woolsthorpe and known as 'Newton's apple tree' is in fact the same specimen which was identified in the middle of the eighteenth century and which may now be 350 years old. In conclusion early results from a radiocarbon dating study being carried out at the University of Oxford on core samples from the Woolsthorpe tree lend support to the contention that the present tree is one and the same as that identified as Newton's apple tree more than 200 years ago. Very recently genetic fingerprinting techniques have been used in an attempt to identify from which sources the various 'Newton apple trees' planted throughout the world originate. The tentative result of this work suggests that there are two separate varieties of apple tree in existence which have been accepted as 'the tree'. One may conclude that at least some of

  7. DATING OF LATE PLEISTOCENE TREE-RING SERIES FROM JAPAN

    NARCIS (Netherlands)

    van der Plicht, J.; Imamura, M.; Sakamoto, M.; Boaretto, E.; Rebollo Franco, N.R.

    2012-01-01

    We have radiocarbon dated series of tree rings from 2 fossil trees (named ND-113 and the Fuji tree) buried in fossil volcanic avalanche deposits in Japan. They are dendrochronologically floating, dating beyond the tree-ring part of the C-14 calibration curve. The trees show about 350 and 400 annual

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-07-31

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

  9. Genealogical Trees of Scientific Papers.

    Science.gov (United States)

    Waumans, Michaël Charles; Bersini, Hugues

    2016-01-01

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

  10. Tree and nontree multiparticle amplitudes

    International Nuclear Information System (INIS)

    Goldberg, H.; Vaughn, M.T.

    1991-01-01

    We examine the behavior of the connected n-point function in a zero-dimensional scalar theory (scrL=-1/2m 2 φ 2 -1/4λφ 4 ). The problematic n exclamation point(√λ ) n behavior for large n, previously found for tree graphs in scalar field theory, is again obtained in saddle-point approximation in this model. However, a similar behavior, n exclamation point[f(λ)] n , persists in the full theory, where f∼ √λ for λ→0, f∼λ -1/4 for λ much-gt 1. This behavior can be traced to the existence of zeros in the complex J plane of the generating functional Z(J), which in turn is controlled by the asymptotic behavior in |J| of Z(J) calculated in saddle-point approximation. The application of these results to field theory is discussed

  11. A coinductive calculus of binary trees

    NARCIS (Netherlands)

    A.M. Silva (Alexandra); J.J.M.M. Rutten (Jan)

    2007-01-01

    htmlabstractWe study the set T_A of infinite binary trees with nodes labelled in a semiring A from a coalgebraic perspective. We present coinductive definition and proof principles based on the fact that T_A carries a final coalgebra structure. By viewing trees as formal power series, we develop a

  12. Efficient Computation of Popular Phylogenetic Tree Measures

    DEFF Research Database (Denmark)

    Tsirogiannis, Constantinos; Sandel, Brody Steven; Cheliotis, Dimitris

    2012-01-01

    Given a phylogenetic tree $\\mathcal{T}$ of n nodes, and a sample R of its tips (leaf nodes) a very common problem in ecological and evolutionary research is to evaluate a distance measure for the elements in R. Two of the most common measures of this kind are the Mean Pairwise Distance ($\\ensurem...... software package for processing phylogenetic trees....

  13. Sprouting of dormant buds on border trees

    Science.gov (United States)

    G.R., Jr. Trimble; H. Clay Smith; H. Clay Smith

    1970-01-01

    As part of an evaluation of silvicultura1 systems used in managing Appalachian hardwoods, we are studying degrade of border trees surrounding harvest-cut openings made in the patch cutting and group selection systems. One facet of this research dealt with determining what portion of visually evident dormant buds on border tree boles sprouted when the openings were cut...

  14. Do Trees Tell About the Past?

    Indian Academy of Sciences (India)

    Tree, chronos = time, logos = study. .... The heart- wood in many species has different colors and hues. The ratio of sapwood to heartwood varies across species. Some of the climate change models that use tree physiology for .... The principle of limiting factors states that the rate of plant process constrained by the primary.

  15. Structure, composition, and condition of overstory trees

    Science.gov (United States)

    Daniel A. Yaussy; Todd F. Hutchinson; Elaine Kennedy Sutherland

    2003-01-01

    The structure, composition, and condition of overstory trees in the four study areas prior to prescribed fire treatments are summarized. Stand initiation dates were similar among the study areas (ca. 1885), and coincided with the decline of the charcoal iron industry in southern Ohio. Tree basal area averaged 26.8m²/ha and was not significantly different among...

  16. Market-based approaches to tree valuation

    Science.gov (United States)

    Geoffrey H. Donovan; David T. Butry

    2008-01-01

    A recent four-part series in Arborist News outlined different appraisal processes used to value urban trees. The final article in the series described the three generally accepted approaches to tree valuation: the sales comparison approach, the cost approach, and the income capitalization approach. The author, D. Logan Nelson, noted that the sales comparison approach...

  17. Navigation and Tree Mapping in Orchards

    DEFF Research Database (Denmark)

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

    . The average accuracy for the center point estimation is 0.2 m in the along track direction and 0.35 m in the across track direction. The goal of the tree mapping algorithm is create a database of individual trees, and be the basis for creation of a graph map that can be used for mission planning...

  18. A Fuzzy Neural Tree for Possibilistic Reliability

    NARCIS (Netherlands)

    Ciftcioglu, O.

    2008-01-01

    An innovative neural fuzzy system is considered for possibilistic reliability using a neural tree structure with nodes of neuronal type. The total tree structure works effectively as a fuzzy logic system where the possibility theory plays important role with Gaussian possibility distribution at the

  19. The "Ride for Russia" Tree Lichen Survey

    Science.gov (United States)

    Young, Simon

    2013-01-01

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

  20. The production of homozygous tree material

    Science.gov (United States)

    Reinhard F. Stettler; George E. Howe

    1966-01-01

    Homozygous trees will never be the desired ultimate step in a forest tree improvement program. However, they will serve many purposes in forest genetics research: (1) in the detection of genetic markers; (2) in the isolation of traits under simple genetic control for the study of growth and differentiation phenomena; (3) as a tool as well as reference material in the...

  1. Induced chemical defences in Colophospermum mopane trees ...

    African Journals Online (AJOL)

    A field experiment was conducted in which Mopane (Colophospermum mopane) trees were subjected to three different canopy treatments:felling of trees at a mean height of 0.7m above ground level, felling at a height of 2m, or pruning of selected branches. These treatments were intended to simulate wood harvesting by ...

  2. Binary trees equipped with semivaluations | Pajoohesh ...

    African Journals Online (AJOL)

    Our interest in this lattice stems from its application to binary decision trees. Binary decision trees form a crucial tool for algorithmic time analysis. The lattice properties of Tn are studied and we show that every Tn has a sublattice isomorphic to Tn-1 and prove that Tn is generated by Tn-1. Also we show that the distance from ...

  3. Structure of an urban Christmas tree market

    Science.gov (United States)

    Thomas H. Pendleton; Lawrence D. Garrett; Lawrence D. Garrett

    1973-01-01

    The retail Christmas tree market in Winston-Salem, N.C., was studied 3 years. Types of retailers and their sales are described. Best sales were made by dealers who had lots on heavily traveled streets in business districts, had ample parking facilities, advertised, and displayed their trees well.

  4. Elimination of Constraints from Feature Trees

    NARCIS (Netherlands)

    van den Broek, P.M.; Galvao, I.; Noppen, J.A.R.

    2008-01-01

    We present an algorithm which eliminates constraints from a feature model whose feature diagram is a tree and whose constraints are "requires" or "excludes" constraints. The algorithm constructs a feature tree which has the same semantics as the original feature model. The computational complexity

  5. Understanding search trees via statistical physics

    Indian Academy of Sciences (India)

    Abstract. We study the random m-ary search tree model (where m stands for the number of branches of the search tree), an important problem for data storage in computer science, using a variety of statistical physics techniques that allow us to obtain exact asymptotic results. In particular, we show that the probability ...

  6. Demography of threatened tree species in Vietnam

    NARCIS (Netherlands)

    Chien, P.D.

    2006-01-01

    Demography of threatened tree species in Vietnam (Summary for the library) Effective conservation of threatened tree species requires information on natural dynamics and future prospects of populations of these species. Such information can be obtained from demographic studies. We investigated the

  7. Exploring connections between trees and human health

    Science.gov (United States)

    Geoffrey Donovan; Marie. Oliver

    2014-01-01

    Humans have intuitively understood the value of trees to their physical and mental health since the beginning of recorded time. A scientist with the Pacific Northwest Research Station wondered if such a link could be scientifically validated. His research team took advantage of an infestation of emerald ash borer, an invasive pest that kills ash trees, to conduct a...

  8. Naive Fault Tree : formulation of the approach

    NARCIS (Netherlands)

    Rajabalinejad, M

    2017-01-01

    Naive Fault Tree (NFT) accepts a single value or a range of values for each basic event and returns values for the top event. This accommodates the need of commonly used Fault Trees (FT) for precise data making them prone to data concerns and limiting their area of application. This paper extends

  9. Language distance and tree reconstruction

    International Nuclear Information System (INIS)

    Petroni, Filippo; Serva, Maurizio

    2008-01-01

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

  10. Language distance and tree reconstruction

    Science.gov (United States)

    Petroni, Filippo; Serva, Maurizio

    2008-08-01

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

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

    Science.gov (United States)

    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.

  12. Tree growth studies on uranium mill tailings

    International Nuclear Information System (INIS)

    Murray, D.R.; Turcotte, M.

    1982-01-01

    Coniferous trees planted in 1974 and deciduous species that have volunteered since 1970 on uranium mill tailings that had been stabilized to varying degrees using limestone and vegetation were evaluated. Their survival and growth rates were compared with those from other investigations. Competition for light appears to be a major contributor to mortality. Differences in soil moisture conditions under a tree stand as compared to those under a grass sward are potentially significant enough to affect the tailings hydrology and effluent contamination. Recommendations include planting seeds of deciduous species or deciduous and coniferous seedlings on strips of freshly disturbed tailings. The disturbed strips would provide reduced competition for the initial year and assist in tree survival. The planting of block stands of coniferous or deciduous trees would be useful for evaluating the hydrological impact of the trees as compared to the present grass sward

  13. Big data of tree species distributions

    DEFF Research Database (Denmark)

    Serra-Diaz, Josep M.; Enquist, Brian J.; Maitner, Brian

    2018-01-01

    are currently available in big databases, several challenges hamper their use, notably geolocation problems and taxonomic uncertainty. Further, we lack a complete picture of the data coverage and quality assessment for open/public databases of tree occurrences. Methods: We combined data from five major......Background: Trees play crucial roles in the biosphere and societies worldwide, with a total of 60,065 tree species currently identified. Increasingly, a large amount of data on tree species occurrences is being generated worldwide: from inventories to pressed plants. While many of these data...... aggregators of occurrence data (e.g. Global Biodiversity Information Facility, Botanical Information and Ecological Network v.3, DRYFLOR, RAINBIO and Atlas of Living Australia) by creating a workflow to integrate, assess and control data quality of tree species occurrences for species distribution modeling...

  14. Success tree method of resources evaluation

    International Nuclear Information System (INIS)

    Chen Qinglan; Sun Wenpeng

    1994-01-01

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

  15. Timing-Driven-Testable Convergent Tree Adders

    Directory of Open Access Journals (Sweden)

    Johnnie A. Huang

    2002-01-01

    Full Text Available Carry lookahead adders have been, over the years, implemented in complex arithmetic units due to their regular structure which leads to efficient VLSI implementation for fast adders. In this paper, timing-driven testability synthesis is first performed on a tree adder. It is shown that the structure of the tree adder provides for a high fanout with an imbalanced tree structure, which likely contributes to a racing effect and increases the delay of the circuit. The timing optimization is then realized by reducing the maximum fanout of the adder and by balancing the tree circuit. For a 56-b testable tree adder, the optimization produces a 6.37%increase in speed of the critical path while only contributing a 2.16% area overhead. The full testability of the circuit is achieved in the optimized adder design.

  16. Interactive wood combustion for botanical tree models

    KAUST Repository

    Pirk, Sören

    2017-11-22

    We present a novel method for the combustion of botanical tree models. Tree models are represented as connected particles for the branching structure and a polygonal surface mesh for the combustion. Each particle stores biological and physical attributes that drive the kinetic behavior of a plant and the exothermic reaction of the combustion. Coupled with realistic physics for rods, the particles enable dynamic branch motions. We model material properties, such as moisture and charring behavior, and associate them with individual particles. The combustion is efficiently processed in the surface domain of the tree model on a polygonal mesh. A user can dynamically interact with the model by initiating fires and by inducing stress on branches. The flames realistically propagate through the tree model by consuming the available resources. Our method runs at interactive rates and supports multiple tree instances in parallel. We demonstrate the effectiveness of our approach through numerous examples and evaluate its plausibility against the combustion of real wood samples.

  17. Representing Boolean Functions by Decision Trees

    KAUST Repository

    Chikalov, Igor

    2011-01-01

    A Boolean or discrete function can be represented by a decision tree. A compact form of decision tree named binary decision diagram or branching program is widely known in logic design [2, 40]. This representation is equivalent to other forms, and in some cases it is more compact than values table or even the formula [44]. Representing a function in the form of decision tree allows applying graph algorithms for various transformations [10]. Decision trees and branching programs are used for effective hardware [15] and software [5] implementation of functions. For the implementation to be effective, the function representation should have minimal time and space complexity. The average depth of decision tree characterizes the expected computing time, and the number of nodes in branching program characterizes the number of functional elements required for implementation. Often these two criteria are incompatible, i.e. there is no solution that is optimal on both time and space complexity. © Springer-Verlag Berlin Heidelberg 2011.

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

    Science.gov (United States)

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

    2018-04-06

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

  19. Cache-Oblivious Search Trees via Binary Trees of Small Height

    DEFF Research Database (Denmark)

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

    2002-01-01

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

  20. An efficient and extensible approach for compressing phylogenetic trees

    KAUST Repository

    Matthews, Suzanne J

    2011-01-01

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

  1. Tree decline and the future of Australian farmland biodiversity

    OpenAIRE

    Fischer, Joern; Zerger, Andre; Gibbons, Phil; Stott, Jenny; Law, Bradley S.

    2010-01-01

    Farmland biodiversity is greatly enhanced by the presence of trees. However, farmland trees are declining worldwide, including in North America, Central America, and parts of southern Europe. We show that tree decline and its likely consequences are particularly severe in Australia's temperate agricultural zone, which is a threatened ecoregion. Using field data on trees, remotely sensed imagery, and a demographic model for trees, we predict that by 2100, the number of trees on an average farm...

  2. Cafts: computer aided fault tree analysis

    International Nuclear Information System (INIS)

    Poucet, A.

    1985-01-01

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

  3. A biophysical analysis of latitudinal tree line

    Science.gov (United States)

    Goetz, S. J.; Loranty, M. M.; Berner, L.; Jin, Y.; Randerson, J. T.

    2011-12-01

    Northern latitudinal tree line represents the interface between boreal forests and tundra ecosystems, and is the ecophysiological limit of tree recruitment and persistence. The transition between tundra and forest is typically gradual, occurring over tens to hundreds of kilometers. This gradient represents a substantial change in the biophysical properties of the earth surface, one that is particularly important in ecosystems that are snow covered for much of the year. Tree line is, however, commonly delineated by the point of the northern most tree, with no gradient between forested and non-forested ecosystems. As a consequence crisp delineations of tree line incorporated into models introduce error in surface radiation budgets due to inaccurate albedo representations. Errors in modeled carbon and water fluxes are likely as well. Here we use satellite observations to quantify several key biophysical properties across latitudinal tree line for a series of sites throughout the pan-boreal region We find decreases in NDVI and increases in albedo across the transition from boreal forest to tundra, as expected. However, in the absence of topographical barriers we find that these transitions can occur over upwards of 100 km, and that biophysical properties characteristic of tundra ecosystems can occur as far as 100 km south of tree line. This suggests that land surface models likely overestimate surface radiation budgets and carbon fluxes in the boreal biome. We discuss our results in the context of land surface models, noting specific examples from archived model runs.

  4. Atmospheric carbon reduction by urban trees

    International Nuclear Information System (INIS)

    Nowak, D.J.

    1993-01-01

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

  5. Reconciliation of Gene and Species Trees

    Directory of Open Access Journals (Sweden)

    L. Y. Rusin

    2014-01-01

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

  6. Nodal distances for rooted phylogenetic trees.

    Science.gov (United States)

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

    2010-08-01

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

  7. National assessment of Tree City USA participation

    Science.gov (United States)

    Tree City USA is a national program that recognizes municipal commitment to community forestry. In return for meeting program requirements, Tree City USA participants expect social, economic, and/or environmental benefits. Understanding the geographic distribution and socioeconomic characteristics of Tree City USA communities at the national scale can offer insights into the motivations or barriers to program participation, and provide context for community forestry research at finer scales. In this study, researchers assessed patterns in Tree City USA participation for all U.S. communities with more than 2,500 people according to geography, community population size, and socioeconomic characteristics, such as income, education, and race. Nationally, 23.5% of communities studied were Tree City USA participants, and this accounted for 53.9% of the total population in these communities. Tree City USA participation rates varied substantially by U.S. region, but in each region participation rates were higher in larger communities, and long-term participants tended to be larger communities than more recent enrollees. In logistic regression models, owner occupancy rates were significant negative predictors of Tree City USA participation, education and percent white population were positive predictors in many U.S. regions, and inconsistent patterns were observed for income and population age. The findings indicate that communities with smaller populations, lower educat

  8. Topological and categorical properties of binary trees

    Directory of Open Access Journals (Sweden)

    H. Pajoohesh

    2008-04-01

    Full Text Available Binary trees are very useful tools in computer science for estimating the running time of so-called comparison based algorithms, algorithms in which every action is ultimately based on a prior comparison between two elements. For two given algorithms A and B where the decision tree of A is more balanced than that of B, it is known that the average and worst case times of A will be better than those of B, i.e., ₸A(n ≤₸B(n and TWA (n≤TWB (n. Thus the most balanced and the most imbalanced binary trees play a main role. Here we consider them as semilattices and characterize the most balanced and the most imbalanced binary trees by topological and categorical properties. Also we define the composition of binary trees as a commutative binary operation, *, such that for binary trees A and B, A * B is the binary tree obtained by attaching a copy of B to any leaf of A. We show that (T,* is a commutative po-monoid and investigate its properties.

  9. Evaluation of larch trees (Larix Mill., Pinaceae

    Directory of Open Access Journals (Sweden)

    Firsov Gennadii

    2016-12-01

    Full Text Available Peter the Great Botanical Garden of the Komarov Boranical Institute has 148 larch samples (Larix Mill., Pinaceae which represent 22 taxa. They are long-lived large trees, up to 200 years of age, representing the base for a forest stand of an arboretum and forming alleys in the oldest regular part of the Garden. The tallest trees reach 31,6 m (L. dahurica and 113 cm in diameter (L. decidua and L. dahurica. Due to the warming in the St. Petersburg area, there is a noticeable drying found on the trees' crowns. Based on the results of an inventory in 2015, 43 trees can be assigned to the first category; the other 105 trees suffer from drying of shoots, twigs and branches. The degree of drying corresponds with the age of trees. One of the possible reasons of the deterioration in the conditions of larch trees at the arboretum of the Komarov Botanical Institute may be the influence of the Phytophthora species. Soil research samples show presence of Phytophthora syringae (Berk. Kleb. in the risosphere of L. decidua. It is the first time, this species of Phytophthora has been discovered at the Peter the Great Botanical Garden.

  10. Urban tree effects on soil organic carbon.

    Directory of Open Access Journals (Sweden)

    Jill L Edmondson

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

  11. The Importance of Tree Height in Estimating Individual Tree Biomass While Considering Errors in Measurements and Allometric Models

    OpenAIRE

    Phalla, Thuch; Ota, Tetsuji; Mizoue, Nobuya; Kajisa, Tsuyoshi; Yoshida, Shigejiro; Vuthy, Ma; Heng, Sokh

    2018-01-01

    This study evaluated the uncertainty of individual tree biomass estimated by allometric models by both including and excluding tree height independently. Using two independent sets of measurements on the same trees, the errors in the measurement of diameter at breast height and tree height were quantified, and the uncertainty of individual tree biomass estimation caused by errors in measurement was calculated. For both allometric models, the uncertainties of the individual tree biomass estima...

  12. Comprehensive decision tree models in bioinformatics.

    Science.gov (United States)

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

    2012-01-01

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

  13. Comprehensive decision tree models in bioinformatics.

    Directory of Open Access Journals (Sweden)

    Gregor Stiglic

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

  14. Fruit load governs transpiration of olive trees.

    Science.gov (United States)

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

    2016-03-01

    We tested the hypothesis that whole-tree water consumption of olives (Olea europaea L.) is fruit load-dependent and investigated the driving physiological mechanisms. Fruit load was manipulated in mature olives grown in weighing-drainage lysimeters. Fruit was thinned or entirely removed from trees at three separate stages of growth: early, mid and late in the season. Tree-scale transpiration, calculated from lysimeter water balance, was found to be a function of fruit load, canopy size and weather conditions. Fruit removal caused an immediate decline in water consumption, measured as whole-plant transpiration normalized to tree size, which persisted until the end of the season. The later the execution of fruit removal, the greater was the response. The amount of water transpired by a fruit-loaded tree was found to be roughly 30% greater than that of an equivalent low- or nonyielding tree. The tree-scale response to fruit was reflected in stem water potential but was not mirrored in leaf-scale physiological measurements of stomatal conductance or photosynthesis. Trees with low or no fruit load had higher vegetative growth rates. However, no significant difference was observed in the overall aboveground dry biomass among groups, when fruit was included. This case, where carbon sources and sinks were both not limiting, suggests that the role of fruit on water consumption involves signaling and alterations in hydraulic properties of vascular tissues and tree organs. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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

    Science.gov (United States)

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

    2015-09-01

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

  16. Mechanical stimuli regulate the allocation of biomass in trees: demonstration with young Prunus avium trees.

    Science.gov (United States)

    Coutand, Catherine; Dupraz, Christian; Jaouen, Gaëlle; Ploquin, Stéphane; Adam, Boris

    2008-06-01

    Plastic tree-shelters are increasingly used to protect tree seedlings against browsing animals and herbicide drifts. The biomass allocation in young seedlings of deciduous trees is highly disturbed by common plastic tree-shelters, resulting in poor root systems and reduced diameter growth of the trunk. The shelters have been improved by creating chimney-effect ventilation with holes drilled at the bottom, resulting in stimulated trunk diameter growth, but the root deficit has remained unchanged. An experiment was set up to elucidate the mechanisms behind the poor root growth of sheltered Prunus avium trees. Tree seedlings were grown either in natural windy conditions or in tree-shelters. Mechanical wind stimuli were suppressed in ten unsheltered trees by staking. Mechanical stimuli (bending) of the stem were applied in ten sheltered trees using an original mechanical device. Sheltered trees suffered from poor root growth, but sheltered bent trees largely recovered, showing that mechano-sensing is an important mechanism governing C allocation and the shoot-root balance. The use of a few artificial mechanical stimuli increased the biomass allocation towards the roots, as did natural wind sway. It was demonstrated that there was an acclimation of plants to the imposed strain. This study suggests that if mechanical stimuli are used to control plant growth, they should be applied at low frequency in order to be most effective. The impact on the functional equilibrium hypothesis that is used in many tree growth models is discussed. The consequence of the lack of mechanical stimuli should be incorporated in tree growth models when applied to environments protected from the wind (e.g. greenhouses, dense forests).

  17. Lateglacial environmental variability from Swiss tree rings

    DEFF Research Database (Denmark)

    Schaub, Matthias; Büntgen, Ulf; Kaiser, Klaus Felix

    2008-01-01

    Evidence of annually resolved environmental variations during the Allerød interstadial is presented using 81 fossil Scots pine tree-ring series from Gaenziloo and Landikon, near Zurich, Switzerland. The absolute age of the trees ranges between 11,920 and 10,610 14C BP, which was determined...... by wiggle-matching radiocarbon ages to the Cariaco 14C data set. From the two sites we created a composite floating Allerød chronology on the basis of their 632 years of overlap (r = 0.57), after individual spline detrending. Merging both data sets resulted in a Lateglacial tree-ring chronology covering...

  18. Fault tree analysis for vital area identification

    International Nuclear Information System (INIS)

    Varnado, G.B.; Ortiz, N.R.

    1978-01-01

    This paper discusses the use of fault tree analysis to identify those areas of nuclear fuel cycle facilities which must be protected to prevent acts of sabotage that could lead to sifnificant release of radioactive material. By proper manipulation of the fault trees for a plant, an analyst can identify vital areas in a manner consistent with regulatory definitions. This paper discusses the general procedures used in the analysis of any nuclear facility. In addition, a structured, generic approach to the development of the fault trees for nuclear power reactors is presented along with selected results of the application of the generic approach to several plants

  19. Algorithms for optimal dyadic decision trees

    Energy Technology Data Exchange (ETDEWEB)

    Hush, Don [Los Alamos National Laboratory; Porter, Reid [Los Alamos National Laboratory

    2009-01-01

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

  20. {sup 137}Cs distribution in guava trees

    Energy Technology Data Exchange (ETDEWEB)

    Mosquera, B.; Veiga, R.; Mangia, L.; Carvalho, C.; Estellita, L.; Uzeda, D.; Facure, A.; Violini, B.; Anjos, R.M. [Universidade Federal Fluminense, Niteroi, RJ (Brazil). Inst. de Fisica

    2004-09-15

    This paper presents results of {sup 137}Cs concentration measured from a guava tree cultivated after the first decontamination work of one of the sites where the worst Brazilian radiological accident occurred. The present work aims to verify how the {sup 137}Cs is transported and distributed along the tropical trees. Bi-dimensional analyses of the radial distribution of {sup 137}Cs in the main trunk are also presented. Neither symmetrical nor homogeneous behaviors of the specific activity distribution in the tree rings were observed. (author)