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Sample records for tupaia tree shrew

  1. Tree shrew (Tupaia belangeri as a novel laboratory disease animal model

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    Ji Xiao

    2017-05-01

    Full Text Available The tree shrew (Tupaia belangeri is a promising laboratory animal that possesses a closer genetic relationship to primates than to rodents. In addition, advantages such as small size, easy breeding, and rapid reproduction make the tree shrew an ideal subject for the study of human disease. Numerous tree shrew disease models have been generated in biological and medical studies in recent years. Here we summarize current tree shrew disease models, including models of infectious diseases, cancers, depressive disorders, drug addiction, myopia, metabolic diseases, and immune-related diseases. With the success of tree shrew transgenic technology, this species will be increasingly used in biological and medical studies in the future.

  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. Architectonic subdivisions of neocortex in the tree shrew (Tupaia belangeri)

    OpenAIRE

    Wong, Peiyan; Kaas, Jon H.

    2009-01-01

    Tree shrews are small mammals that bear some semblance to squirrels, but are actually close relatives of primates. Thus, they have been extensively studied as a model for the early stages of primate evolution. In the present study, subdivisions of cortex were reconstructed from brain sections cut in the coronal, sagittal or horizontal planes, and processed for parvalbumin (PV), SMI-32 immunopositive neurofilament protein epitopes, vesicle glutamate transporter 2 (VGluT2), free ionic zinc, mye...

  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. Identification of the full-length β-actin sequence and expression profiles in the tree shrew (Tupaia belangeri).

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

    2015-02-01

    The tree shrew (Tupaia belangeri) diverges from the primate order (Primates) and is classified as a separate taxonomic group of mammals - Scandentia. It has been suggested that the tree shrew can be used as an animal model for studying human diseases; however, the genomic sequence of the tree shrew is largely unidentified. In the present study, we reported the full-length cDNA sequence of the housekeeping gene, β-actin, in the tree shrew. The amino acid sequence of β-actin in the tree shrew was compared to that of humans and other species; a simple phylogenetic relationship was discovered. Quantitative polymerase chain reaction (qPCR) and western blot analysis further demonstrated that the expression profiles of β-actin, as a general conservative housekeeping gene, in the tree shrew were similar to those in humans, although the expression levels varied among different types of tissue in the tree shrew. Our data provide evidence that the tree shrew has a close phylogenetic association with humans. These findings further enhance the potential that the tree shrew, as a species, may be used as an animal model for studying human disorders.

  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).

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    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. Aspects of masticatory form and function in common tree shrews, Tupaia glis.

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    Fish, D R

    1983-04-01

    Tree shrews have relatively primitive tribosphenic molars that are apparently similar to those of basal eutherians; thus, these animals have been used as a model to describe mastication in early mammals. In this study the gross morphology of the bony skull, joints, dentition, and muscles of mastication are related to potential jaw movements and cuspal relationships. Potential for complex mandibular movements is indicated by a mobile mandibular symphysis, shallow mandibular fossa that is large compared to its resident condyle, and relatively loose temporomandibular joint ligaments. Abrasive tooth wear is noticeable, and is most marked at the first molars and buccal aspects of the upper cheek teeth distal to P2. Muscle morphology is basically similar to that previously described for Tupaia minor and Ptilocercus lowii. However, in T. glis, an intraorbital part of deep temporalis has the potential for inducing lingual translation of its dentary, and the large medial pterygoid has extended its origin anteriorly to the floor of the orbit, which would enhance protrusion. The importance of the tongue and hyoid muscles during mastication is suggested by broadly expanded anterior bellies of digastrics, which may assist mylohyoids in tensing the floor of the mouth during forceful tongue actions, and by preliminary electromyography, which suggests that masticatory muscles alone cannot fully account for jaw movements in this species.

  10. Identification and characterization of toll-like receptors (TLRs) in the Chinese tree shrew (Tupaia belangeri chinensis).

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    Yu, Dandan; Wu, Yong; Xu, Ling; Fan, Yu; Peng, Li; Xu, Min; Yao, Yong-Gang

    2016-07-01

    In mammals, the toll-like receptors (TLRs) play a major role in initiating innate immune responses against pathogens. Comparison of the TLRs in different mammals may help in understanding the TLR-mediated responses and developing of animal models and efficient therapeutic measures for infectious diseases. The Chinese tree shrew (Tupaia belangeri chinensis), a small mammal with a close relationship to primates, is a viable experimental animal for studying viral and bacterial infections. In this study, we characterized the TLRs genes (tTLRs) in the Chinese tree shrew and identified 13 putative TLRs, which are orthologs of mammalian TLR1-TLR9 and TLR11-TLR13, and TLR10 was a pseudogene in tree shrew. Positive selection analyses using the Maximum likelihood (ML) method showed that tTLR8 and tTLR9 were under positive selection, which might be associated with the adaptation to the pathogen challenge. The mRNA expression levels of tTLRs presented an overall low and tissue-specific pattern, and were significantly upregulated upon Hepatitis C virus (HCV) infection. tTLR4 and tTLR9 underwent alternative splicing, which leads to different transcripts. Phylogenetic analysis and TLR structure prediction indicated that tTLRs were evolutionarily conserved, which might reflect an ancient mechanism and structure in the innate immune response system. Taken together, TLRs had both conserved and unique features in the Chinese tree shrew. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

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    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

  12. 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)

  13. 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.

  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. Preservation of hippocampal neuron numbers and hippocampal subfield volumes in behaviorally characterized aged tree shrews

    NARCIS (Netherlands)

    Keuker, J.I.H.; de Biurrun, G.; Luiten, P.G.M.; Fuchs, E.

    2004-01-01

    Aging is associated with a decreased ability to store and retrieve information. The hippocampal formation plays a critical role in such memory processes, and its integrity is affected during normal aging. We used tree shrews (Tupaia belangeri) as an animal model of aging, because in many

  18. Identification and Characterization of Liver MicroRNAs of the Chinese Tree Shrew via Deep Sequencing.

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    Feng, Yue; Feng, Yue-Mei; Feng, Yang; Lu, Caixia; Liu, Li; Sun, Xiaomei; Dai, Jiejie; Xia, Xueshan

    2015-10-01

    Chinese tree shrew (Tupaia belangeri chinensis) is a small animal that possess many features, which are valuable in biomedical research, as experimental models. Currently, there are numerous attempts to utilize tree shrews as models for hepatitis C virus (HCV) infection. This study aimed to construct a liver microRNA (miRNA) data of the tree shrew. Three second filial generation tree shrews were used in this study. Total RNA was extracted from each liver of the tree shrew and equal quality mixed, then reverse-transcribed to complementary DNA (cDNA). The cDNAs were amplified by polymerase chain reaction and subjected to high-throughput sequencing. A total of 2060 conserved miRNAs were identified through alignment with the mature miRNAs in miRBase 20.0 database. The gene ontology and Kyoto encyclopedia of genes and genomes analyses of the target genes of the miRNAs revealed several candidate miRNAs, genes and pathways that may involve in the process of HCV infection. The abundance of miR-122 and Let-7 families and their other characteristics provided us more evidences for the utilization of this animal, as a potential model for HCV infection and other related biomedical research. Moreover, 80 novel microRNAs were predicted using the software Mireap. The top 3 abundant miRNAs were validated in other tree samples, based on stem-loop quantitative reverse transcription-polymerase chain reaction. According to the liver microRNA data of Chinese tree shrew, characteristics of the miR-122 and Let-7 families further highlight the suitability of tree shrew as the animal model in HCV research.

  19. Isolation and identification of symbiotic bacteria from the skin, mouth, and rectum of wild and captive tree shrews.

    Science.gov (United States)

    Li, Gui; Lai, Ren; Duan, Gang; Lyu, Long-Bao; Zhang, Zhi-Ye; Liu, Huang; Xiang, Xun

    2014-11-18

    Endosymbionts influence many aspects of their hosts' health conditions, including physiology, development, immunity, metabolism, etc. Tree shrews (Tupaia belangeri chinensis) have attracted increasing attention in modeling human diseases and therapeutic responses due to their close relationship with primates. To clarify the situation of symbiotic bacteria from their body surface, oral cavity, and anus, 12 wild and 12 the third generation of captive tree shrews were examined. Based on morphological and cultural characteristics, physiological and biochemical tests, as well as the 16S rDNA full sequence analysis, 12 bacteria strains were isolated and identified from the wild tree shrews: body surface: Bacillus subtilis (detection rate 42%), Pseudomonas aeruginosa (25%), Staphlococcus aureus (33%), S. Epidermidis (75%), Micrococcus luteus (25%), Kurthia gibsonii (17%); oral cavity: Neisseria mucosa (58%), Streptococcus pneumonia (17%); anus: Enterococcus faecalis (17%), Lactococus lactis (33%), Escherichia coli (92%), Salmonella typhosa (17%); whereas, four were indentified from the third generation captive tree shrews: body surface: S. epidermidis (75%); oral cavity: N.mucosa (67%); anus: L. lactis (33%), E. coli (100%). These results indicate that S. epidermidis, N. mucosa, L. lactis and E. coli were major bacteria in tree shrews, whereas, S. aureus, M. luteus, K. gibsonii, E. faecalis and S. typhosa were species-specific flora. This study facilitates the future use of tree shrews as a standard experimental animal and improves our understanding of the relationship between endosymbionts and their hosts.

  20. Common tree shrews and primates share leukocyte membrane antigens.

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    Palley, L S; Schlossman, S F; Letvin, N L

    1984-01-01

    Monoclonal antibodies reactive with human peripheral blood lymphocyte and myeloid cell surface antigens were utilized to study the phylogeny of the common tree shrew. Blood cells from the common tree shrew, but not the bat or short-tailed shrew, react with certain of these antibodies. These data strengthen the argument that the Tupaiidae are primitive primates rather than insectivores. They also indicate that this approach should be useful for further work in taxonomic systemization.

  1. Tupaia belangeri as an experimental animal model for viral infection.

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    Tsukiyama-Kohara, Kyoko; Kohara, Michinori

    2014-01-01

    Tupaias, or tree shrews, are small mammals that are similar in appearance to squirrels. The morphological and behavioral characteristics of the group have been extensively characterized, and despite previously being classified as primates, recent studies have placed the group in its own family, the Tupaiidae. Genomic analysis has revealed that the genus Tupaia is closer to humans than it is to rodents. In addition, tupaias are susceptible to hepatitis B virus and hepatitis C virus. The only other experimental animal that has been demonstrated to be sensitive to both of these viruses is the chimpanzee, but restrictions on animal testing have meant that experiments using chimpanzees have become almost impossible. Consequently, the development of the tupaia for use as an animal infection model could become a powerful tool for hepatitis virus research and in preclinical studies on drug development.

  2. The Formation and Extinction of Fear Memory in Tree Shrews

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    Shujiang eShang

    2015-07-01

    Full Text Available Fear is an emotion that is well studied due to its importance for animal survival. Experimental animals, such as rats and mice, have been widely used to model fear. However, higher animals such as nonhuman primates have rarely been used to study fear due to ethical issues and high costs. Tree shrews are small mammals that are closely related to primates; they have been used to model human-related psychosocial conditions such as stress and alcohol tolerance. Here, we describe an experimental paradigm to study the formation and extinction of fear memory in tree shrews. We designed an experimental apparatus of a light/dark box with a voltage foot shock. We found that tree shrews preferred staying in the dark box in the daytime without stimulation and showed avoidance to voltage shocks applied to the footplate in a voltage-dependent manner. Foot shocks applied to the dark box for 5 days (10 minutes per day effectively reversed the light–dark preference of the tree shrews, and this memory lasted for more than 50 days without any sign of memory decay (extinction in the absence of further stimulation. However, this fear memory was reversed with 4 days of reverse training by applying the same stimulus to the light box. When reducing the stimulus intensity during the training period, a memory extinction and subsequently reinstatement effects were observed. Thus, our results describe an efficient method of monitoring fear memory formation and extinction in tree shrews.

  3. Phylogenetic affinity of tree shrews to Glires is attributed to fast evolution rate.

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    Lin, Jiannan; Chen, Guangfeng; Gu, Liang; Shen, Yuefeng; Zheng, Meizhu; Zheng, Weisheng; Hu, Xinjie; Zhang, Xiaobai; Qiu, Yu; Liu, Xiaoqing; Jiang, Cizhong

    2014-02-01

    Previous phylogenetic analyses have led to incongruent evolutionary relationships between tree shrews and other suborders of Euarchontoglires. What caused the incongruence remains elusive. In this study, we identified 6845 orthologous genes between seventeen placental mammals. Tree shrews and Primates were monophyletic in the phylogenetic trees derived from the first or/and second codon positions whereas tree shrews and Glires formed a monophyly in the trees derived from the third or all codon positions. The same topology was obtained in the phylogeny inference using the slowly and fast evolving genes, respectively. This incongruence was likely attributed to the fast substitution rate in tree shrews and Glires. Notably, sequence GC content only was not informative to resolve the controversial phylogenetic relationships between tree shrews, Glires, and Primates. Finally, estimation in the confidence of the tree selection strongly supported the phylogenetic affiliation of tree shrews to Primates as a monophyly. Copyright © 2013 Elsevier Inc. All rights reserved.

  4. Pathogenesis of Hepatitis C Virus Infection in Tupaia belangeri▿†

    Science.gov (United States)

    Amako, Yutaka; Tsukiyama-Kohara, Kyoko; Katsume, Asao; Hirata, Yuichi; Sekiguchi, Satoshi; Tobita, Yoshimi; Hayashi, Yukiko; Hishima, Tsunekazu; Funata, Nobuaki; Yonekawa, Hiromichi; Kohara, Michinori

    2010-01-01

    The lack of a small-animal model has hampered the analysis of hepatitis C virus (HCV) pathogenesis. The tupaia (Tupaia belangeri), a tree shrew, has shown susceptibility to HCV infection and has been considered a possible candidate for a small experimental model of HCV infection. However, a longitudinal analysis of HCV-infected tupaias has yet to be described. Here, we provide an analysis of HCV pathogenesis during the course of infection in tupaias over a 3-year period. The animals were inoculated with hepatitis C patient serum HCR6 or viral particles reconstituted from full-length cDNA. In either case, inoculation caused mild hepatitis and intermittent viremia during the acute phase of infection. Histological analysis of infected livers revealed that HCV caused chronic hepatitis that worsened in a time-dependent manner. Liver steatosis, cirrhotic nodules, and accompanying tumorigenesis were also detected. To examine whether infectious virus particles were produced in tupaia livers, naive animals were inoculated with sera from HCV-infected tupaias, which had been confirmed positive for HCV RNA. As a result, the recipient animals also displayed mild hepatitis and intermittent viremia. Quasispecies were also observed in the NS5A region, signaling phylogenic lineage from the original inoculating sequence. Taken together, these data suggest that the tupaia is a practical animal model for experimental studies of HCV infection. PMID:19846521

  5. Neurochemical characterization of the tree shrew dorsal striatum

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    MATTHEW W RICE

    2011-08-01

    Full Text Available The striatum is a major component of the basal ganglia and is associated with motor and cognitive functions. Striatal pathologies have been linked to several disorders, including Huntington's, Tourette's syndrome, obsessive-compulsive disorders and schizophrenia. For the study of these striatal pathologies different animal models have been used, including rodents and non-human primates. Rodents lack on morphological complexity (for example, the lack of well defined caudate and putamen nuclei, which makes it difficult to translate data to the human paradigm. Primates, and especially higher primates, are the closest model to humans, but there are ever-increasing restrictions to the use of these animals for research. In our search for a non-primate animal model with a striatum that anatomically (and perhaps functionally can resemble that of humans, we turned our attention to the tree shrew. Evolutionary genetic studies have provided strong data supporting that the tree shrews (Scadentia are one of the closest groups to primates, although their brain anatomy has only been studied in detail for specific brain areas. Morphologically, the tree shrew striatum resembles the primate striatum with the presence of an internal capsule separating the caudate and putamen, but little is known about its neurochemical composition. Here we analyzed the expression of calcium-binding proteins, the presence and distribution of the striosome and matrix compartments (by the use of calbindin, tyrosine hydroxylase and acetylcholinesterase immunohistochemistry, and the GABAergic system by immunohistochemistry against glutamic acid decarboxylase and Golgi impregnation. In summary, our results show that when compared to primates, the tree shrew dorsal striatum presents striking similarities in the distribution of most of the markers studied, while presenting some marked divergences when compared to the rodent striatum.

  6. 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

  7. Establishment of an intermittent cold stress model using Tupaia belangeri and evaluation of compound C737 targeting neuron-restrictive silencer factor

    Science.gov (United States)

    Hai-Ying, Chi; Nagano, Kiori; Ezzikouri, Sayeh; Yamaguchi, Chiho; Kayesh, Mohammad Enamul Hoque; Rebbani, Khadija; Kitab, Bouchra; Nakano, Hirohumi; Kouji, Hiroyuki; Kohara, Michinori; Tsukiyama-Kohara, Kyoko

    2016-01-01

    Previous studies have shown that intermittent cold stress (ICS) induces depression-like behaviors in mammals. Tupaia belangeri (the tree shrew) is the only experimental animal other than the chimpanzee that has been shown to be susceptible to infection by hepatitis B and C viruses. Moreover, full genome sequence analysis has revealed strong homology between host proteins in Tupaia and in humans and other primates. Tupaia neuromodulator receptor proteins are also known to have a high degree of homology with their corresponding primate proteins. Based on these similarities, we hypothesized that induction of ICS in Tupaia would provide a useful animal model of stress responses. We exposed young adult Tupaia to ICS and observed decreases in body temperature and body weight in both female and male Tupaia, suggesting that Tupaia are an appropriate animal model for ICS studies. We further examined the efficacy of a new small-molecule compound, C737, against the effects of ICS. C737 mimics the helical structure of neuron-restrictive silencer factor (NRSF/REST), which regulates a wide range of target genes involved in neuronal function and pain modulation. Treatment with C737 significantly reduced stress-induced weight loss in female Tupaia; these effects were stronger than those elicited by the antidepressant agomelatine. These results suggest that Tupaia represents a useful non-rodent ICS model. Our data also provide new insights into the function of NRSF/REST in stress-induced depression and other disorders with epigenetic influences or those with high prevalence in women. PMID:27041457

  8. Extensive characterization of Tupaia belangeri neuropeptidome using an integrated mass spectrometric approach.

    Science.gov (United States)

    Petruzziello, Filomena; Fouillen, Laetitia; Wadensten, Henrik; Kretz, Robert; Andren, Per E; Rainer, Gregor; Zhang, Xiaozhe

    2012-02-03

    Neuropeptidomics is used to characterize endogenous peptides in the brain of tree shrews (Tupaia belangeri). Tree shrews are small animals similar to rodents in size but close relatives of primates, and are excellent models for brain research. Currently, tree shrews have no complete proteome information available on which direct database search can be allowed for neuropeptide identification. To increase the capability in the identification of neuropeptides in tree shrews, we developed an integrated mass spectrometry (MS)-based approach that combines methods including data-dependent, directed, and targeted liquid chromatography (LC)-Fourier transform (FT)-tandem MS (MS/MS) analysis, database construction, de novo sequencing, precursor protein search, and homology analysis. Using this integrated approach, we identified 107 endogenous peptides that have sequences identical or similar to those from other mammalian species. High accuracy MS and tandem MS information, with BLAST analysis and chromatographic characteristics were used to confirm the sequences of all the identified peptides. Interestingly, further sequence homology analysis demonstrated that tree shrew peptides have a significantly higher degree of homology to equivalent sequences in humans than those in mice or rats, consistent with the close phylogenetic relationship between tree shrews and primates. Our results provide the first extensive characterization of the peptidome in tree shrews, which now permits characterization of their function in nervous and endocrine system. As the approach developed fully used the conservative properties of neuropeptides in evolution and the advantage of high accuracy MS, it can be portable for identification of neuropeptides in other species for which the fully sequenced genomes or proteomes are not available.

  9. Early embryonic development and transplantation in tree shrews

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    Lan-Zhen YAN

    2016-07-01

    Full Text Available As a novel experimental animal model, tree shrews have received increasing attention in recent years. Despite this, little is known in regards to the time phases of their embryonic development. In this study, surveillance systems were used to record the behavior and timing of copulations; embryos at different post-copulation stages were collected and cultured in vitro; and the developmental characteristics of both early-stage and in vitro cultured embryos were determined. A total of 163 females were collected following effective copulation, and 150 were used in either unilateral or bilateral oviduct embryo collections, with 307 embryos from 111 females obtained (conception rate=74%. Among them, 237 embryos were collected from 78 females, bilaterally, i.e., the average embryo number per female was 3.04; 172 fertilized eggs collected from 55 females, bilaterally, were cultured for 24-108 h in vitro for developmental observations; finally, 65 embryos from 23 bilateral cases and 70 embryos from 33 unilateral cases were used in embryo transplantation.

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

    Science.gov (United States)

    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.

  11. 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.

  12. 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

    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...

  13. 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.

  14. Astrocytic and neuronal oxidative metabolism are coupled to the rate of glutamate-glutamine cycle in the tree shrew visual cortex.

    Science.gov (United States)

    Sonnay, Sarah; Poirot, Jordan; Just, Nathalie; Clerc, Anne-Catherine; Gruetter, Rolf; Rainer, Gregor; Duarte, João M N

    2018-03-01

    Astrocytes play an important role in glutamatergic neurotransmission, namely by clearing synaptic glutamate and converting it into glutamine that is transferred back to neurons. The rate of this glutamate-glutamine cycle (V NT ) has been proposed to couple to that of glucose utilization and of neuronal tricarboxylic acid (TCA) cycle. In this study, we tested the hypothesis that glutamatergic neurotransmission is also coupled to the TCA cycle rate in astrocytes. For that we investigated energy metabolism by means of magnetic resonance spectroscopy (MRS) in the primary visual cortex of tree shrews (Tupaia belangeri) under light isoflurane anesthesia at rest and during continuous visual stimulation. After identifying the activated cortical volume by blood oxygenation level-dependent functional magnetic resonance imaging, 1 H MRS was performed to measure stimulation-induced variations in metabolite concentrations. Relative to baseline, stimulation of cortical activity for 20 min caused a reduction of glucose concentration by -0.34 ± 0.09 µmol/g (p glucose infusion was employed to measure fluxes of energy metabolism. Stimulation of glutamatergic activity, as indicated by a 20% increase of V NT , resulted in increased TCA cycle rates in neurons by 12% ( VTCAn, p glucose oxidation and to mitochondrial metabolism in both neurons and astrocytes. © 2017 Wiley Periodicals, Inc.

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

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    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.

  16. 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.

  17. Long-wavelength (red) light produces hyperopia in juvenile and adolescent tree shrews.

    Science.gov (United States)

    Gawne, Timothy J; Ward, Alexander H; Norton, Thomas T

    2017-11-01

    In infant tree shrews, exposure to narrow-band long-wavelength (red) light, that stimulates long-wavelength sensitive cones almost exclusively, slows axial elongation and produces hyperopia. We asked if red light produces hyperopia in juvenile and adolescent animals, ages when plus lenses are ineffective. Animals were raised in fluorescent colony lighting (100-300 lux) until they began 13days of red-light treatment at 11 (n=5, "infant"), 35 (n=5, "juvenile") or 95 (n=5, "adolescent") days of visual experience (DVE). LEDs provided 527-749 lux on the cage floor. To control for the higher red illuminance, a fluorescent control group (n=5) of juvenile (35 DVE) animals was exposed to ∼975 lux. Refractions were measured daily; ocular component dimensions at the start and end of treatment and end of recovery in colony lighting. These groups were compared with normals (n=7). In red light, the refractive state of both juvenile and adolescent animals became significantly (Prefractions (0.6±0.3D) were normal. In red-treated juveniles the vitreous chamber was significantly smaller than normal (Plight-induced slowed growth and hyperopia in juvenile and adolescent tree shrews demonstrates that the emmetropization mechanism is still capable of restraining eye growth at these ages. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Somatostatin-immunoreactive senile plaque-like structures in the frontal cortex and nucleus accumbens of aged tree shrews and Japanese macaques.

    Science.gov (United States)

    Yamashita, Akiko; Fuchs, Eberhard; Taira, Masato; Yamamoto, Takamitsu; Hayashi, Motoharu

    2012-06-01

    Previously, we demonstrated decreased expression of somatostatin mRNA in aged macaque brain, particularly in the prefrontal cortex. To investigate whether or not this age-dependent decrease in mRNA is related to morphological changes, we analyzed somatostatin cells in the cerebra of aged Japanese macaques and compared them with those in rats and tree shrews, the latter of which are closely related to primates. Brains of aged macaques, tree shrews, and rats were investigated by immunohistochemistry with special emphasis on somatostatin. We observed degenerating somatostatin-immunoreactive cells in the cortices of aged macaques and tree shrews. Somatostatin-immunoreactive senile plaque-like structures were found in areas 6 and 8 and in the nucleus accumbens of macaques, as well as in the nucleus accumbens and the cortex of aged tree shrews, where amyloid accumulations were observed. Somatostatin degenerations may be related to amyloid accumulations and may play roles in impairments of cognitive functions during aging. © 2012 John Wiley & Sons A/S.

  19. Occurrence of the Madras Tree Shrew Anathana ellioti (Waterhouse (Scandentia: Tupaiidae in the Biligirirangan Hills, Karnataka, India

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    U. Srinivasan

    2009-05-01

    Full Text Available The Madras Tree Shrew Anathana ellioti (Waterhouse 1850 is a small mammal belonging to the order Scandentia, and is endemic to peninsular India. It inhabits deciduous forests and has till date not been reported from the Biligiriranga Swamy Temple Wildlife Sanctuary (BRT WLS or the contiguous hill ranges or from anywhere else in the state of Karnataka. We provide details of nine independent sightings of this species from six locations in the BRT WLS between 2003 and 2008. Photographs of the three individuals from different locations are also presented. These records indicate an extension of the range of this species in the BRT WLS, and possibly the forests contiguous to the protected area.

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

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    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.

  1. Ectoparasite of Tupaia glis (Scandentia: Tupaiidae from Lingai agricultural area, Terengganu

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    Muhammad Hafiz Sulaiman

    2016-01-01

    Full Text Available Objective: To investigate ectoparasite fauna on the common tree shrew [Tupaia glis (T. glis] in Lingai agriculture area, Terengganu. Methods: The sampling was conducted once a month with five consecutive days from November 2012 to February 2013. Five mammal cage traps (60 cm × 30 cm × 30 cm and 30 rat cage traps (45 cm × 15 cm × 15 cm baited with banana, salt fish or fleshy-grilled coconut were used. One line transect was built and each trap was set up along the line transect with 5 m intervals. Ectoparasite was collected by combing host’s fur vigorously and kept in vials containing 70% ethanol. Results: Out of 23 hosts examined, 20 individuals (87% of T. glis in Lingai agricultural area were infested by three species of ticks and two species of mites. It was found that Laelaps echidninus showed higher mean intensity (5 as compared to the other ectoparasites. However, the prevalence was higher on Ixodes sp. (43.5% though its mean intensity was among the lowest (1.9 from the rest. Conclusions: This study provides useful information of ectoparasite fauna infesting T. glis in the agricultural area. It is important to have knowledge regarding what type of ectoparasite infests small animals in agricultural area, which in turn can assist responsible agencies to take precaution if epidemic outbreaks caused by tick-borne zoonotic diseases occur in the future.

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

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    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.

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

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    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

  4. 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.

  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. Injection of Aβ1-40 into hippocampus induced cognitive lesion associated with neuronal apoptosis and multiple gene expressions in the tree shrew.

    Science.gov (United States)

    Lin, Na; Xiong, Liu-Lin; Zhang, Rong-Ping; Zheng, Hong; Wang, Lei; Qian, Zhong-Yi; Zhang, Piao; Chen, Zhi-Wei; Gao, Fa-Bao; Wang, Ting-Hua

    2016-05-01

    Alzheimer's disease (AD) can incur significant health care costs to the patient, their families, and society; furthermore, effective treatments are limited, as the mechanisms of AD are not fully understood. This study utilized twelve adult male tree shrews (TS), which were randomly divided into PBS and amyloidbetapeptide1-40 (Aβ1-40) groups. AD model was established via an intracerebroventricular (icv) injection of Aβ1-40 after being incubated for 4 days at 37 °C. Behavioral, pathophysiological and molecular changes were evaluated by hippocampal-dependent tasks, magnetic resonance imaging (MRI), silver staining, hematoxylin-eosin (HE) staining, TUNEL assay and gene sequencing, respectively. At 4 weeks post-injection, as compared with the PBS group, in Aβ1-40 injected animals: cognitive impairments happened, and the hippocampus had atrophied indicated by MRI findings; meanwhile, HE staining showed the cells of the CA3 and DG were significantly thinner and smaller. The average number of cells in the DG, but not the CA3, was also significantly reduced; furthermore, silver staining revealed neurotic plaques and neurofibrillary tangles (NFTs) in the hippocampi; TUNEL assay showed many cells exhibited apoptosis, which was associated with downregulated BCL-2/BCL-XL-associated death promoter (Bad), inhibitor of apoptosis protein (IAP), Cytochrome c (CytC) and upregulated tumor necrosis factor receptor 1 (TNF-R1); lastly, gene sequencing reported a total of 924 mobilized genes, among which 13 of the downregulated and 19 of the upregulated genes were common to the AD pathway. The present study not only established AD models in TS, but also reported on the underlying mechanism involved in neuronal apoptosis associated with multiple gene expression.

  7. Neural coding of image structure and contrast polarity of Cartesian, hyperbolic, and polar gratings in the primary and secondary visual cortex of the tree shrew.

    Science.gov (United States)

    Poirot, Jordan; De Luna, Paolo; Rainer, Gregor

    2016-04-01

    We comprehensively characterize spiking and visual evoked potential (VEP) activity in tree shrew V1 and V2 using Cartesian, hyperbolic, and polar gratings. Neural selectivity to structure of Cartesian gratings was higher than other grating classes in both visual areas. From V1 to V2, structure selectivity of spiking activity increased, whereas corresponding VEP values tended to decrease, suggesting that single-neuron coding of Cartesian grating attributes improved while the cortical columnar organization of these neurons became less precise from V1 to V2. We observed that neurons in V2 generally exhibited similar selectivity for polar and Cartesian gratings, suggesting that structure of polar-like stimuli might be encoded as early as in V2. This hypothesis is supported by the preference shift from V1 to V2 toward polar gratings of higher spatial frequency, consistent with the notion that V2 neurons encode visual scene borders and contours. Neural sensitivity to modulations of polarity of hyperbolic gratings was highest among all grating classes and closely related to the visual receptive field (RF) organization of ON- and OFF-dominated subregions. We show that spatial RF reconstructions depend strongly on grating class, suggesting that intracortical contributions to RF structure are strongest for Cartesian and polar gratings. Hyperbolic gratings tend to recruit least cortical elaboration such that the RF maps are similar to those generated by sparse noise, which most closely approximate feedforward inputs. Our findings complement previous literature in primates, rodents, and carnivores and highlight novel aspects of shape representation and coding occurring in mammalian early visual cortex. Copyright © 2016 the American Physiological Society.

  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......, our results indicate that pitfall traps are the most efficient for capturing shrews: not only do they have a higher efficiency (yield), but the taxonomic diversity of shrews is also higher when pitfall traps are used....

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

    Science.gov (United States)

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

    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(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. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  10. 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.

  11. The Taming of the Shrew

    Science.gov (United States)

    Gad-El-Hak, M.

    1996-11-01

    Considering the extreme complexity of the turbulence problem in general and the unattainability of first-principles analytical solutions in particular, it is not surprising that controlling a turbulent flow remains a challenging task, mired in empiricism and unfulfilled promises and aspirations. Brute force suppression, or taming, of turbulence via active control strategies is always possible, but the penalty for doing so often exceeds any potential savings. The artifice is to achieve a desired effect with minimum energy expenditure. Spurred by the recent developments in chaos control, microfabrication and neural networks, efficient reactive control of turbulent flows, where the control input is optimally adjusted based on feedforward or feedback measurements, is now in the realm of the possible for future practical devices. But regardless of how the problem is approached, combating turbulence is always as arduous as the taming of the shrew. The former task will be emphasized during the oral presentation, but for this abstract we reflect on a short verse from the latter. From William Shakespeare's The Taming of the Shrew. Curtis (Petruchio's servant, in charge of his country house): Is she so hot a shrew as she's reported? Grumio (Petruchio's personal lackey): She was, good Curtis, before this frost. But thou know'st winter tames man, woman, and beast; for it hath tamed my old master, and my new mistress, and myself, fellow Curtis.

  12. 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.

  13. Persistence and diversification of the Holarctic shrew, Sorex tundrensis (Family Soricidae), in response to climate change

    Science.gov (United States)

    Hope, Andrew G.; Waltari, Eric; Fedorov, Vadim B.; Goropashnaya, Anna V.; Talbot, Sandra; Cook, Joseph A.

    2011-01-01

    Environmental processes govern demography, species movements, community turnover and diversification and yet in many respects these dynamics are still poorly understood at high latitudes. We investigate the combined effects of climate change and geography through time for a widespread Holarctic shrew, Sorex tundrensis. We include a comprehensive suite of closely related outgroup taxa and three independent loci to explore phylogeographic structure and historical demography. We then explore the implications of these findings for other members of boreal communities. The tundra shrew and its sister species, the Tien Shan shrew (Sorex asper), exhibit strong geographic population structure across Siberia and into Beringia illustrating local centres of endemism that correspond to Late Pleistocene refugia. Ecological niche predictions for both current and historical distributions indicate a model of persistence through time despite dramatic climate change. Species tree estimation under a coalescent process suggests that isolation between populations has been maintained across timeframes deeper than the periodicity of Pleistocene glacial cycling. That some species such as the tundra shrew have a history of persistence largely independent of changing climate, whereas other boreal species shifted their ranges in response to climate change, highlights the dynamic processes of community assembly at high latitudes.

  14. Persistence and diversification of the Holarctic shrew, Sorex tundrensis (Family Soricidae), in response to climate change

    Science.gov (United States)

    Hope, Andrew G.; Waltari, Eric; Fedorov, V.B.; Goropashnaya, A.V.; Talbot, Sandra; Cook, Joseph A.

    2014-01-01

    Environmental processes govern demography, species movements, community turnover and diversification and yet in many respects these dynamics are still poorly understood at high latitudes. We investigate the combined effects of climate change and geography through time for a widespread Holarctic shrew, Sorex tundrensis. We include a comprehensive suite of closely related outgroup taxa and three independent loci to explore phylogeographic structure and historical demography. We then explore the implications of these findings for other members of boreal communities. The tundra shrew and its sister species, the Tien Shan shrew (Sorex asper), exhibit strong geographic population structure across Siberia and into Beringia illustrating local centres of endemism that correspond to Late Pleistocene refugia. Ecological niche predictions for both current and historical distributions indicate a model of persistence through time despite dramatic climate change. Species tree estimation under a coalescent process suggests that isolation between populations has been maintained across timeframes deeper than the periodicity of Pleistocene glacial cycling. That some species such as the tundra shrew have a history of persistence largely independent of changing climate, whereas other boreal species shifted their ranges in response to climate change, highlights the dynamic processes of community assembly at high latitudes.

  15. Multilocus phylogeography and systematic revision of North American water shrews (genus: Sorex)

    Science.gov (United States)

    Hope, Andrew G.; Panter, Nicholas; Cook, Joseph A.; Talbot, Sandra L.; Nagorsen, David W.

    2014-01-01

    North American water shrews, which have traditionally included Sorex alaskanus, S. bendirii, and S. palustris, are widely distributed through Nearctic boreal forests and adapted for life in semiaquatic environments. Molecular mitochondrial signatures for these species have recorded an evolutionary history with variable levels of regional divergence, suggesting a strong role of Quaternary environmental change in speciation processes. We expanded molecular analyses, including more-comprehensive rangewide sampling of specimens representing North American water shrew taxa, except S. alaskanus, and sequencing of 4 independent loci from the nuclear and mitochondrial genomes. We investigated relative divergence of insular populations along the North Pacific Coast, and newly recognized diversity from southwestern montane locations, potentially representing refugial isolates. Congruent independent genealogies, lack of definitive evidence for contemporary gene flow, and high support from coalescent species trees indicated differentiation of 4 major geographic lineages over multiple glacial cycles of the late Quaternary, similar to a growing number of boreal taxa. Limited divergence of insular populations suggested colonization following the last glacial. Characterization of southwestern montane diversity will require further sampling but divergence over multiple loci is indicative of a relictual sky-island fauna. We have reviewed and revised North American water shrew taxonomy including the recognition of 3 species within what was previously known as S. palustris. The possibility of gene flow between most distantly related North American water shrew lineages coupled with unresolved early diversification of this group and other sibling species reflects a complex but potentially productive system for investigating speciation processes.

  16. 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

  17. 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

  18. The relative host status of rock elephant shrews Elephantulus ...

    African Journals Online (AJOL)

    1991-10-18

    Oct 18, 1991 ... rocky terrain, occur in South Africa (Smithers 1983) and the distribution of ... elephant shrews on northern and on southern slopes on the farm 'Preezfon- .... this has caused paralysis in Angora goat kids (Fourie et al. 1988a).

  19. 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.

  20. Trees

    Science.gov (United States)

    Al-Khaja, Nawal

    2007-01-01

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

  1. 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.

  2. New status for two African giant forest shrews, Crocidura goliath ...

    African Journals Online (AJOL)

    New status for two African giant forest shrews, Crocidura goliath goliath and C. ... that C. g. nimbasilvanus is the sister taxon of C. nimbae, a species also endemic to ... Crocidura g. goliath is part of the C. olivieri group and closely related to C.

  3. 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....

  4. Preliminary report of shrews and rodents in and around Lake ...

    African Journals Online (AJOL)

    Surveys during October 2004 and July 2005, in and around Lake Bogoria National Reserve, Kenya, collected evidence of nine rodent species, and one species of shrew. The diversity of small mammals live-trapped within a single habitat type was low compared to similar studies in Africa. The low diversity may be due to the ...

  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. 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

  7. 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...

  8. 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.

  9. 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...

  10. 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.

  11. 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

    2009-01-01

    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 Denmark. Results 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. Conclusion 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. PMID:19152713

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

    Directory of Open Access Journals (Sweden)

    Olsen Henrik

    2009-01-01

    Full Text Available 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 Denmark. Results 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. Conclusion 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.

  13. 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.

  14. 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, s...

  15. 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.

  16. Estimation of body surface area in the musk shrew ( Suncus murinus): a small animal for testing chemotherapy-induced emesis.

    Science.gov (United States)

    Eiseman, Julie L; Sciullo, Michael; Wang, Hong; Beumer, Jan H; Horn, Charles C

    2017-10-01

    Several cancer chemotherapies cause nausea and vomiting, which can be dose-limiting. Musk shrews are used as preclinical models for chemotherapy-induced emesis and for antiemetic effectiveness. Unlike rats and mice, shrews possess a vomiting reflex and demonstrate an emetic profile similar to humans, including acute and delayed phases. As with most animals, dosing of shrews is based on body weight, while translation of such doses to clinically equivalent exposure requires doses based on body surface area. In the current study body surface area in musk shrews was directly assessed to determine the Meeh constant (K m ) conversion factor (female = 9.97, male = 9.10), allowing estimation of body surface area based on body weight. These parameters can be used to determine dosing strategies for shrew studies that model human drug exposures, particularly for investigating the emetic liability of cancer chemotherapeutic agents.

  17. 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.

  18. High shrew diversity on Alaska's Seward Peninsula: Community assembly and environmental change

    Science.gov (United States)

    Hope, Andrew G.

    2012-01-01

    In September 2010, 6 species of shrews (genus: Sorex) were collected at a single locality on the Seward Peninsula of Alaska. Such high sympatric diversity within a single mammalian genus is seldom realized. This phenomenon at high latitudes highlights complex Arctic community dynamics that reflect significant turnover through time as a consequence of environmental change. Each of these shrew species occupies a broad geographic distribution collectively spanning the entire Holarctic, although the study site lies within Eastern Beringia, near the periphery of all individual ranges. A review of published genetic evidence reflects a depauperate shrew community within ice-free Beringia through the last glaciation, and recent assembly of current diversity during the Holocene.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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 obtain...... by two pairs of septal folds. A similar arrangement has been described for representatives of each of the remaining five orders within Afrotheria. This is significant because previous anatomical studies have failed to establish a single synapomorphy in support of Afrotheria....

  4. "The Taming of the Shrew." A Play Packet To Accompany "Elementary, My Dear Shakespeare."

    Science.gov (United States)

    Engen, Barbara; Campbell, Joy

    Intended for use by elementary school teachers as a supplement to the book, "Elementary, My Dear Shakespeare," or for use by itself to produce one Shakespeare play, this play packet contains ready-to-reproduce materials for the production of "The Taming of the Shrew." Materials include: staging suggestions for scenery, props,…

  5. 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.

  6. 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...

  7. Two new species of shrews (Soricidae) from the western highlands of Guatemala

    Science.gov (United States)

    Woodman, Neal

    2010-01-01

    The broad-clawed shrews (Soricomorpha: Soricidae: Cryptotis) encompass a clade of 5 species—Cryptotis alticolus (Merriam), C. goldmani (Merriam), C. goodwini Jackson, C. griseoventris Jackson, and C. peregrinus (Merriam)—that is known collectively as the Cryptotis goldmani group and is characterized by broadened forefeet, elongated and broadened fore claws, and broadened humeri. These shrews are distributed in highland regions from central Mexico to Honduras. Two broad-clawed shrews, C. goodwini and C. griseoventris, occur in southern Mexico and Guatemala and are presumed sister species whose primary distinguishing feature is the larger size of C. goodwini. In an investigation of variation within and between these 2 species, I studied characteristics of the postcranial skeleton. Statistical analyses of a variety of character suites indicate that the forelimb morphology in this group exhibits less intraspecific variation and greater interspecific variation than cranio-mandibular morphology, although most skull characters support groupings based on forelimb characters. Together, these characters define 4 distinct groups among the specimens examined. C. griseoventris is restricted to the northern highlands of Chiapas, Mexico, and C. goodwini occurs in the southern highlands of Chiapas and Guatemala. Herein, I describe 2 new species of broad-clawed shrews from the Sierra de los Cuchumatanes, Guatemala.

  8. 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,

  9. 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

  10. Improved Starch Digestion of Sucrase-deficient Shrews Treated With Oral Glucoamylase Enzyme Supplements.

    Science.gov (United States)

    Nichols, Buford L; Avery, Stephen E; Quezada-Calvillo, Roberto; Kilani, Shadi B; Lin, Amy Hui-Mei; Burrin, Douglas G; Hodges, Benjamin E; Chacko, Shaji K; Opekun, Antone R; Hindawy, Marwa El; Hamaker, Bruce R; Oda, Sen-Ichi

    2017-08-01

    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 congenital sucrase-isomaltase deficiency.Starch digestion is much more complex than sucrose digestion. Six enzyme activities, 2 α-amylases (Amy), and 4 mucosal α-glucosidases (maltases), including maltase-glucoamylase (Mgam) and sucrase-isomaltase (Si) subunit activities, are needed to digest starch to absorbable free glucose. Amy breaks down insoluble starch to soluble dextrins; mucosal Mgam and Si can either directly digest starch to glucose or convert the post-α-amylolytic dextrins to glucose. Starch digestion is reduced because of sucrase deficiency and oral glucoamylase enzyme supplement can correct the starch maldigestion. The aim of the present study was to measure glucogenesis in suc/suc shrews after feeding of starch and improvement of glucogenesis by oral glucoamylase supplements. Sucrase mutant (suc/suc) and heterozygous (+/suc) shrews were fed with C-enriched starch diets. Glucogenesis derived from starch was measured as blood C-glucose enrichment and oral recombinant C-terminal Mgam glucoamylase (M20) was supplemented to improve starch digestion. After feedings, suc/suc and +/suc shrews had different starch digestions as shown by blood glucose enrichment and the suc/suc had lower total glucose concentrations. Oral supplements of glucoamylase increased suc/suc total blood glucose and quantitative starch digestion to glucose. Sucrase deficiency, in this model of congenital sucrase-isomaltase deficiency, reduces blood glucose response to starch feeding. Supplementing the diet with oral recombinant glucoamylase significantly improved starch digestion in the sucrase-deficient shrew.

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

    NARCIS (Netherlands)

    Kole, MHP; Czeh, B; Fuchs, E

    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

  12. The use of albendazole for the treatment of trematodiasis in two tree shrews (Tupala glis)

    Science.gov (United States)

    Beehler, B.A.; Tuggle, B.N.

    1983-01-01

    Albendazole is a broad-spectrum anthelmintic of the benzimidazole group which has been tested in several rodents and domestic animals. Albendazole has been used effectively to treat trematodes in sheep, cattle, dogs, and cats. The use of this anthelmintic in exotic small mammals has not been reported to the authors' knowledge.

  13. 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

  14. 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 ...

  15. AFLP diversity between the Novosibirsk and Tomsk chromosome races of the common shrew (Sorex araneus

    Directory of Open Access Journals (Sweden)

    Andrey Polyakov

    2009-12-01

    Full Text Available Genetic diversity between of the Novosibirsk and Tomsk chromosome races of the common shrew (Sorex araneus was analyzed using 39 polymorphic AFLP (amplified fragments length polymorphism markers. Exact and F-statistics tests for population differentiation demonstrated significant interracial difference in allele frequencies and significant subdivision between the races. The value of the genetic distance between the chromosome races observed in this study corresponds to that found between subspecies of mammals studied so far.

  16. 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

  17. 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.

  18. A new species of small-eared shrew from Colombia and Venezuela (Mammalia: Soricomorpha: Soricidae: Genus Cryptotis)

    Science.gov (United States)

    Woodman, N.

    2002-01-01

    Populations of small-eared shrews inhabiting the northern Cordillera Oriental of Colombia and adjoining Venezuelan highlands in the vicinity of Paramo de Tama have been referred alternatively to Cryptotis thomssi or Cryptotis meridensis. Morphological and morphometrical study of this population indicates that it belongs to neither taxon, but represents a distinct, previously unrecognized species. I describe this new species as Cryptotis tamensis and redescribe C. meridensis. Recognition of the population at Paramo de Tama as a separate taxon calls into question the identities of populations of shrews currently represented only by single specimens from Cerro Pintado in the Sierra de Perija, Colombia, and near El Junquito in the coastal highlands of Venezuela.

  19. 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

    Mass-specific metabolic rate varies inversely with size, while pulmonary transit time, muscle O2 storage capacity, and the ability to exploit anaerobic metabolism vary directly with this variable. Thus, small mammals must exploit a suite of morphological and physiological adjustments to supply...... and moles. Despite these constraints, several shrew (and mole) species flourish at elevations exceeding 4500 m (where atmospheric PO2 is ... operating near their upper limits, what if any additional functional properties of the Hb of these species make these achievements possible? Our findings suggest that changes in the intrinsic O2-affinity of the Hb moiety (rather than phosphate sensitivity) underlie transitions to and from hypoxic...

  20. [Life cycle of Maupasina weissi Seurat, 1913, Subuluroidea Nematode, parasite of the elephant shrew (author's transl)].

    Science.gov (United States)

    Quentin, J C; Verdier, J M

    1979-01-01

    The life cycle of Maupasina weissi Seurat, 1913, the parasite of the elephant shrew, has been experimentally obtained from the intermediate host Locusta migratoria. The biology of this Nematoda is considered as being more primitive than the Subuluridae: -- egg maturation in external environment is in fact necessary to the Maupasina larvae to penetrate into the insect, -- The different localizations of the infective larvae, such as mesenteron regeneration crypta, fat body, demonstrate that the parasite is not completely adaptated to its intermediate host, -- the ontogenesis of cephalic structures is characterized by an hypertrophy of the archaic structures mainly from cuticular origin.

  1. 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.

  2. Prevalence and diversity of gastrointestinal helminths in free-ranging Asian house shrew (Suncus murinus in Bangladesh

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    Mizanur Rahman

    2018-04-01

    Full Text Available Background and Aim: Asian house shrew (Suncus murinus, a widely distributed small mammal in the South Asian region, can carry helminths of zoonotic importance. The aim of the study was to know the prevalence and diversity of gastrointestinal (GI helminths in free-ranging Asian house shrew (S. murinus in Bangladesh. Materials and Methods: A total of 86 Asian house shrews were captured from forest areas and other habitats of Bangladesh in 2015. Gross examination of the whole GI tract was performed for gross helminth detection, and coproscopy was done for identification of specific eggs or larvae. Results: The overall prevalence of GI helminth was 77.9% (67/86, with six species including nematodes (3, cestodes (2, and trematodes (1. Of the detected helminths, the dominant parasitic group was from the genus Hymenolepis spp. (59%, followed by Strongyloides spp. (17%, Capillaria spp. (10%, Physaloptera spp. (3%, and Echinostoma spp. (3%. Conclusion: The finding shows that the presence of potential zoonotic parasites (Hymenolepis spp. and Capillaria spp. in Asian house shrew is ubiquitous in all types of habitat (forest land, cropland and dwelling in Bangladesh. Therefore, further investigation is crucial to examine their role in the transmission of human helminthiasis.

  3. Prevalence and diversity of gastrointestinal helminths in free-ranging Asian house shrew (Suncus murinus) in Bangladesh

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    Rahman, Mizanur; Islam, Shariful; Masuduzzaman, Md.; Alam, Mahabub; Chawdhury, Mohammad Nizam Uddin; Ferdous, Jinnat; Islam, Md. Nurul; Hassan, Mohammad Mahmudul; Hossain, Mohammad Alamgir; Islam, Ariful

    2018-01-01

    Background and Aim Asian house shrew (Suncus murinus), a widely distributed small mammal in the South Asian region, can carry helminths of zoonotic importance. The aim of the study was to know the prevalence and diversity of gastrointestinal (GI) helminths in free-ranging Asian house shrew (S. murinus) in Bangladesh. Materials and Methods A total of 86 Asian house shrews were captured from forest areas and other habitats of Bangladesh in 2015. Gross examination of the whole GI tract was performed for gross helminth detection, and coproscopy was done for identification of specific eggs or larvae. Results The overall prevalence of GI helminth was 77.9% (67/86), with six species including nematodes (3), cestodes (2), and trematodes (1). Of the detected helminths, the dominant parasitic group was from the genus Hymenolepis spp.(59%), followed by Strongyloides spp.(17%), Capillaria spp. (10%), Physaloptera spp. (3%), and Echinostoma spp.(3%). Conclusion The finding shows that the presence of potential zoonotic parasites (Hymenolepis spp. and Capillaria spp.) in Asian house shrew is ubiquitous in all types of habitat (forest land, cropland and dwelling) in Bangladesh. Therefore, further investigation is crucial to examine their role in the transmission of human helminthiasis. PMID:29805224

  4. Prevalence and diversity of gastrointestinal helminths in free-ranging Asian house shrew (Suncus murinus) in Bangladesh.

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    Rahman, Mizanur; Islam, Shariful; Masuduzzaman, Md; Alam, Mahabub; Chawdhury, Mohammad Nizam Uddin; Ferdous, Jinnat; Islam, Md Nurul; Hassan, Mohammad Mahmudul; Hossain, Mohammad Alamgir; Islam, Ariful

    2018-04-01

    Asian house shrew ( Suncus murinus ), a widely distributed small mammal in the South Asian region, can carry helminths of zoonotic importance. The aim of the study was to know the prevalence and diversity of gastrointestinal (GI) helminths in free-ranging Asian house shrew ( S. murinus ) in Bangladesh. A total of 86 Asian house shrews were captured from forest areas and other habitats of Bangladesh in 2015. Gross examination of the whole GI tract was performed for gross helminth detection, and coproscopy was done for identification of specific eggs or larvae. The overall prevalence of GI helminth was 77.9% (67/86), with six species including nematodes (3), cestodes (2), and trematodes (1). Of the detected helminths, the dominant parasitic group was from the genus Hymenolepis spp.(59%), followed by Strongyloides spp.(17%), Capillaria spp. (10%), Physaloptera spp. (3%), and Echinostoma spp.(3%). The finding shows that the presence of potential zoonotic parasites (Hymenolepis spp. and Capillaria spp.) in Asian house shrew is ubiquitous in all types of habitat (forest land, cropland and dwelling) in Bangladesh. Therefore, further investigation is crucial to examine their role in the transmission of human helminthiasis.

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

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    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.

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

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    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.

  7. Dual mechanism of chromatin remodeling in the common shrew sex trivalent (XY 1Y 2

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    Sergey N. Matveevsky

    2017-11-01

    Full Text Available Here we focus on the XY1Y2 condition in male common shrew Sorex araneus Linnaeus, 1758, applying electron microscopy and immunocytochemistry for a comprehensive analysis of structure, synapsis and behaviour of the sex trivalent in pachytene spermatocytes. The pachytene sex trivalent consists of three distinct parts: short and long synaptic SC fragments (between the X and Y1 and between the X and Y2, respectively and a long asynaptic region of the X in-between. Chromatin inactivation was revealed in the XY1 synaptic region, the asynaptic region of the X and a very small asynaptic part of the Y2. This inactive part of the sex trivalent, that we named the ‘head’, forms a typical sex body and is located at the periphery of the meiotic nucleus at mid pachytene. The second part or ‘tail’, a long region of synapsis between the X and Y2 chromosomes, is directed from the periphery into the nucleus. Based on the distribution patterns of four proteins involved in chromatin inactivation, we propose a model of meiotic silencing in shrew sex chromosomes. Thus, we conclude that pachytene sex chromosomes are structurally and functionally two different chromatin domains with specific nuclear topology: the peripheral inactivated ‘true’ sex chromosome regions (part of the X and the Y1 and more centrally located transcriptionally active autosomal segments (part of the X and the Y2.

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

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    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.

  9. Size evolution in Goodwin’s small-eared shrew, Cryptotis goodwini

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    Woodman, N.; Merritt, J.F.; Churchfield, S.; Hutterer, R.; Sheftel, B.A.

    2005-01-01

    Fossils of Cryptotis goodwini from Honduras indicate that body sizes of modern individuals average at least 18% larger than among members of the late Pleistocene population of this species. Palynological and other paleoenvironmental studies provide evidence that the Neotropical montane environments that these shrews inhabit were cooler and drier in the late Pleistocene than at present and supported communities of plants without modern analog. Therefore, the most likely cause of this change in size ultimately was related to climatic change at the end of the Pleistocene?but to what specific factors did the species respond? I examined the possibilities that this species changed in size: to accommodate a change in temperature regime; to escape from predators; as a response to a change in intensity of interspecific competition; to take advantage of a newly abundant food resource. Based on evidence from studies of modern communities of shrews and niche partitioning, I hypothesized that size evolution in C. goodwini was directly related to changes in the community of soil and soil-surface invertebrates upon which the species depends, specifically an increase in the availability of earthworms (Annelida).

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

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    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.

  11. 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.

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

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    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.

  13. Effect of land cover, habitat fragmentation and ant colonies on the distribution and abundance of shrews in southern California

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    Laakkonen, Juha; Fisher, Robert N.; Case, Ted J.

    2001-01-01

    Because effects of habitat fragmentation and anthropogenic disturbance on native animals have been relatively little studied in arid areas and in insectivores, we investigated the roles of different land covers, habitat fragmentation and ant colonies on the distribution and abundance of shrews, Notiosorex crawfordi and Sorex ornatus, in southern California.Notiosorex crawfordi was the numerically dominant species (trap-success rate 0·52) occurring in 21 of the 22 study sites in 85% of the 286 pitfall arrays used in this study.Sorex ornatus was captured in 14 of the sites, in 52% of the arrays with a total trap-success rate of 0·2. Neither of the species was found in one of the sites.The population dynamics of the two shrew species were relatively synchronous during the 4–5-year study; the peak densities usually occurred during the spring. Precipitation had a significant positive effect, and maximum temperature a significant negative effect on the trap-success rate of S. ornatus.Occurrence and abundance of shrews varied significantly between sites and years but the size of the landscape or the study site had no effect on the abundance of shrews. The amount of urban edge had no significant effect on the captures of shrews but increased edge allows invasion of the Argentine ants, which had a highly significant negative impact on the abundance of N. crawfordi.At the trap array level, the percentage of coastal sage scrub flora had a significant positive, and the percentage of other flora had a significant negative effect on the abundance of N. crawfordi. The mean canopy height and the abundance of N. crawfordi had a significant positive effect on the occurrence of S. ornatus.Our study suggests that the loss of native coastal sage scrub flora and increasing presence of Argentine ant colonies may significantly effect the distribution and abundance of N. crawfordi. The very low overall population densities of both shrew species in most study sites make both species

  14. The taming of the shrew: batterers' constructions of their wives' narratives.

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    Borochowitz, Dalit Yassour

    2008-10-01

    Constructing a life story is a need shared by all humans to give their lives meaning and coherence. This article explores some of the narrative devices that batterers use to achieve a sense of coherence when telling their stories and justifying their violent behavior. A central theme that emerged from these stories centered on the men's perception of their wives as the embodiment of their own emotions and inner world. Two narrative strategies were identified in this context: (a) The construction of a "couple narrative" that focused on an idealized marital relationship rather than "allowing" the wife her story and (b) constructing a story around the theme of "she's not the same woman I married," which portrays the wife as "a shrew" and the violence as an attempt to discipline her. The stories of 18 batterers were used for this analysis, and two narratives were used to illustrate these strategies.

  15. Tranio Transformed: Social Anxieties and Social Metamorphosis in The Taming of the Shrew

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    Sonya L. Brockman

    2015-03-01

    Full Text Available The article discusses Elizabethan anxieties about the increasing fluidity of social status through an examination of the servant Tranio in Shakespeare’s The Taming of the Shrew. It argues that Tranio’s informed and willing participation in this social performance embodies the anxieties about social mobility held by members of the Elizabethan elite. In contrast to other figures of social metamorphosis in the play, Tranio’s social transformation is temporary, even though, like Christopher Sly, he is transformed into a gentleman at the behest of his Lord. He must return to his servile status in the final act, however, not only because he can so successfully perform the role of master, but because he knowingly participates in his own social metamorphosis. The article suggests, in conclusion, that it is the servant’s knowledge of his own performative power that makes him a threat in Elizabethan society. 

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

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    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.

  17. Species interactions during diversification and community assembly in an island radiation of shrews.

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    Jacob A Esselstyn

    Full Text Available BACKGROUND: Closely related, ecologically similar species often have adjacent distributions, suggesting competitive exclusion may contribute to the structure of some natural communities. In systems such as island archipelagos, where speciation is often tightly associated with dispersal over oceanic barriers, competitive exclusion may prevent population establishment following inter-island dispersal and subsequent cladogenesis. METHODOLOGY/PRINCIPAL FINDINGS: Using a combination of tools, we test the hypothesis that the distributions of shrew (Crocidura species in the Philippines are the result of competitive exclusion preventing secondary invasion of occupied islands. We first compare ecological niche models between two widespread, allopatric species and find statistical support for their ecological similarity, implying that competition for habitat between these species is possible. We then examine dispersion patterns among sympatric species and find some signal for overdispersion of body size, but not for phylogenetic branch length. Finally, we simulate the process of inter-island colonization under a stochastic model of dispersal lacking ecological forces. Results are dependent on the geographic scope and colonization probability employed. However, some combinations suggest that the number of inter-island dispersal events necessary to populate the archipelago may be much higher than the minimum number of colonization events necessary to explain current estimates of species richness and phylogenetic relationships. If our model is appropriate, these results imply that alternative factors, such as competitive exclusion, may have influenced the process of inter-island colonization and subsequent cladogenesis. CONCLUSIONS/SIGNIFICANCE: We interpret the combined results as providing tenuous evidence that similarity in body size may prevent co-occurrence in Philippine shrews and that competitive exclusion among ecologically similar species, rather

  18. 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

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    Sonsthagen, Sarah A.; Sage, G. Kevin; Fowler, Megan C.; Hope, Andrew G.; Cook, J.A.; Talbot, Sandra 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.

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

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    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.

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

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    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.

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

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    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.

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

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    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.

  3. Aging is accompanied by a subfield-specific reduction of serotonergic fibers in the tree shrew hippocampal formation

    NARCIS (Netherlands)

    Keuker, Jeanine I H; Keijser, Jan N.; Nyakas, Csaba; Luiten, Paul G.M.; Fuchs, Eberhard

    2005-01-01

    The hippocampal formation is a crucial structure for learning and memory, and serotonin together with other neurotransmitters is essential in these processes. Although the effects of aging on various neurotransmitter systems in the hippocampus have been extensively investigated, it is not entirely

  4. 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.

  5. Neonatal DHT but not E2 speeds induction of sexual receptivity in the musk shrew.

    Science.gov (United States)

    Ewton, Tiffany A; Siboni, Ruth B; Jackson, Andrea; Freeman, Louise M

    2010-06-01

    Neural aromatization of testosterone (T) to estrogen during development is thought to be important for sexual differentiation of many altricial mammals. We evaluated the effects of neonatal injections of the non-aromatizable androgen dihydrotestosterone propionate (DHTP) and estradiol (E2) on the copulatory behavior of the female musk shrew, an altricial insectivore. Following adult ovariectomy and replacement T, animals were paired with a stimulus female for two 60-minute copulatory behavior tests. The latency to induce sexual receptivity (in the form of tail-wagging by the female), mount latency and total number of mounts were recorded in experimental females and in a group of untreated control males. While neither hormone treatment significantly affected mounting behavior, DHTP-treated animals induced receptivity faster and with latencies not significantly different from intact males, suggesting that early non-aromatizable androgens can have masculinizing actions by either increasing sexual motivation or making the treated animal more attractive to the stimulus female. Reliance on androgenic rather than estrogenic metabolites for the differentiation of courtship behaviors conforms to the pattern seen more typically in primates than rodents. Copyright 2009 Elsevier Inc. All rights reserved.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Bibliography of studies on hybrid zones of the common shrew chromosome races distributed in Russia

    Directory of Open Access Journals (Sweden)

    Rena Nadjafova

    2013-11-01

    Full Text Available The common shrew, Sorex araneus Linnaeus, 1758, has become a model species for cytogenetical and evolutionary studies after discovery of extraordinary Robertsonian polymorphism at the within-species level. Development of differential staining techniques (Q-, R-and G-banding made it possible to identify the chromosomal arms and their combination in racial karyotypes. Entering into contact with each other, the chromosomal races might form hybrid zones which represent a great interest for understanding of the process of speciation. Until recently all known hybrid zones of S. araneus were localized in Western Europe and only one was identified in Siberia (Russia between Novosibirsk and Tomsk races (Aniskin and Lukianova 1989, Searle and Wójcik 1998, Polyakov et al. 2011. However, rapidly growing number of reports on discovery of interracial hybrid zones of Sorex araneus in the European part of Russia and neighboring territories appeared lately. The aim of the present work is to compile the bibliography of all studies covering this topic regardless of the original language and the publishing source which hopefully could make research data more accessible to international scientists.It could also be a productive way to save current history of Sorex araneus researches in full context of the ISACC (International Sorex araneus Cytogenetics Committee heritage (Searle et al. 2007, Zima 2008.

  13. Flowering Trees

    Indian Academy of Sciences (India)

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

  14. Flowering Trees

    Indian Academy of Sciences (India)

    IAS Admin

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

  15. Flowering Trees

    Indian Academy of Sciences (India)

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

  16. Flowering Trees

    Indian Academy of Sciences (India)

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

  17. 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...

  18. 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...

  19. Invading and expanding: range dynamics and ecological consequences of the greater white-toothed shrew (Crocidura russula invasion in Ireland.

    Directory of Open Access Journals (Sweden)

    Allan D McDevitt

    Full Text Available 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.

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

    DEFF Research Database (Denmark)

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

    2009-01-01

    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. Results: High grazing...... as well as in most other European countries, the amount of land covered by semi-natural grassland has decreased dramatically during the 20th century concurrent with the general intensification of the agricultural production. To reverse this trend, actions are being taken in many places to either maintain...

  1. 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

  2. Tree Nut Allergies

    Science.gov (United States)

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

  3. 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

  4. 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...

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. A New Approach to the Shrew Group in Strange Tales from a Chinese Studio%《聊斋志异》悍妇群新论

    Institute of Scientific and Technical Information of China (English)

    张宇

    2016-01-01

    Shrews in Strange Tales from a Chinese Studio not only are great in number but also forms a complete picture of its group. In the past, studies on the shrews in this novel were from such aspects as views on marriage and religions, and the most typical views were to redress customs, reflect social practice and patri-archy projection. These theories, however, fail to satisfactorily explain the prevailing of shrews in this novel. Under the unique circumstances of Ming and Qing Dynasty, Pu Songling, the novelist, was deeply influenced by the ideology of “distinguishing Central China from its neighbors”, which has a profound influence on his literary works. As literacy inquisition occurred repeatedly in Qing Dynasty, writers had to seek a roundabout way to express his feeling. The group of shrews in Strange Tales from a Chinese Studio was thus formed. The novelist found his voice in the shrews and the shrews carry with them more symbolic meaning than realistic meaning. To know the symbolic meaning of the shrews helps readers understand Pu Songling and his literary recreation.%《聊斋志异》中的悍妇不仅数量众多,且可构成一体系完备的悍妇群。对《聊斋志异》悍妇的研究,多从婚姻观、宗教观角度分析,以“正风俗”、现实反映论以及男权投射论最为典型。然这些理论都不能尽解《聊斋志异》悍妇盛行之因。在明末清初特殊的社会背景下,蒲松龄深受“夷夏之辨”的思想意识影响,并深深影响其《聊斋志异》的创作;但清代文字狱迭发,抒发自己家国情怀,只能以迂回委婉的方式表达。悍妇便是这一家国情怀抒发的载体之一,其象征意义大于现实意义。了解悍妇的象征意义,对研究蒲松龄《聊斋志异》的创作有一定的意义。

  10. Flowering Trees

    Indian Academy of Sciences (India)

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

  11. Flowering Trees

    Indian Academy of Sciences (India)

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

  12. Flowering Trees

    Indian Academy of Sciences (India)

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

  13. Flowering Trees

    Indian Academy of Sciences (India)

    user

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

  14. 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.

  15. Talking Trees

    Science.gov (United States)

    Tolman, Marvin

    2005-01-01

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

  16. Drawing Trees

    DEFF Research Database (Denmark)

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

    2018-01-01

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

  17. 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.

  18. Phylogenetic trees

    OpenAIRE

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

    2016-01-01

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

  19. 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....

  20. 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.

  1. 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.

  2. 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.

  3. Abundance & distribution of trombiculid mites & Orientia tsutsugamushi, the vectors & pathogen of scrub typhus in rodents & shrews collected from Puducherry & Tamil Nadu, India.

    Science.gov (United States)

    Candasamy, Sadanandane; Ayyanar, Elango; Paily, Kummankottil; Karthikeyan, Patricia Anitha; Sundararajan, Agatheswaran; Purushothaman, Jambulingam

    2016-12-01

    Human cases of scrub typhus are reported every year from Puducherry and adjoining areas in southern India. However, information on the presence of causative agent, Orientia tsutsugamushi, and its vectors is lacking. Hence, the objective of the study was to find out the vector as well as pathogen distribution in rodents and shrews present in the scrub typhus-reported areas in southern India. Trombiculid mites were collected by combing rats and shrews collected using Sherman traps and identified to species level following standard taxonomical keys. The serum samples of the animals were used for Weil-Felix test and the clots containing blood cells were used for DNA extraction and polymerase chain reaction (PCR). A total of 181 animals comprising four rodent species and one shrew species were collected from 12 villages. High proportion of chiggers was collected from the shrew, Suncus murinus (79.1%) and Rattus rattus (47.6%). A total of 10,491 trombiculid mites belonging to nine species were collected. Leptotrombidium deliense, the known vector of scrub typhus pathogen, was the predominant species (71.0%) and the chigger (L. deliense) index was 41.1 per animal. Of the 50 animals screened for the pathogen, 28 showed agglutination against OX-K in Weil-Felix test indicating the presence of antibodies against O. tsutsugamushi, the causative agent of scrub typhus. PCR carried out with the DNA extracted from blood samples of two of the animals were positive for GroEl gene of O. tsutsugamushi. L. deliense index was well above the critical limit of chigger load, indicating that all the villages were receptive for high risk of transmission of scrub typhus to human. Pathogen positivity was higher among animals collected from villages recorded for higher chigger indices due to active transmission between the chigger mites and reservoir host animals. The results are suggestive of routine vector/pathogen surveillance at hot spots to initiate timely preventive measures.

  4. [Identification of a novel WART-like chromosome rearrangement in complex heterozygotes in an interracial hybrid zone of the common shrew Sorex araneus L].

    Science.gov (United States)

    Pavlova, S V; Bulatova, N Sh

    2010-09-01

    Karyotypes uncharacteristic of pure races or hybrids were identified in the interracial hybrid zones of the common shrew Sorex araneus L. that were recently discovered in the European part of Russia. This suggests the actual existence in natural populations of WART-like rearrangements (whole-arm reciprocal translocations) along with Robertsonian fusions of acrocentrics. Demonstration of new and still rare chromosome variants is the aim of this communication.

  5. The impact of fire on habitat use by the short-snouted elephant shrew ('Elephantulus brachyrhynchus') in North West Province, South Africa

    OpenAIRE

    Yarnell, R; Metcalfe, D; Dunstone, N; Burnside, N; Scott, D

    2008-01-01

    Several studies have investigated the response of small mammal populations to fire, but few have investigated behavioural responses to habitat modification. In this study we investigated the impact of fire on home range, habitat use and activity patterns of the short-snouted elephant shrew (Elephantulus brachyrhynchus) by radio-tracking individuals before and after a fire event. All animals survived the passage of fire in termite mound refugia. Before the fire, grassland was used more than th...

  6. Bioaccumulation of lead, mercury, and cadmium in the greater white-toothed shrew, Crocidura russula, from the Ebro Delta (NE Spain); Sex- and age-dependent variation

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez-Chardi, Alejandro [Departament de Biologia Animal (Vertebrats), Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 645, 08028 Barcelona (Spain)]. E-mail: a.sanchez.chardi@ub.edu; Lopez-Fuster, Maria Jose [Departament de Biologia Animal (Vertebrats), Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 645, 08028 Barcelona (Spain); Nadal, Jacint [Departament de Biologia Animal (Vertebrats), Facultat de Biologia, Universitat de Barcelona, Avinguda Diagonal 645, 08028 Barcelona (Spain)

    2007-01-15

    We quantified bioaccumulation of lead, mercury, and cadmium in bones from 105 greater white-toothed shrews (Crocidura russula) collected at the Ebro Delta, a polluted area, and the Medas Islands, a control site. Lead and mercury levels varied with site, age, and sex, although statistical significances depended on each factor. Globally, shrews from the polluted area exhibited significantly higher concentrations of Pb and Hg. Increment of Pb with age was particularly remarkable in wetland animals and was interpreted in relation to human activities, namely hunting. Unlike males, females from the Ebro Delta maintained low Hg levels, which were associated with gestation and lactation. Cadmium levels did not differ between sites, sexes, or ages. This study provides the first data on heavy metals in mammals from this wetland and suggests that C. russula is a good bioindicator of metal pollution. We concluded that sex and age may represent an important source of variation in the bioaccumulation of these metals in wild populations. - Bioaccumulation patterns of Pb and Hg reveal sex and age-related differences in the large bones of the greater white-toothed shrew from a polluted Mediterranean wetland.

  7. 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.

  8. Flowering Trees

    Indian Academy of Sciences (India)

    Berrya cordifolia (Willd.) Burret (Syn. B. ammonilla Roxb.) – 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 ...

  9. 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 ...

  10. Flowering Trees

    Indian Academy of Sciences (India)

    sriranga

    Hook.f. ex Brandis (Yellow. Cadamba) of Rubiaceae is a large and handsome deciduous tree. Leaves are simple, large, orbicular, and drawn abruptly at the apex. Flowers are small, yellowish and aggregate into small spherical heads. The corolla is funnel-shaped with five stamens inserted at its mouth. Fruit is a capsule.

  11. Flowering Trees

    Indian Academy of Sciences (India)

    Celtis tetrandra Roxb. of Ulmaceae is a moderately large handsome deciduous tree with green branchlets and grayish-brown bark. Leaves are simple with three to four secondary veins running parallel to the mid vein. Flowers are solitary, male, female and bisexual and inconspicuous. Fruit is berry-like, small and globose ...

  12. Flowering Trees

    Indian Academy of Sciences (India)

    IAS Admin

    Aglaia elaeagnoidea (A.Juss.) Benth. of Meliaceae is a small-sized evergreen tree of both moist and dry deciduous forests. The leaves are alternate and pinnately compound, terminating in a single leaflet. Leaflets are more or less elliptic with entire margin. Flowers are small on branched inflorescence. Fruit is a globose ...

  13. Flowering Trees

    Indian Academy of Sciences (India)

    user

    Flowers are borne on stiff bunches terminally on short shoots. They are 2-3 cm across, white, sweet-scented with light-brown hairy sepals and many stamens. Loquat fruits are round or pear-shaped, 3-5 cm long and are edible. A native of China, Loquat tree is grown in parks as an ornamental and also for its fruits.

  14. Flowering Trees

    Indian Academy of Sciences (India)

    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. Leaves are thick, oblong, leathery and bright red when young. The female flowers are drooping and are larger than male flowers. Fruit is large, red in color and velvety.

  15. 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.

  16. 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.

  17. 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 ...

  18. ~{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.

  19. 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....

  20. 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.

  1. 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.

  2. Chromosome Synapsis and Recombination in Male Hybrids between Two Chromosome Races of the Common Shrew (Sorex araneus L., Soricidae, Eulipotyphla

    Directory of Open Access Journals (Sweden)

    Nadezhda M. Belonogova

    2017-10-01

    Full Text Available Hybrid zones between chromosome races of the common shrew (Sorex araneus provide exceptional models to study the potential role of chromosome rearrangements in the initial steps of speciation. The Novosibirsk and Tomsk races differ by a series of Robertsonian fusions with monobrachial homology. They form a narrow hybrid zone and generate hybrids with both simple (chain of three chromosomes and complex (chain of eight or nine synaptic configurations. Using immunolocalisation of the meiotic proteins, we examined chromosome pairing and recombination in males from the hybrid zone. Homozygotes and simple heterozygotes for Robertsonian fusions showed a low frequency of synaptic aberrations (<10%. The carriers of complex synaptic configurations showed multiple pairing abnormalities, which might lead to reduced fertility. The recombination frequency in the proximal regions of most chromosomes of all karyotypes was much lower than in the other regions. The strong suppression of recombination in the pericentromeric regions and co-segregation of race specific chromosomes involved in the long chains would be expected to lead to linkage disequilibrium between genes located there. Genic differentiation, together with the high frequency of pairing aberrations in male carriers of the long chains, might contribute to maintenance of the narrow hybrid zone.

  3. 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.

  4. Study of male–mediated gene flow across a hybrid zone in the common shrew (Sorex araneus using Y chromosome

    Directory of Open Access Journals (Sweden)

    Andrei V. Polyakov

    2017-06-01

    Full Text Available Despite many studies, the impact of chromosome rearrangements on gene flow between chromosome races of the common shrew (Sorex araneus Linnaeus, 1758 remains unclear. Interracial hybrids form meiotic chromosome complexes that are associated with reduced fertility. Nevertheless comprehensive investigations of autosomal and mitochondrial markers revealed weak or no barrier to gene flow between chromosomally divergent populations. In a narrow zone of contact between the Novosibirsk and Tomsk races hybrids are produced with extraordinarily complex configurations at meiosis I. Microsatellite markers have not revealed any barrier to gene flow, but the phenotypic differentiation between races is greater than may be expected if gene flow was unrestricted. To explore this contradiction we analyzed the distribution of the Y chromosome SNP markers within this hybrid zone. The Y chromosome variants in combination with race specific autosome complements allow backcrosses to be distinguished and their proportion among individuals within the hybrid zone to be evaluated. The balanced ratio of the Y variants observed among the pure race individuals as well as backcrosses reveals no male mediated barrier to gene flow. The impact of reproductive unfitness of backcrosses on gene flow is discussed as a possible mechanism of the preservation of race-specific morphology within the hybrid zone.

  5. 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.

    2014-01-01

    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.

  6. 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...

  7. 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...

  8. 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...

  9. The Mother, Who Is Not One: Reflections Of Motherhood In Shakespeare's Romeo And Juliet, The Tempest, And The Taming Of The Shrew

    Directory of Open Access Journals (Sweden)

    KARAMAN HATICE

    2014-12-01

    Full Text Available The lack of proper motherhood in Shakespeare's plays has been a point of attraction for many feminist critics actively engaged in emphasizing the patriarchal aspect of Shakespeare's plays. This paper aims to analyze motherhood and the lack of mother/mother-figure in The Tempest, Romeo and Juliet and The Taming of the Shrew through Luce Irigaray's theory of gender and the work of other feminist critics. The issues of gender, father-daughter relations and the reflections of the absent mothers will be discussed. Male/Female Subjectivity will also be questioned, in view of Irigaray's conceptualization of gender by relating it to Subject.

  10. ‘Misure‘ e ‘Flyting’: il linguaggio dell'inversione in The Taming of the Shrew di William Shakespeare

    Directory of Open Access Journals (Sweden)

    Bianca Del Villano

    2016-11-01

    Rilevante, in questo senso, è una delle prime commedie di Shakespeare, The Taming of the Shrew, in cui il tropo dell’inversione si articola attraverso l’originale elaborazione di una ‘inversione dell’inversione’, un device drammaturgico che reinterpreta il Misrule della tradizione, attraverso: 1 espedienti metateatrali; 2 fusione tra linguaggio cortese e scortese presentando esempi dell'antica pratica del flyting; 3 la problematizzazione dei ruoli sociali e di genere. La comunicazione che propongo analizza brevemente le forme del popolaresco in Inghilterra per soffermarsi con maggiore attenzione sul teatro shakespeariano e in particolare su La bisbetica domata.

  11. 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.

  12. 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...

  13. 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

  14. 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.

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

    Science.gov (United States)

    Fisler, Marie; Lecointre, Guillaume

    2013-01-01

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

  16. 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...

  17. 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,...

  18. Chronic psychosocial stress in tree shrews : effect of the substance P (NK1 receptor) antagonist L-760735 and clomipramine on endocrine and behavioral parameters

    NARCIS (Netherlands)

    van der Hart, MGC; de Biurrun, G; Czeh, B; Rupniak, NMJ; den Boer, JA; Fuchs, E

    Rationale: Substance P and its preferred receptor, the neurokinin 1 receptor (NK1R), have been proposed as possible targets for new antidepressant therapies, although results of a recently completed phase III trial failed to demonstrate that the NK1R antagonist MK-869 is more effective than placebo

  19. 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.

  20. 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

  1. There's Life in Hazard Trees

    Science.gov (United States)

    Mary Torsello; Toni McLellan

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

  2. 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

  3. 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...

  4. Pulvinar projections to the striatum and amygdala

    Directory of Open Access Journals (Sweden)

    Jonathan D Day-Brown

    2010-11-01

    Full Text Available Visually-guided movement is possible in the absence of conscious visual perception, a phenomenon referred to as blindsight. Similarly, fearful images can elicit emotional responses in the absence of their conscious perception. Both capabilities are thought to be mediated by pathways from the retina through the superior colliculus (SC and pulvinar nucleus. To define potential pathways that underlie behavioral responses to unperceived visual stimuli, we examined the projections from the pulvinar nucleus to the striatum and amygdala in the tree shrew (Tupaia belangeri, a species considered to be a protypical primate. The tree shrew brain has a large pulvinar nucleus that contains two SC-recipient subdivisions; the dorsal (Pd and central (Pc pulvinar both receive topographic (specific projections from SC, and Pd receives an additional nontopographic (diffuse projection from SC (Chomsung et al., 2008; JCN 510:24-46. Anterograde and retrograde tract tracing revealed that both Pd and Pc project to the caudate and putamen, and Pd, but not Pc, additionally projects to the lateral amygdala. Using immunocytochemical staining for substance P (SP and parvalbumin (PV to reveal the patch/matrix organization of tree shrew striatum, we found that SP-rich/PV-poor patches interlock with a PV-rich/SP-poor matrix. Confocal microscopy revealed that tracer-labeled pulvinostriatal terminals preferentially innervate the matrix. Electron microscopy revealed that the postsynaptic targets of tracer-labeled pulvino-striatal and pulvino-amygdala terminals are spines, demonstrating that the pulvinar nucleus projects to the spiny output cells of the striatum matrix and the lateral amygdala, potentially relaying: 1 topographic visual information from SC to striatum to aid in guiding precise movements, and 2 nontopographic visual information from SC to the amygdala alerting the animal to potentially dangerous visual images.

  5. 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...

  6. Phylogeography and recolonization of the Swiss Alps by the Valais shrew (Sorex antinorii), inferred with autosomal and sex-specific markers.

    Science.gov (United States)

    Yannic, G; Basset, P; Hausser, J

    2008-09-01

    Using one male-inherited, one female-inherited and eight biparentally inherited markers, we investigate the population genetic structure of the Valais shrew (Sorex antinorii) in the Swiss Alps. Bayesian analysis on autosomal microsatellites suggests a clear genetic differentiation between two groups of populations. This geographically based structure is consistent with two separate postglacial recolonization routes of the species into Switzerland from Italian refugia after the last Pleistocene glaciations. Sex-specific markers also confirm genetic structuring among western and eastern areas, since very few haplotypes for either Y chromosome or mtDNA genome are shared between the two regions. Overall, these results suggest that two already well-differentiated genetic lineages colonized the Swiss Alps and came into secondary contact in the Rhône Valley. Low level of admixture between the two lineages is likely explained by the mountainous landscape structure of lateral valleys orthogonal to the main Rhône valley.

  7. 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.

  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. 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.

  10. Minnesota's Forest Trees. Revised.

    Science.gov (United States)

    Miles, William R.; Fuller, Bruce L.

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

  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...

  12. 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 ...

  13. 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…

  14. 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....

  15. 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.

  16. Spectra of chemical trees

    International Nuclear Information System (INIS)

    Balasubramanian, K.

    1982-01-01

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

  17. Refining discordant gene trees.

    Science.gov (United States)

    Górecki, Pawel; Eulenstein, Oliver

    2014-01-01

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

  18. shrew, Croeidura bieolor

    African Journals Online (AJOL)

    Mealworms, used as a supplement when insect catches were low, were not preferred and dung beetles were refused. On March 14, at 22h50 the female gave birth to two offspring (sexes undetermined). Parturition of the first young was not seen but that of the second was followed to com- pletion. A typical parturition posture ...

  19. 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.

  20. 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...

  1. 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,...

  2. 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...

  3. Fragmentation of random trees

    International Nuclear Information System (INIS)

    Kalay, Z; Ben-Naim, E

    2015-01-01

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

  4. 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...

  5. Tree growth visualization

    Science.gov (United States)

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

    2005-01-01

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

  6. Flowering T Flowering Trees

    Indian Academy of Sciences (India)

    Adansonia digitata L. ( The Baobab Tree) of Bombacaceae is a tree with swollen trunk that attains a dia. of 10m. Leaves are digitately compound with leaflets up to 18cm. long. Flowers are large, solitary, waxy white, and open at dusk. They open in 30 seconds and are bat pollinated. Stamens are many. Fruit is about 30 cm ...

  7. Fault tree graphics

    International Nuclear Information System (INIS)

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

    1975-01-01

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

  8. 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...

  9. 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...

  10. 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.

  11. 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…

  12. 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...

  13. 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)

  14. Generalising tree traversals and tree transformations to DAGs

    DEFF Research Database (Denmark)

    Bahr, Patrick; Axelsson, Emil

    2017-01-01

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

  15. Patterns of morphological variation amongst semifossorial shrews in the highlands of Guatemala, with the description of a new species (Mammalia, Soricomorpha, Soricidae)

    Science.gov (United States)

    Woodman, Neal

    2011-01-01

    Members of the Cryptotis goldmani group of small-eared shrews (Mammalia, Soricomorpha, Soricidae) represent a clade within the genus that is characterized by modifications of the forelimb that include broadened forefeet, elongated and broadened foreclaws, and massive humeri with enlarged processes. These modifications are consistent with greater adaptation to their semifossorial habits than other members of the genus. The species in this group occur discontinuously in temperate highlands from southern Tamaulipas, Mexico, to Honduras. In Guatemala, there are three species: the relatively widespread Cryptotis goodwini and two species (Cryptotis lacertosus, Cryptotis mam) endemic to highland forests in the Sierra de los Cuchumatanes of western Guatemala. Ongoing studies focusing on the relationships of variation in cranial and postcranial skeletal morphology have revealed a fourth species from remnant cloud forest in the Sierra de Yalijux, central Guatemala. In this paper, I describe this new species and characterize its morphology relative to other species in the C. goldmani group and to other species of Cryptotis in Guatemala. In addition, I summarize available details of its habitat and ecology.

  16. A recursive algorithm for trees and forests

    OpenAIRE

    Guo, Song; Guo, Victor J. W.

    2017-01-01

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

  17. 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.

  18. 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...

  19. The gravity apple tree

    International Nuclear Information System (INIS)

    Aldama, Mariana Espinosa

    2015-01-01

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

  20. Visualizing phylogenetic tree landscapes.

    Science.gov (United States)

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

    2017-02-02

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

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

    NARCIS (Netherlands)

    Eilmann, B.; Rigling, A.

    2012-01-01

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

  2. 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...

  3. A bijection between phylogenetic trees and plane oriented recursive trees

    OpenAIRE

    Prodinger, Helmut

    2017-01-01

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

  4. A Suffix Tree Or Not a Suffix Tree?

    DEFF Research Database (Denmark)

    Starikovskaya, Tatiana; Vildhøj, Hjalte Wedel

    2015-01-01

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

  5. 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...

  6. Trees for future forests

    DEFF Research Database (Denmark)

    Lobo, Albin

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

  7. 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

  8. 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....

  9. 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....

  10. 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

  11. Benefit-based tree valuation

    Science.gov (United States)

    E.G. McPherson

    2007-01-01

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

  12. 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

  13. 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

  14. 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.

  15. 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...

  16. 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...

  17. 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....

  18. ColorTree: a batch customization tool for phylogenic trees.

    Science.gov (United States)

    Chen, Wei-Hua; Lercher, Martin J

    2009-07-31

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

  19. 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...... 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....

  20. 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.

  1. Rediscovery of the type series of the Acadian Masked Shrew, Sorex acadicus Gilpin, 1865 (Mammalia: Soricidae), with the designation of a neotype and a reevaluation of its taxonomic status

    Science.gov (United States)

    Woodman, Neal

    2018-01-01

    The name Sorex acadicus Gilpin, 1865 is currently recognized as the valid name for the Nova Scotian subspecies of the masked shrew, S. cinereus Kerr, 1792 (Mammalia: Soricidae), but a holotype for the taxon was never designated, and the location of the type series has been a mystery. The authority for this species, John Bernard Gilpin, was associated with the Nova Scotia Museum, Halifax, NS, but that institution has no Gilpin specimens in its possession, and I could find no record of Gilpin shrews in any other Canadian Museum. I recently discovered a series of Gilpin specimens in the Mammal Collection of the National Museum of Natural History, Washington, DC (USNM), some of which may have been part of the original type series of S. acadicus, and I show that these specimens best represent Gilpin's concept of the taxon. From this series, I designate a neotype for S. acadicus. I also evaluate the distinctiveness of Nova Scotian S. c. acadicus compared with S. c. cinereus from Maine, New Brunswick, and New Hampshire and determine that S. acadicus should be considered a junior synonym of S. c. cinereus.

  2. Synaptonemal complex analysis of interracial hybrids between the Moscow and Neroosa chromosomal races of the common shrew Sorex araneus showing regular formation of a complex meiotic configuration (ring-of-four).

    Science.gov (United States)

    Matveevsky, Sergey N; Pavlova, Svetlana V; Maret M Acaeva; Oxana L Kolomiets

    2012-01-01

    Immunocytochemical and electron microscopic analysis of synaptonemal complexes (SCs) was carried out for the first time in homozygotes and complex Robertsonian heterozygotes (hybrids) of the common shrew, Sorex araneus Linnaeus, 1758, from a newly discovered hybrid zone between the Moscow and the Neroosa chromosomal races. These races differ in four monobrachial homologous metacentrics, and closed SC tetravalent is expected to be formed in meiosis of a hybrid. Indeed, such a multivalent was found at meiotic prophase I in hybrids. Interactions between multivalent and both autosomes and/or the sex chromosomes were observed. For the first time we have used immunocytochemical techniques to analyse asynapsis in Sorex araneus and show that the multivalent pairs in an orderly fashion with complete synapsis. Despite some signs of spermatocytes arrested in the meiotic prophase I, hybrids had large number of active sperm. Thus, Moscow - Neroosa hybrid males that form a ring-of-four meiotic configuration are most likely not sterile. Our results support previous demonstrations that monobrachial homology of metacentrics of the common shrew does not lead to complete reproductive isolation between parapatric chromosomal races of the species.

  3. Synaptonemal complex analysis of interracial hybrids between the Moscow and Neroosa chromosomal races of the common shrew Sorex araneus showing regular formation of a complex meiotic configuration (ring-of-four

    Directory of Open Access Journals (Sweden)

    Sergey Matveevsky

    2012-09-01

    Full Text Available Immunocytochemical and electron microscopic analysis of synaptonemal complexes (SCs was carried out for the first time in homozygotes and complex Robertsonian heterozygotes (hybrids of the common shrew, Sorex araneus Linnaeus, 1758, from a newly discovered hybrid zone between the Moscow and the Neroosa chromosomal races. These races differ in four monobrachial homologous metacentrics, and closed SC tetravalent is expected to be formed in meiosis of a hybrid. Indeed, such a multivalent was found at meiotic prophase I in hybrids. Interactions between multivalent and both autosomes and/or the sex chromosomes were observed. For the first time we have used immunocytochemical techniques to analyse asynapsis in S. araneus and show that the multivalent pairs in an orderly fashion with complete synapsis. Despite some signs of spermatocytes arrested in the meiotic prophase I, hybrids had large number of active sperm. Thus, Moscow – Neroosa hybrid males that form a ring-of-four meiotic configuration are most likely not sterile. Our results support previous demonstrations that monobrachial homology of metacentrics of the common shrew does not lead to complete reproductive isolation between parapatric chromosomal races of the species.

  4. Embedding complete ternary tree in hypercubes using AVL trees

    NARCIS (Netherlands)

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

    2008-01-01

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

  5. 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

  6. 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 ...

  7. Programming macro tree transducers

    DEFF Research Database (Denmark)

    Bahr, Patrick; Day, Laurence E.

    2013-01-01

    transducers can be concisely represented in Haskell, and demonstrate the benefits of utilising such an approach with a number of examples. In particular, tree transducers afford a modular programming style as they can be easily composed and manipulated. Our Haskell representation generalises the original...

  8. 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....

  9. A Universal Phylogenetic Tree.

    Science.gov (United States)

    Offner, Susan

    2001-01-01

    Presents a universal phylogenetic tree suitable for use in high school and college-level biology classrooms. Illustrates the antiquity of life and that all life is related, even if it dates back 3.5 billion years. Reflects important evolutionary relationships and provides an exciting way to learn about the history of life. (SAH)

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. Adjustable chain trees for proteins

    DEFF Research Database (Denmark)

    Winter, Pawel; Fonseca, Rasmus

    2012-01-01

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

  15. Introduction to fault tree analysis

    International Nuclear Information System (INIS)

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

    1975-01-01

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

  16. The Re-Think Tree.

    Science.gov (United States)

    Gear, Jim

    1993-01-01

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

  17. 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…

  18. 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...

  19. 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...

  20. Genetic transformation of forest trees

    African Journals Online (AJOL)

    Admin

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

  1. TREE SELECTING AND TREE RING MEASURING IN DENDROCHRONOLOGICAL INVESTIGATIONS

    Directory of Open Access Journals (Sweden)

    Sefa Akbulut

    2004-04-01

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

  2. 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.

  3. "European" race-specific metacentrics in East Siberian common shrews (Sorex araneus): a description of two new chromosomal races, Irkutsk and Zima.

    Science.gov (United States)

    Pavlova, Svetlana V; Borisov, Sergei A; Timoshenko, Alexander F; Sheftel, Boris I

    2017-01-01

    Karyotype studies of common shrews in the vicinity of Lake Baikal (Irkutsk Region, Eastern Siberia) resulted in the description of two new chromosomal races of Sorex araneus Linnaeus, 1758 (Lypotyphla, Mammalia), additional to 5 races formerly found in Siberia. In the karyotypes of 12 specimens from 3 locations, the polymorphism of metacentric and acrocentric chromosomes of the Robertsonian type was recorded and two distinct groups of karyotypes interpreted as the chromosomal races were revealed. They are geographically distant and described under the racial names Irkutsk (Ir) and Zima (Zi). Karyotypes of both races were characterized by species-specific (the same for all 74 races known so far) metacentric autosomes af, bc, tu and jl , and the typical sex chromosome system - XX/XY 1 Y 2 . The race-specific arm chromosome combinations include three metacentrics and four acrocentrics in the Irkutsk race ( gk, hi, nq, m, o, p, r ) and four metacentrics and two acrocentrics in the Zima race ( gm, hi, ko, nq, p, r ). Within the races, individuals with polymorphic chromosomes were detected ( g/m, k/o, n/q, p/r ). The presence of the specific metacentric gk allowed us to include the Irkutsk race into the Siberian Karyotypic Group (SKG), distributed in surrounding regions. The Zima race karyotype contained two metacentrics, gm and ko , which have been never found in the Siberian part of the species range, but appear as the common feature of chromosomal races belonging to the West European Karyotypic Group (WEKG). Moreover, the metacentrics of that karyotype are almost identical to the Åkarp race (except the heterozygous pair p/r ) locally found in the southern Sweden. One of two Siberian races described here for the first time, the Zima race, occurs in an area considerably distant from Europe and shares the common metacentrics ( gm, hi, ko ) with races included in WEKG. This fact may support a hypothesis of independent formation of identical arm chromosome combinations

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

    Science.gov (United States)

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

    2014-03-06

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

  5. Fault tree analysis

    International Nuclear Information System (INIS)

    1981-09-01

    Suggestion are made concerning the method of the fault tree analysis, the use of certain symbols in the examination of system failures. This purpose of the fault free analysis is to find logical connections of component or subsystem failures leading to undesirable occurrances. The results of these examinations are part of the system assessment concerning operation and safety. The objectives of the analysis are: systematical identification of all possible failure combinations (causes) leading to a specific undesirable occurrance, finding of reliability parameters such as frequency of failure combinations, frequency of the undesirable occurrance or non-availability of the system when required. The fault tree analysis provides a near and reconstructable documentation of the examination. (orig./HP) [de

  6. Tree-level formalism

    International Nuclear Information System (INIS)

    Brandhuber, Andreas; Spence, Bill; Travaglini, Gabriele

    2011-01-01

    We review two novel techniques used to calculate tree-level scattering amplitudes efficiently: MHV diagrams, and on-shell recursion relations. For the MHV diagrams, we consider applications to tree-level amplitudes and focus in particular on the N=4 supersymmetric formulation. We also briefly describe the derivation of loop amplitudes using MHV diagrams. For the recursion relations, after presenting their general proof, we discuss several applications to massless theories with and without supersymmetry, to theories with massive particles, and to graviton amplitudes in general relativity. This article is an invited review for a special issue of Journal of Physics A: Mathematical and Theoretical devoted to 'Scattering amplitudes in gauge theories'. (review)

  7. Tree Rings: Timekeepers of the Past.

    Science.gov (United States)

    Phipps, R. L.; McGowan, J.

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

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. Making CSB + -Trees Processor Conscious

    DEFF Research Database (Denmark)

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

    2005-01-01

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

  13. 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...

  14. (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.

  15. 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.

  16. On Determining if Tree-based Networks Contain Fixed Trees.

    Science.gov (United States)

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

    2016-05-01

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

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

    Science.gov (United States)

    G.H. Donovan; D.T. Butry

    2010-01-01

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

  18. Systolic trees and systolic language recognition by tree automata

    Energy Technology Data Exchange (ETDEWEB)

    Steinby, M

    1983-01-01

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

  19. 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...

  20. 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

  1. Phylogenetic trees and Euclidean embeddings.

    Science.gov (United States)

    Layer, Mark; Rhodes, John A

    2017-01-01

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

  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. 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...

  4. 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.

  5. 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.

  6. 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

  7. 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.

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

    African Journals Online (AJOL)

    PROF HORSFALL

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

  9. 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.

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

    Science.gov (United States)

    Vaughn, Brandon K.; Wang, Qiu

    2010-01-01

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

  11. 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%; ...

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

    Science.gov (United States)

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

    2004-01-01

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

  13. Better trees through systematic breeding

    Science.gov (United States)

    Robert Z. Callaham

    1957-01-01

    Today I would like to tell you briefly about the efforts of forest geneticists to improve the quality of forest trees. What do we mean by quality? Here, the consumer has the first word. The trees we produce are primarily for timber production, and the timber growing and wood-using industries give us our guidelines. Nevertheless, many of the characteristics sought by...

  14. 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,...

  15. 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…

  16. Boosted decision trees and applications

    International Nuclear Information System (INIS)

    Coadou, Y.

    2013-01-01

    Decision trees are a machine learning technique more and more commonly used in high energy physics, while it has been widely used in the social sciences. After introducing the concepts of decision trees, this article focuses on its application in particle physics. (authors)

  17. 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...

  18. Mean-field lattice trees

    NARCIS (Netherlands)

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

    1999-01-01

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

  19. 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

  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. Totally optimal decision trees for Boolean functions

    KAUST Repository

    Chikalov, Igor; Hussain, Shahid; Moshkov, Mikhail

    2016-01-01

    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

  3. Are There Infinite Irrigation Trees?

    Science.gov (United States)

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

    2006-08-01

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

  4. Molecular evolution of the neurohypophysial hormone precursors in mammals: Comparative genomics reveals novel mammalian oxytocin and vasopressin analogues.

    Science.gov (United States)

    Wallis, Michael

    2012-11-01

    Among vertebrates the neurohypophysial hormones show considerable variation. However, in eutherian mammals they have been considered rather conserved, with arginine vasopressin (AVP) and oxytocin (OT) in all species except pig and some relatives, where lysine vasopressin replaces AVP. The availability of genomic data for a wide range of mammals makes it possible to assess whether these peptides and their precursors may be more variable in Eutheria than previously suspected. A survey of these data confirms that AVP and OT occur in most eutherians, but with exceptions. In a New-World monkey (marmoset, Callithrix jacchus) and in tree shrew (Tupaia belangeri), Pro(8)OT replaces OT, confirming a recent report for these species. In armadillo (Dasypus novemcinctus) Leu(3)OT replaces OT, while in tenrec (Echinops telfairi) Thr(4)AVP replaces AVP. In these two species there is also evidence for additional genes/pseudogenes, encoding much-modified forms of AVP, but in most other eutherian species there is no evidence for additional neurohypophysial hormone genes. Evolutionary analysis shows that sequences of eutherian neurohypophysial hormone precursors are generally strongly conserved, particularly those regions encoding active peptide and neurophysin. The close association between OT and VP genes has led to frequent gene conversion of sequences encoding neurophysins. A monotreme, platypus (Ornithorhynchus anatinus) has genes for OT and AVP, organized tail-to-tail as in eutherians, but in marsupials 3-4 genes are present for neurohypophysial hormones, organized tail-to-head as in lower vertebrates. Copyright © 2012 Elsevier Inc. All rights reserved.

  5. 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.

  6. Linking and Cutting Spanning Trees

    Directory of Open Access Journals (Sweden)

    Luís M. S. Russo

    2018-04-01

    Full Text Available We consider the problem of uniformly generating a spanning tree for an undirected connected graph. This process is useful for computing statistics, namely for phylogenetic trees. We describe a Markov chain for producing these trees. For cycle graphs, we prove that this approach significantly outperforms existing algorithms. For general graphs, experimental results show that the chain converges quickly. This yields an efficient algorithm due to the use of proper fast data structures. To obtain the mixing time of the chain we describe a coupling, which we analyze for cycle graphs and simulate for other graphs.

  7. 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.

  8. 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...... 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...... images such as halftones. By utilizing randomized subsampling in the template selection, the speed becomes acceptable for practical image coding...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1979-01-01

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

  10. 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...... is not sound. Therefore, we complement our implementation of the recursion scheme with a number of correspondence theorems that ensure soundness for various classes of traversals. We illustrate the practical applicability of the implementation as well as the complementing theory with a number of examples....

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

    Science.gov (United States)

    Eilmann, Britta; Rigling, Andreas

    2012-02-01

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

  12. 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...

  13. 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 ...

  14. 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.

  15. 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

  16. Trees as metal scavengers

    International Nuclear Information System (INIS)

    Hallman, N.

    2000-01-01

    Full text: Tree roots extract metal ions form wet soils in two different ways. At the soil/root hair interface soluble ions in contact with the cellulose wall move through it and enter the cell through the plasmalemma; the semi permeable membrane that encloses every living cell. Some ions, especially those that are part of cellular metabolic processes eg. Na, K, Fe, Mg, S move into the cytoplasm, are bound into organic complexes and travel from cell to cell within the cytoplasm. This requires energy, and the amount of any of these metabolically active ions taken in tends to be regulated by the plant. The movement of the ions from cell to cell is slow, selective, and regulated by requirements of synthesis of for example Mg in the chlorophyll molecule. This means that more Mg is transported to cells of leaves than of cells of roots. This movement of ions is simplistic, or within the cytoplasm. Other ions are swept along in the transpiration stream and enter the complex plumbing system that brings water to the leaves for metabolism and cooling. Water in this apoplastic pathway travels within the pipes (xylem) of the wood and in the cellulose of the walls. It travels along essentially non-living parts of the plant. Ions such as As, Pb, Ni, Cr accumulate in sites such as leaves and bark. Analysis of plant parts can indicate the presence of heavy metals and can give an indication of ore bodies within the root zone

  17. The Tree of Industrial Life

    DEFF Research Database (Denmark)

    Andersen, Esben Sloth

    2002-01-01

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

  18. Fremont Tree-Well Filter

    Science.gov (United States)

    Information about the SFBWQP Fremont Tree-Well Filter Spine project, part of an EPA competitive grant program to improve SF Bay water quality focused on restoring impaired waters and enhancing aquatic resources.

  19. 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.

  20. 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.

  1. 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...... that is suitable for large contour trees and efficiently conveys the topological structure of the most important isosurface components. This visualization is integrated into a histogram of the volume data; thus, it offers strictly more information than a traditional histogram. We present algorithms...... to automatically compute the graph layout and to calculate appropriate approximations of the contour tree and the surface area of the relevant isosurface components. The benefits of this new visualization are demonstrated with the help of several publicly available volume data sets....

  2. 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...

  3. 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

  4. Border trees of complex networks

    International Nuclear Information System (INIS)

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

    2008-01-01

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

  5. 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.

  6. Objective consensus from decision trees

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  7. 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.

  8. 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...

  9. 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...

  10. 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...

  11. 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.

  12. Field guide to red tree vole nests

    Science.gov (United States)

    Damon B. Lesmeister; James K. Swingle

    2017-01-01

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

  13. Mitered fractal trees: constructions and properties

    NARCIS (Netherlands)

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

    2012-01-01

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

  14. Critical wind speed at which trees break.

    Science.gov (United States)

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

    2016-02-01

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

  15. 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

  16. Colourings of (k-r,k-trees

    Directory of Open Access Journals (Sweden)

    M. Borowiecki

    2017-01-01

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

  17. 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.

  18. Tree Notation: an antifragile program notation

    OpenAIRE

    Yunits, Breck

    2017-01-01

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

  19. 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

  20. Leucismo en la musaraña de orejas cortas Cryptotis mexicana (Mammalia: Soricomorpha, endémica de México Leucism in Mexican small-eared shrew Cryptotis mexicana (Mammalia: Soricomorpha, endemic to Mexico

    Directory of Open Access Journals (Sweden)

    Lázaro Guevara

    2011-06-01

    Full Text Available El leucismo es la reducción de la pigmentación parcial o total del pelaje, pero que mantiene la coloración normal de los ojos y la piel. Aquí se presenta el registro de un individuo de la musaraña endémica de México Cryptotis mexicana recolectado en Veracruz, México, que presenta esta condición. Esta coloración, considerada anormal en estado silvestre, puede incrementar la presión de selección sobre esos individuos. Además, es un reflejo indirecto de la baja variabilidad genética en las poblaciones naturales.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, México, that displays leucism. This lack of pigmentation, uncommon in the wild, may result in negative selective pressure on these mammals. Moreover, this genetic-based condition reflects on the low levels of genetic variability within natural populations.

  1. 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.

  2. Isoprene emission from Indian trees

    Science.gov (United States)

    Varshney, C. K.; Singh, Abhai Pratap

    2003-12-01

    Isoprene is the most dominant non-methane volatile organic compound (NMVOC) emitted by plants. NMVOCs play an important role in regulating the composition of atmospheric trace gases including global concentration of tropospheric ozone. Our present knowledge about NMVOCs emission is mainly from studies on temperate tree species. So far information on biogenic NMVOCs emission from tropical tree species is limited. In this study, isoprene emission rates from 40 tropical Indian tree species belonging to 33 genera and 17 families were measured for the first time using a dynamic flow through enclosure chamber technique. The isoprene emission rate from plants (30°C and PAR 1000 μmolm-2s-1) ranged from undetectable to 81.5 μg g-1 h-1 and values were found to be comparable with other studies on tropical tree species. Tree species screened for isoprene emission in the present study may be grouped into the four categories, proposed by [2001], namely, 18 species were negligible or BDL isoprene emitting (Morus alba Linn., which were earlier reported as BDL or non isoprene emitters in US [, 1998; , 2001] were found to be appreciably high isoprene emitters (0.61-21.60 μg g-1 h-1) in the present study.

  3. Automated Generation of Attack Trees

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  4. Stress-Induced Neurodegeneration: Mechanisms and Interventions

    National Research Council Canada - National Science Library

    Meyerhoff, James

    2000-01-01

    .... chronic stress in several species, including mouse, rat, tree shrew and monkey, have been reported to develop alterations in hippocampal morphology, including apical dendritic atrophy, depletion...

  5. 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.

  6. 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.

  7. 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

  8. Interpreting the universal phylogenetic tree

    Science.gov (United States)

    Woese, C. R.

    2000-01-01

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

  9. Columnar apple tree named 'Moonlight'

    OpenAIRE

    Tupý, J. (Jaroslav); Louda, O. (Otto); Zima, J. (Jan)

    2010-01-01

    A new and distinct Malus domestica (Borkh.) apple tree variety is provided which exhibits a columnar tree type, weakly vigorous compact growth, predominant bearing on spurs and V.sub.f-resistance against scab. The new variety yields late maturing, medium-sized, globose-conical to conical fruits having good storage quality. The fruit color is yellow-green to yellow with a partial red to orange blush. The fruits have a yellow-colored firm flesh that is crisp and juicy with a good sweet/sour bal...

  10. 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....

  11. 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 ...

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

    Science.gov (United States)

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

    2012-11-15

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

  13. 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…

  14. 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.

  15. 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.

  16. On Tree-Based Phylogenetic Networks.

    Science.gov (United States)

    Zhang, Louxin

    2016-07-01

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

  17. 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.

  18. Integrating cyber attacks within fault trees

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-09-15

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

  19. Recursive algorithms for phylogenetic tree counting.

    Science.gov (United States)

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

    2013-10-28

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

  20. A Metric on Phylogenetic Tree Shapes.

    Science.gov (United States)

    Colijn, C; Plazzotta, G

    2018-01-01

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

  1. 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.

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

    Science.gov (United States)

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

    2011-06-01

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

  3. GumTree: Data reduction

    Energy Technology Data Exchange (ETDEWEB)

    Rayner, Hugh [Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia)]. E-mail: hrz@ansto.gov.au; Hathaway, Paul [Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia); Hauser, Nick [Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia); Fei, Yang [Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia); Franceschini, Ferdi [Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia); Lam, Tony [Bragg Institute, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW (Australia)

    2006-11-15

    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.

  4. 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...

  5. Induction of Ordinal Decision Trees

    NARCIS (Netherlands)

    J.C. Bioch (Cor); V. Popova (Viara)

    2003-01-01

    textabstractThis paper focuses on the problem of monotone decision trees from the point of view of the multicriteria decision aid methodology (MCDA). By taking into account the preferences of the decision maker, an attempt is made to bring closer similar research within machine learning and MCDA.

  6. 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.

  7. 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.

  8. Eucalyptus as a landscape tree

    Science.gov (United States)

    W. Douglas Hamilton

    1983-01-01

    Ninety-two species of Eucalyptus were evaluated at the University of California re- search station in San Jose. The purpose: to find acceptable new street and park trees. Growth rates and horticultural characteristics were noted. Forty-three species were studied in locations statewide to evaluate site adaptation and landscape usefulness; flooded, cold, dry, saline....

  9. 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...

  10. 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)…

  11. The Trees that surround us

    Science.gov (United States)

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

    2012-04-01

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

  12. Wellhead and tree standards updated

    International Nuclear Information System (INIS)

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

    1996-01-01

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

  13. The Tree of Life Project

    Science.gov (United States)

    Milbrath, Sherry

    2009-01-01

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

  14. 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

  15. 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

  16. Can Children Read Evolutionary Trees?

    Science.gov (United States)

    Ainsworth, Shaaron; Saffer, Jessica

    2013-01-01

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

  17. Top tips from tree tops

    Science.gov (United States)

    Ornes, Stephen

    2018-04-01

    The ability of trees to cool by transporting water from their roots to the leaves has been known for centuries. But as Stephen Ornes discovers, the principles of transpiration are also inspiring innovative techniques to cool vehicles travelling at hypersonic speeds, where unwanted heat is a problem too

  18. 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 comm...

  19. 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...

  20. Interactive wood combustion for botanical tree models

    KAUST Repository

    Pirk, Sö ren; Jarząbek, Michał; Hadrich, Torsten; Michels, Dominik L.; Palubicki, Wojciech

    2017-01-01

    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

  1. EDITORIAL Development Linkages between Tree Breeding ...

    African Journals Online (AJOL)

    EDITORIAL Development Linkages between Tree Breeding Programmes and National/Regional Tree Seed Centres in Africa. ... Discovery and Innovation. Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current Issue · Archives.

  2. Systolic automata for VLSI on balanced trees

    Energy Technology Data Exchange (ETDEWEB)

    Culik, K Ii; Gruska, J; Salomaa, A

    1983-01-01

    Systolic tree automata with a binary (or, more generally, balanced) underlying tree are investigated. The main emphasis is on input conditions, decidability, and characterization of acceptable languages. 4 references.

  3. 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

  4. Computing Refined Buneman Trees in Cubic Time

    DEFF Research Database (Denmark)

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

    2003-01-01

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

  5. 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.

  6. 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

  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. Locating a tree in a phylogenetic network

    OpenAIRE

    van Iersel, Leo; Semple, Charles; Steel, Mike

    2010-01-01

    Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a phylogenetic network and a cluster of species, the Cluster Containment problem asks whether the given cluster is a cluster of some phylogenetic tree embedded in the network. Both problems are known to be NP-complete in general. In this article, we consider t...

  10. The transposition distance for phylogenetic trees

    OpenAIRE

    Rossello, Francesc; Valiente, Gabriel

    2006-01-01

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

  11. 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.

  12. The national tree-list layer

    Science.gov (United States)

    Stacy A. Drury; Jason M. Herynk

    2011-01-01

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

  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. Measuring and analyzing urban tree cover

    Science.gov (United States)

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

    1996-01-01

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

  15. Understanding the challenges of municipal tree planting

    Science.gov (United States)

    E.G. McPherson; R. Young

    2010-01-01

    Nine of the twelve largest cities in the U.S. have mayoral tree planting initiatives (TPIs), with pledges to plant nearly 20 million trees. Although executive-level support for trees has never been this widespread, many wonder if this support will endure as administrations change and budgets tighten. In an effort to share lessons learned from successes and setbacks, a...

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

    African Journals Online (AJOL)

    philiph

    contribution of agro-forestry tree products to the livelihood of rural farmers was high and accounted for ... systems in which trees are grown with ... livelihood of farmers in rural areas and .... pulp, the seed are boiled in water and dried .... treatment of fracture/dislocation of bones. Some agroforestry trees that provides the rural ...

  17. Sampling the quality of hardwood trees

    Science.gov (United States)

    Adrian M. Gilbert

    1959-01-01

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

  18. Locating a tree in a phylogenetic network

    NARCIS (Netherlands)

    Iersel, van L.J.J.; Semple, C.; Steel, M.A.

    2010-01-01

    Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a phylogenetic network and a cluster of species, the Cluster

  19. Finding small equivalent decision trees is hard

    NARCIS (Netherlands)

    Zantema, H.; Bodlaender, H.L.

    2000-01-01

    Two decision trees are called decision equivalent if they represent the same function, i.e., they yield the same result for every possible input. We prove that given a decision tree and a number, to decide if there is a decision equivalent decision tree of size at most that number is NPcomplete. As

  20. 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

  1. 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

  2. Coalescent methods for estimating phylogenetic trees.

    Science.gov (United States)

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

    2009-10-01

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

  3. 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...

  4. 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...

  5. 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...

  6. Carbon dynamics in trees: feast or famine?

    Science.gov (United States)

    Anna Sala; David R. Woodruff; Fredrick C. Meinzer

    2012-01-01

    Research on the degree to which carbon (C) availability limits growth in trees, as well as recent trends in climate change and concurrent increases in drought related tree mortality, have led to a renewed focus on the physiological mechanisms associated with tree growth responses to current and future climate. This has led to some dispute over the role of stored...

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

    NARCIS (Netherlands)

    Soliz Gamboa, C.C.

    2010-01-01

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

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

    Science.gov (United States)

    Thomas B. Lynch; Robert F. Wittwer

    2002-01-01

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

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

    Science.gov (United States)

    E. Gregory McPherson

    2014-01-01

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

  11. Identification of the sexually dimorphic gastrin-releasing peptide system in the lumbosacral spinal cord that controls male reproductive function in the mouse and Asian house musk shrew (Suncus murinus).

    Science.gov (United States)

    Tamura, Kei; Kobayashi, Yasuhisa; Hirooka, Asuka; Takanami, Keiko; Oti, Takumi; Jogahara, Takamichi; Oda, Sen-Ichi; Sakamoto, Tatsuya; Sakamoto, Hirotaka

    2017-05-01

    Several regions of the brain and spinal cord control male reproductive function. We previously demonstrated that the gastrin-releasing peptide (GRP) system, located in the lumbosacral spinal cord of rats, controls spinal centers to promote penile reflexes during male copulatory behavior. However, little information exists on the male-specific spinal GRP system in animals other than rats. The objective of this study was to examine the functional generality of the spinal GRP system in mammals using the Asian house musk shrew (Suncus murinus; suncus named as the laboratory strain), a specialized placental mammal model. Mice are also used for a representative model of small laboratory animals. We first isolated complementary DNA encoding GRP in suncus. Phylogenetic analysis revealed that suncus preproGRP was clustered to an independent branch. Reverse transcription-PCR showed that GRP and its receptor mRNAs were both expressed in the lumbar spinal cord of suncus and mice. Immunohistochemistry for GRP demonstrated that the sexually dimorphic GRP system and male-specific expression/distribution patterns of GRP in the lumbosacral spinal cord in suncus are similar to those of mice. In suncus, we further found that most GRP-expressing neurons in males also express androgen receptors, suggesting that this male-dominant system in suncus is also androgen-dependent. Taken together, these results indicate that the sexually dimorphic spinal GRP system exists not only in mice but also in suncus, suggesting that this system is a conserved property in mammals. J. Comp. Neurol. 525:1586-1598, 2017. © 2016 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

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

    Science.gov (United States)

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

    2008-07-01

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

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

    OpenAIRE

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

    2009-01-01

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

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

    Science.gov (United States)

    2013-01-01

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

  15. Navigation and Tree Mapping in Orchards

    DEFF Research Database (Denmark)

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

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

  16. Computer aided construction of fault tree

    International Nuclear Information System (INIS)

    Kovacs, Z.

    1982-01-01

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

  17. Air pollution and tree growth

    Energy Technology Data Exchange (ETDEWEB)

    Scurfield, G

    1960-01-01

    The problem of air pollution is reviewed with emphasis on its origin and its effects on trees and shrubs. These effects are described from two points of view: the effects of general air pollution, and also the effects of specific pollutants. The considerable mixing, dilution and interaction that pollutants undergo in the air often renders it exceedingly difficult to assign pollution damage to any specific chemical or physical entity. Moreover, it is often impossible to assign responsibility for damage to any particular source. The constituents of general air pollution may be subdivided into those potentially incapable, and those potentially capable, of entering the plant either through the leaf stomata or indirectly by way of the soil. Specific pollutants cause damage directly, as well as indirectly from the chemical reactions that occur in the polluted atmosphere. Sulfur dioxide is discussed in detail in relation to tree and shrub damage, with numerous examples of plant injuries.

  18. Spanning Tree Based Attribute Clustering

    DEFF Research Database (Denmark)

    Zeng, Yifeng; Jorge, Cordero Hernandez

    2009-01-01

    Attribute clustering has been previously employed to detect statistical dependence between subsets of variables. We propose a novel attribute clustering algorithm motivated by research of complex networks, called the Star Discovery algorithm. The algorithm partitions and indirectly discards...... 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...

  19. Carbon Sequestration by Urban Trees

    DEFF Research Database (Denmark)

    Fares, Silvano; Paoletti, Elena; Calfapietra, Carlo

    2017-01-01

    Carbon dioxide (CO2) is the most prominent component of anthropogenic greenhouse gas emissions, resulting mainly from fuel combustion in the built environment – for activities such as heating of buildings, urban mobility and cooking. The concentration of near-surface CO2 in cities is affected by ....... In this chapter, we review the most recent studies and highlight emerging research needs for a better understanding of present and future roles of urban trees in removing CO2 from the atmosphere....

  20. Chemicals from trees and shrubs

    Energy Technology Data Exchange (ETDEWEB)

    Halloran, G M

    1978-01-01

    The need for finding economically viable alternatives to crude oil is discussed in the context of Australia's uncertain reserves of black coal, from which crude oil derivatives may have to be obtained when oil supplies become depleted. A table is presented showing the major fractions of crude oil and the likely sources (in general terms) of equivalent substances from forest trees, shrubs and agricultural species.

  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. 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.

  3. The stopping rules for winsorized tree

    Science.gov (United States)

    Ch'ng, Chee Keong; Mahat, Nor Idayu

    2017-11-01

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

  4. Nonbinary Tree-Based Phylogenetic Networks.

    Science.gov (United States)

    Jetten, Laura; van Iersel, Leo

    2018-01-01

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

  5. Deterministic Automata for Unordered Trees

    Directory of Open Access Journals (Sweden)

    Adrien Boiret

    2014-08-01

    Full Text Available Automata for unordered unranked trees are relevant for defining schemas and queries for data trees in Json or Xml format. While the existing notions are well-investigated concerning expressiveness, they all lack a proper notion of determinism, which makes it difficult to distinguish subclasses of automata for which problems such as inclusion, equivalence, and minimization can be solved efficiently. In this paper, we propose and investigate different notions of "horizontal determinism", starting from automata for unranked trees in which the horizontal evaluation is performed by finite state automata. We show that a restriction to confluent horizontal evaluation leads to polynomial-time emptiness and universality, but still suffers from coNP-completeness of the emptiness of binary intersections. Finally, efficient algorithms can be obtained by imposing an order of horizontal evaluation globally for all automata in the class. Depending on the choice of the order, we obtain different classes of automata, each of which has the same expressiveness as CMso.

  6. Carbon-14 in tree rings

    International Nuclear Information System (INIS)

    Cain, W.F.; Suess, H.E.

    1976-01-01

    In order to investigate how reliably the carbon 14 content of tree rings reflects that of atmospheric carbon dioxide, two types of determinations were carried out: (1) carbon 14 determinations in annual rings from the beginning of this century until 1974 and (2) carbon 14 determinations in synchronous wood from the North American bristlecone pine and from European oak trees, dendrochronologically dated to have grown in the third and fourth century B.C. The first series of measurements showed that bomb-produced radiocarbon was incorporated in wood at a time when it was converted from sapwood to heartwood, whenever radiocarbon from bomb testing was present in the atmosphere. The second series showed that wood more than 2000 years old and grown on two different continents at different altitudes had, within the limits of experimental error, the same radiocarbon content. This work and other experimental evidence, obtained in part by other laboratories, show that tree rings reflect the average radiocarbon content of global atmospheric carbon dioxide accurately within several parts per mil. In rare cases, deviations of up to 10 parts per thousand may be possible. This means that a typical single radiocarbon date for wood or charcoal possesses an intrinsic uncertainty (viz., an estimated ''one-sigma error'' in addition to all the other errors) of the order of +-50 years. This intrinsic uncertainty is independent of the absolute age of the sample. More accurate dates can, in principle, be obtained by the so-called method of ''wiggle matching.''

  7. 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.

  8. 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

  9. Folding and unfolding phylogenetic trees and networks.

    Science.gov (United States)

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

    2016-12-01

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

  10. Fuzzy tree automata and syntactic pattern recognition.

    Science.gov (United States)

    Lee, E T

    1982-04-01

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

  11. The dynamics of strangling among forest trees.

    Science.gov (United States)

    Okamoto, Kenichi W

    2015-11-07

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

  12. 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.

  13. ETE: a python Environment for Tree Exploration

    Directory of Open Access Journals (Sweden)

    Gabaldón Toni

    2010-01-01

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

  14. 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...

  15. Nitrogen fixation in trees - 1

    Energy Technology Data Exchange (ETDEWEB)

    Dobereiner, J.; Gauthier, D.L.; Diem, H.G.; Dommergues, Y.R.; Bonetti, R.; Oliveira, L.A.; Magalhaes, F.M.M.; Faria, S.M. de; Franco, A.A.; Menandro, M.S.

    1984-01-01

    Six papers are presented from the symposium. Dobereiner, J.; Nodulation and nitrogen fixation in leguminous trees, 83-90, (15 ref.), reviews studies on Brazilian species. Gauthier, D.L., Diem, H.G., Dommergues, Y.R., Tropical and subtropical actinorhizal plants, 119-136, (Refs. 50), reports on studies on Casuarinaceae. Bonetti, R., Oliveira, L.A., Magalhaes, F.M.M.; Rhizobium populations and occurrence of VA mycorrhizae in plantations of forest trees, 137-142, (Refs. 15), studies Amazonia stands of Cedrelinga catenaeformis, Calophyllum brasiliense, Dipteryx odorata, D. potiphylla, Carapa guianensis, Goupia glabra, Tabebuia serratifolia, Clarisia racemosa, Pithecellobium racemosum, Vouacapoua pallidior, Eperua bijuga, and Diplotropis species. Nodulation was observed in Cedrelinga catenaeformis and V. pallidior. Faria, S.M. de, Franco, A.A., Menandro, M.S., Jesus, R.M. de, Baitello, J.B.; Aguiar, O.T. de, Doebereiner, J; survey of nodulation in leguminous tree species native to southeastern Brazil, 143-153, (Refs. 7), reports on 119 species, with first reports of nodulation in the genera Bowdichia, Poecilanthe, Melanoxylon, Moldenhaurea (Moldenhawera), and Pseudosamanea. Gaiad, S., Carpanezzi, A.A.; Occurrence of Rhizobium in Leguminosae of silvicultural interest for south Brazil, 155-158, (Refs. 2). Nodulation is reported in Mimosa scabrella, Acacia mearnsii, A. longifolia various trinervis, Enterolobium contortisiliquum, and Erythrina falcata. Magalhaes, L.M.S., Blum, W.E.H., Nodulation and growth of Cedrelinga catanaeformis in experimental stands in the Manaus region - Amazonas, 159-164, (Refs. 5). Results indicate that C. catenaeformis can be used in degraded areas of very low soil fertility.

  16. Optimal Monotone Drawings of Trees

    OpenAIRE

    He, Dayu; He, Xin

    2016-01-01

    A monotone drawing of a graph G is a straight-line drawing of G such that, for every pair of vertices u,w in G, there exists abpath P_{uw} in G that is monotone in some direction l_{uw}. (Namely, the order of the orthogonal projections of the vertices of P_{uw} on l_{uw} is the same as the order they appear in P_{uw}.) The problem of finding monotone drawings for trees has been studied in several recent papers. The main focus is to reduce the size of the drawing. Currently, the smallest drawi...

  17. Helping to increase tree crops

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1970-07-01

    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)

  18. 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)

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

    Science.gov (United States)

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

    2018-04-01

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

  20. TreeNetViz: revealing patterns of networks over tree structures.

    Science.gov (United States)

    Gou, Liang; Zhang, Xiaolong Luke

    2011-12-01

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

  1. 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.

  2. Geodesic atlas-based labeling of anatomical trees

    DEFF Research Database (Denmark)

    Feragen, Aasa; Petersen, Jens; Owen, Megan

    2015-01-01

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

  3. On the structure of path-like trees

    OpenAIRE

    Muntaner Batle, Francesc Antoni; Rius Font, Miquel

    2007-01-01

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

  4. The spectral dimension of random trees

    International Nuclear Information System (INIS)

    Destri, Claudio; Donetti, Luca

    2002-01-01

    We present a simple yet rigorous approach to the determination of the spectral dimension of random trees, based on the study of the massless limit of the Gaussian model on such trees. As a by-product, we obtain evidence in favour of a new scaling hypothesis for the Gaussian model on generic bounded graphs and in favour of a previously conjectured exact relation between spectral and connectivity dimensions on more general tree-like structures

  5. Reconciliation with non-binary species trees.

    Science.gov (United States)

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

    2008-10-01

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

  6. Nonbinary tree-based phylogenetic networks

    OpenAIRE

    Jetten, Laura; van Iersel, Leo

    2016-01-01

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

  7. Transforming phylogenetic networks: Moving beyond tree space

    OpenAIRE

    Huber, Katharina T.; Moulton, Vincent; Wu, Taoyang

    2016-01-01

    Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees. In this paper we define two operations on unrooted phylogenetic networks, one of which is a generalization of the well-known nearest-neighbor interchange (NNI) operation on phylogenetic trees. We show that any unrooted phylogenetic network can be transforme...

  8. 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

  9. 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

  10. Maintenance of carbohydrate transport in tall trees

    DEFF Research Database (Denmark)

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

    2017-01-01

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

  11. Breaking the fault tree circular logic

    International Nuclear Information System (INIS)

    Lankin, M.

    2000-01-01

    Event tree - fault tree approach to model failures of nuclear plants as well as of other complex facilities is noticeably dominant now. This approach implies modeling an object in form of unidirectional logical graph - tree, i.e. graph without circular logic. However, genuine nuclear plants intrinsically demonstrate quite a few logical loops (circular logic), especially where electrical systems are involved. This paper shows the incorrectness of existing practice of circular logic breaking by elimination of part of logical dependencies and puts forward a formal algorithm, which enables the analyst to correctly model the failure of complex object, which involves logical dependencies between system and components, in form of fault tree. (author)

  12. Modular representation and analysis of fault trees

    Energy Technology Data Exchange (ETDEWEB)

    Olmos, J; Wolf, L [Massachusetts Inst. of Tech., Cambridge (USA). Dept. of Nuclear Engineering

    1978-08-01

    An analytical method to describe fault tree diagrams in terms of their modular compositions is developed. Fault tree structures are characterized by recursively relating the top tree event to all its basic component inputs through a set of equations defining each of the modulus for the fault tree. It is shown that such a modular description is an extremely valuable tool for making a quantitative analysis of fault trees. The modularization methodology has been implemented into the PL-MOD computer code, written in PL/1 language, which is capable of modularizing fault trees containing replicated components and replicated modular gates. PL-MOD in addition can handle mutually exclusive inputs and explicit higher order symmetric (k-out-of-n) gates. The step-by-step modularization of fault trees performed by PL-MOD is demonstrated and it is shown how this procedure is only made possible through an extensive use of the list processing tools available in PL/1. A number of nuclear reactor safety system fault trees were analyzed. PL-MOD performed the modularization and evaluation of the modular occurrence probabilities and Vesely-Fussell importance measures for these systems very efficiently. In particular its execution time for the modularization of a PWR High Pressure Injection System reduced fault tree was 25 times faster than that necessary to generate its equivalent minimal cut-set description using MOCUS, a code considered to be fast by present standards.

  13. Tritium concentrations in tree ring cellulose

    International Nuclear Information System (INIS)

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

    1989-01-01

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

  14. The space of ultrametric phylogenetic trees.

    Science.gov (United States)

    Gavryushkin, Alex; Drummond, Alexei J

    2016-08-21

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

  15. Creating ensembles of decision trees through sampling

    Science.gov (United States)

    Kamath, Chandrika; Cantu-Paz, Erick

    2005-08-30

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

  16. 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

    2016-01-01

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

  17. 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...... and data aggregation, especially from national forest inventory programs, to improve the current publicly available data.......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...

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

    Science.gov (United States)

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

    2016-12-01

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

  19. 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

  20. Encoding phylogenetic trees in terms of weighted quartets.

    Science.gov (United States)

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

    2008-04-01

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

  1. SOFT TREE: Fault Tree Technique as Applied to Software. Revision.

    Science.gov (United States)

    1983-10-01

    13 12 - 16 03 - 18 09 - 19 01 - 19 02 - 19 03 - 19 05 18. Con’t Non- Nuclear Munition, Non- Nuclear Munition Safety, Fuze Safety, Microprocessor...costucin the’ V’Y wvSoft Tree be ver fam-’il~. iar-a’--. that te persnns conihhsutnge thoftd refec be very familia wthipeetino microprocessosor atd idotwee h...ro 7- qSf" fart~b -To WA0 IFu t TOC6Lf e aF ’t9 q-EN rNz Al fC1~ATOk -1- 1AP6AG $ LA ? To.~ Yujiif’ ToA4. IWOv~:EAii CI~t~J~13Lf ToP5M A~E F CAP Avrif

  2. 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

  3. 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.

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

    NARCIS (Netherlands)

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

    2009-01-01

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

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

    Science.gov (United States)

    2010-07-01

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

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

    Science.gov (United States)

    Lara A. Roman

    2014-01-01

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

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

    Science.gov (United States)

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

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

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

    NARCIS (Netherlands)

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

    2014-01-01

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

  9. 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.

  10. Injective Labeled Oriented Trees are Aspherical

    OpenAIRE

    Harlander, Jens; Rosebrock, Stephan

    2012-01-01

    A labeled oriented tree is called injective if each generator occurs at most once as an edge label. We show that injective labeled oriented trees are aspherical. The proof relies on a new relative asphericity test based on a lemma of Stallings.

  11. Tree root mapping with ground penetrating radar

    CSIR Research Space (South Africa)

    Van Schoor, Abraham M

    2009-09-01

    Full Text Available In this paper, the application of ground penetrating radar (GPR) for the mapping of near surface tree roots is demonstrated. GPR enables tree roots to be mapped in a non-destructive and cost-effective manner and is therefore a useful prospecting...

  12. Portraits of Non-Tree Families

    NARCIS (Netherlands)

    Balgooy, van M.M.J.

    2001-01-01

    This is the third and final volume of the series ‘Malesian Seed Plants’. It contains the ‘portraits’ of 124 non-tree families, i.e. families which are mainly herbaceous, climbing, shrubby, or trees with a stem diameter at breast height of less than 10 cm or a height of less than 10 m. Users of the

  13. Smoothed analysis of binary search trees

    NARCIS (Netherlands)

    Manthey, Bodo; Reischuk, Rüdiger

    2007-01-01

    Binary search trees are one of the most fundamental data structures. While the height of such a tree may be linear in the worst case, the average height with respect to the uniform distribution is only logarithmic. The exact value is one of the best studied problems in average-case complexity. We

  14. Tools for valuing tree and park services

    Science.gov (United States)

    E.G. McPherson

    2010-01-01

    Arborists and urban foresters plan, design, construct, and manage trees and parks in cities throughout the world. These civic improvements create walkable, cool environments, save energy, reduce stormwater runoff, sequester carbon dioxide, and absorb air pollutants. The presence of trees and green spaces in cities is associated with increases in property values,...

  15. 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

  16. 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.

  17. 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...

  18. Improved Anonymity for Key-trees

    NARCIS (Netherlands)

    Veugen, P.J.M.; Beye, M.

    2013-01-01

    Randomized hash-lock protocols for Radio Frequency IDentification (RFID) tags offer forward untraceability, but incur heavy search on the server. Key trees have been proposed as a way to reduce search times, but because partial keys in such trees are shared, key compromise affects several tags.

  19. 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...

  20. 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...