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...

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

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

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.

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.

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

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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.

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.

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

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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...

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.

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.

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

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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.

Shrew trap efficiency

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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....

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

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.

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

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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.

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.

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

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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.

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.

Muscle Aging and Oxidative Stress in Wild-Caught Shrews

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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

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

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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

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

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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.

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

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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.

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

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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.

Tactile Experience Shapes Prey-Capture Behavior in Etruscan Shrews

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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.

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

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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.

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.

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.

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.

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

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...

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

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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.

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.

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

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

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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.

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.

Male Specific Gene Expression in Dioecious Phoenix Dactylifera (Date Palm) Tree at Flowering Stage

International Nuclear Information System (INIS)

Al-Ameri, A. A.; Al-Qurainy, F.; Gaafar, A. R. Z.; Khan, S.; Nadeem, M.

2016-01-01

Date palm is a long-living and evergreen important tree in the semiarid regions. Its fruit is rich in carbohydrate and fibres. Transcriptional profiling was compared among male and female trees of dioecious date palm at flowering stage. Male specific genes are expressed at flowering stage which was studied using the cDNA-SCoT marker. We developed sequence characterized amplified region (SCAR) markers of size 253 bp from male tree based on cDNA-SCoT fingerprinting. Further, developed SCAR marker was validated on the independently collected samples of both types of trees at flowering stage. The unique and specific band (253 bp) was amplified from male samples only whereas it was absent from female samples. (author)

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)

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

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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.

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.

Discovery of Novel Alphacoronaviruses in European Rodents and Shrews

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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.

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.

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...

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

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.

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.

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....

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.

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.

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.

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...

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).

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.

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

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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.

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

Science.gov (United States)

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.

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

Tree roosting by male and female eastern pipistrelles in a forested landscape

Science.gov (United States)

Roger W. Perry; Ronald E. Thill

2007-01-01

Little information has been published on selection of tree roosts by eastern pipistrelles (Perimyotis subflavus) in forested environments, and no radiotelemetry-based studies have been conducted on males in forested settings. Therefore, we used radiotelemetry to characterize summer roost selection by 21 male (33 roosts) and 7 female (14 roosts)...

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

Science.gov (United States)

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

2014-08-01

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

Examining SLV-323, a novel NK1 receptor antagonist, in a chronic psychosocial stress model for depression

NARCIS (Netherlands)

Czeh, B; Pudovkina, O; van der Hart, MGC; Simon, M; Heilbronner, U; Michaelis, T; Watanabe, T; Frahm, J; Fuchs, E

Rationale: Substance P antagonists have been proposed as candidates for a new class of antidepressant compounds. Objectives: We examined the effects of SLV-323, a novel neurokinin 1 receptor (NK1R) antagonist, in the chronic psychosocial stress paradigm of adult male tree shrews. Methods: Animals

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....

[Prediction of the total Japanese cedar pollen counts based on male flower-setting conditions of standard trees].

Science.gov (United States)

Yuta, Atsushi; Ukai, Kotaro; Sakakura, Yasuo; Tani, Hideshi; Matsuda, Fukiko; Yang, Tian-qun; Majima, Yuichi

2002-07-01

We made a prediction of the Japanese cedar (Cryptomeria japonica) pollen counts at Tsu city based on male flower-setting conditions of standard trees. The 69 standard trees from 23 kinds of clones, planted at Mie Prefecture Science and Technology Promotion Center (Hakusan, Mie) in 1964, were selected. Male flower-setting conditions for 276 faces (69 trees x 4 points of the compass) were scored from 0 to 3. The average of scores and total pollen counts from 1988 to 2000 was analyzed. As the results, the average scores from standard trees and total pollen counts except two mass pollen-scattered years in 1995 and 2000 had a positive correlation (r = 0.914) by linear function. On the mass pollen-scattered years, pollen counts were influenced from the previous year. Therefore, the score of the present year minus that of the previous year were used for analysis. The average scores from male flower-setting conditions and pollen counts had a strong positive correlation (r = 0.994) when positive scores by taking account of the previous year were analyzed. We conclude that prediction of pollen counts are possible based on the male flower-setting conditions of standard trees.

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.

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

Science.gov (United States)

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

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

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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.

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.

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

Science.gov (United States)

Sonsthagen, 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.

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.

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

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.

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 ...

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

Science.gov (United States)

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

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

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.

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).

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

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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.

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...

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.

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.

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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.

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

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,

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

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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.

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

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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.

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

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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.

Selection of tree roosts by male Indiana bats during the autumn swarm in the Ozark Highlands, USA

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Roger W. Perry; Stephen C. Brandebura; Thomas S. Risch

2016-01-01

We identified 162 roosts for 36 male Indiana bats (Myotis sodalis) across 3 study areas in the Ozarks of northern Arkansas, USA, during the autumn swarm (late Aug to late Oct, 2005 and 2006). Bats utilized 14 tree species; snags of shortleaf pine (Pinus echinata) were the most utilized (30% of roosts) and pines were selected over hardwoods. Diameter of trees and snags...

"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,…

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.

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).

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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.

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

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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.

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.

Flowering Trees

Indian Academy of Sciences (India)

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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.

"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.

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.

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。

Genetic differentiation for size at first reproduction through male versus female functions in the widespread Mediterranean tree Pinus pinaster.

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Santos-del-Blanco, L; Climent, J; González-Martínez, S C; Pannell, J R

2012-11-01

The study of local adaptation in plant reproductive traits has received substantial attention in short-lived species, but studies conducted on forest trees are scarce. This lack of research on long-lived species represents an important gap in our knowledge, because inferences about selection on the reproduction and life history of short-lived species cannot necessarily be extrapolated to trees. This study considers whether the size for first reproduction is locally adapted across a broad geographical range of the Mediterranean conifer species Pinus pinaster. In particular, the study investigates whether this monoecious species varies genetically among populations in terms of whether individuals start to reproduce through their male function, their female function or both sexual functions simultaneously. Whether differences among populations could be attributed to local adaptation across a climatic gradient is then considered. Male and female reproduction and growth were measured during early stages of sexual maturity of a P. pinaster common garden comprising 23 populations sampled across the species range. Generalized linear mixed models were used to assess genetic variability of early reproductive life-history traits. Environmental correlations with reproductive life-history traits were tested after controlling for neutral genetic structure provided by 12 nuclear simple sequence repeat markers. Trees tended to reproduce first through their male function, at a size (height) that varied little among source populations. The transition to female reproduction was slower, showed higher levels of variability and was negatively correlated with vegetative growth traits. Several female reproductive traits were correlated with a gradient of growth conditions, even after accounting for neutral genetic structure, with populations from more unfavourable sites tending to commence female reproduction at a lower individual size. The study represents the first report of genetic

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.

Preference for Male Traits Differ in Two Female Morphs of the Tree Lizard, Urosaurus ornatus

Science.gov (United States)

Lattanzio, Matthew S.; Metro, Kevin J.; Miles, Donald B.

2014-01-01

Non-random female mating preferences may contribute to the maintenance of phenotypic variation in color polymorphic species. However, the effect of female preference depends on the types of male traits used as signals by receptive females. If preference signals derive from discrete male traits (i.e., morph-specific), female preferences may rapidly fix to a morph. However, female preference signals may also include condition-dependent male traits. In this scenario, female preference may differ depending on the social context (i.e., male morph availability). Male tree lizards (Urosaurus ornatus) exhibit a dewlap color polymorphism that covaries with mating behavior. Blue morph males are aggressive and defend territories, yellow males are less aggressive and defend smaller territories, and orange males are typically nomadic. Female U. ornatus are also polymorphic in dewlap color, but the covariation between dewlap color and female behavior is unknown. We performed an experiment to determine how female mate choice depends on the visual and chemical signals produced by males. We also tested whether female morphs differ in their preferences for these signals. Female preferences involved both male dewlap color and size of the ventral color patch. However, the female morphs responded to these signals differently and depended on the choice between the types of male morphs. Our experiment revealed that females may be capable of distinguishing among the male morphs using chemical signals alone. Yellow females exhibit preferences based on both chemical and visual signals, which may be a strategy to avoid ultra-dominant males. In contrast, orange females may prefer dominant males. We conclude that female U. ornatus morphs differ in mating behavior. Our findings also provide evidence for a chemical polymorphism among male lizards in femoral pore secretions. PMID:25033282

Male sterility in chestnuts. A tentative plan for the seed propagation of fruit trees

Energy Technology Data Exchange (ETDEWEB)

Omura, Mitsuo; Akihama, Tomoya [Fruit Tree Research Station, Yatabe, Ibaraki (Japan)

1982-03-01

A tentative plan was proposed for chestnuts based on their pollination system, male sterility and restoration. The studies on the male sterility of 1,063 cultivars and clones suggested that there were three types of male sterility. The first type (S-1) was characterized by antherless florets. In the second type (S-2), the catkins fell before anthesis, and the third type (S-3) appeared to develop normally in gross floral morphology, but the pollen grains were abnormal in shape and did not have germinating power. In an interspecific hybrid clone CS which belonged to S-1, fertility was restored in an open pollinated progeny. The use of CS and CSO-3 with its restored fertility, permitted the planning of breeding the chestnut hybrid cultivars propagated by seeds. The inbred clones with either male sterility or restorer genes are first bred mainly by back crossing with parents with favorable pollen. The clones are selected individually for early bearing, wasp and disease resistance, and restoration. Then, the hybrid seedling lines between male sterile and restorer inbreds are evaluated for homogenity in nut characters and tree habits. Next, the hybrid seedling lines selected will be examined for crop yield, vigor and cross compatibility. The superior seedling lines are finally selected, and the parental inbreds are grafted to be propagated for seed production orchards.

Ariosto, Gascoigne e The Taming of the Shrew

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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.

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

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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.

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 ...

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

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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.

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.

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

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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.

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

Science.gov (United States)

Joly, Marine; Scheumann, Marina; Zimmermann, Elke

2012-01-01

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

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.

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

Directory of Open Access Journals (Sweden)

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

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...

DIOECY EFFECT ON GROWTH OF PLANTED Araucaria angustifolia Bert. O. Kuntze TREES

Directory of Open Access Journals (Sweden)

Afonso Figueiredo Filho

2015-09-01

Full Text Available The aim of the study was to evaluate the influence of dioecy on the growth in diameter at breast height (DBH, individual basal area, total height and individual volume of planted Araucaria angustifolia trees. The data came from 60 trees (30 male trees and 30 female trees sampled from a 30-year-old plantation in Paraná State. Complete stem analysis was used to recover historical tree growth. The Chapman-Richards model was fitted in order to represent the growth and yield of the dendrometric variables for female and male Araucaria trees. Weighted non-linear least squared method was used in the fitting process and the inverse variance was used as weight to solve the problem of heteroscedasticity. The test to verify the equality of parameters and the identity of non-linear regression models proposed by Regazzi (2003 was used to test the influence of dioecy on growth. Dioecy significantly influenced the growth of Araucaria, and female trees have higher growth in diameter, individual basal area and individual volume, while male trees showed better height development. The asymptotic coefficient of the Chapman-Richards model showed that male trees have a higher asymptotic height than female trees.

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.

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...

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

Science.gov (United States)

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.

Female fruit production depends on female flower production and crown size rather than male density in a continuous population of a tropical dioecious tree (Virola surinamensis).

Science.gov (United States)

Riba-Hernández, Pablo; Segura, Jorge Lobo; Muñoz-Valverde, Jenny

2016-11-01

Factors related to pollen and resource limitation were evaluated to predict female fruit production in a tropical dioecious tree. Pollen limitation via variation in the male density at local scales is expected to limit female reproduction success in dioecious plants. We modeled the roles of local male density, female crown size, crown illumination, and female flower production on female fruit initiation and mature fruit production in a continuous population (62 ha plot) of a tropical dioecious tree (Virola surinamensis). In addition, we used microsatellites to describe the scale of effective pollen flow, the male effective population size, and the spatial genetic structure within/between progenies and males. The local male density was not related to female fruit initiation or mature fruit production. Female floral production had a positive effect on fruit initiation. The female crown size was positively related to fruit maturation. Seeds from the same female and seeds from different but spatially proximal females were generally half-siblings; however, proximal females showed greater variation. Proximal male-female adult pairs were not significantly more genetically related than distant pairs. The probability of paternity was negatively affected by the distance between seeds and males; most effective pollen dispersal events (∼85%) occurred from males located less than 150 m from females. The number of males siring progenies was greater than the number of males found at local scales. Female fecundity in this continuous population of Virola surinamensis is not limited by the availability of pollen from proximal males. Rather, resource allocation to floral production may ultimately determine female reproductive success. © 2016 Botanical Society of America.

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

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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.

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

Science.gov (United States)

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

2015-01-01

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

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...

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...

[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.

Life-history dependent relationships between body condition and immunity, between immunity indices in male Eurasian tree sparrows.

Science.gov (United States)

Zhao, Yuliang; Li, Mo; Sun, Yanfeng; Wu, Wei; Kou, Guanqun; Guo, Lingling; Xing, Danning; Wu, Yuefeng; Li, Dongming; Zhao, Baohua

2017-08-01

In free-living animals, recent evidence indicates that innate, and acquired, immunity varies with annual variation in the demand for, and availability of, food resources. However, little is known about how animals adjust the relationships between immunity and body condition, and between innate and acquired immunity to optimize survival over winter and reproductive success during the breeding stage. Here, we measured indices of body condition (size-corrected mass [SCM], and hematocrit [Hct]), constitutive innate immunity (plasma total complement hemolysis activity [CH 50 ]) and acquired immunity (plasma immunoglobulin A [IgA]), plus heterophil/lymphocyte (H/L) ratios, in male Eurasian tree sparrows (Passer montanus) during the wintering and the breeding stages. We found that birds during the wintering stage had higher IgA levels than those from the breeding stage. Two indices of body condition were both negatively correlated with plasma CH 50 activities, and positively with IgA levels in wintering birds, but this was not the case in the breeding birds. However, there was no correlation between CH 50 activities and IgA levels in both stages. These results suggest that the relationships between body condition and immunity can vary across life-history stage, and there are no correlations between innate and acquired immunity independent of life-history stage, in male Eurasian tree sparrows. Therefore, body condition indices predict immunological state, especially during the non-breeding stage, which can be useful indicators of individual immunocompetences for understanding the variations in innate and acquired immunity in free-living animals. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Characteristic odor of Osmoderma eremita identified as a male-released pheromone.

Science.gov (United States)

Larsson, Mattias C; Hedin, Jonas; Svensson, Glenn P; Tolasch, Till; Francke, Wittko

2003-03-01

Osmoderma eremita (Scopoli) is an endangered scarab beetle living in hollow trees. It has mainly been known for its characteristic odor, typically described as a fruity, peachlike or plumlike aroma. The odor emanating from a single beetle can sometimes be perceived from a distance of several meters. In this paper, we show that the characteristic odor from O. eremita is caused by the compound (R)-(+)-gamma-decalactone, released in large quantities mainly or exclusively by male beetles. Antennae from male and female beetles responded in a similar way to (R)-(+)-gamma-decalactone in electroantennographic recordings. Field trapping experiments showed that (R)-(+)-gamma-decalactone is a pheromone attracting female beetles. Lactones similar to (R)-(+)-gamma-decalactone are frequently used as female-released sex pheromones by phytophagous scarabs. This is, however, the first evidence of a lactone used as a male-produced pheromone in scarab beetles. We propose that the strong signal from males is a sexually selected trait used to compete for females and matings. The signal could work within trees but also act as a guide to tree hollows, which are an essential resource for O. eremita. Males may, thus, attract females dispersing from their natal tree by advertising a suitable habitat. This signal could also be exploited by other males searching for tree hollows or for females, which would explain the catch of several males in our traps.

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 ...

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.

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.

[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.

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.

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...

Sex Change Towards Female in Dying Acer rufinerve Trees

Science.gov (United States)

NANAMI, SATOSHI; KAWAGUCHI, HIDEYUKI; YAMAKURA, TAKUO

2004-01-01

• Background and Aims Sex changes within the genus Acer (Aceraceae) may occur because of associations of sex expression and plant health. In this study, a natural population of Acer rufinerve was monitored to clarify the sex change patterns, the relationship between sex expression and plant health, and the causal environmental conditions that precede sex changes. • Methods Sex expression, growth rate and mortality of A. rufinerve trees in a natural population were monitored from 1992 to 1997. • Key Results Three types of sex expression were observed among A. rufinerve: male, female and bisexual. Among the three types of sex expression, sex changes occurred in all directions. In the growing season of 1994, precipitation was reduced. Stem growth rate decreased and mortality was high in 1994. In the spring of 1995, a drastic sex change from male to female or to bisexual occurred. As a result, the sex ratio became female‐biased in 1995, although it had been male‐biased from 1992 to 1994. In 1996 and 1997, the proportion of males in the population increased, partly as a result of female mortality and partly as a result of female‐to‐male sex changes. Sex expression of A. rufinerve was associated with their growth rate and mortality. The growth rate decreased for trees whose sex changed from male to female or to bisexual, and increased for trees whose sex changed from female to male or to bisexual. Dead trees reproduced as females before they died, except for those that died as males in 1994. • Conclusions One explanation for the sex change towards increasing femaleness for this A. rufinerve population in 1995 was the deterioration of plant health in the previous growing season, because of reduced precipitation. Sex changes of unhealthy and dying A. rufinerve towards femaleness may facilitate re‐occupancy by offspring in gaps created by the death of A. rufinerve trees. PMID:15102611

‘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.

Feeding Response of Tree Fodder Bhimal (Grewia optiva on Growth Performance of Castrated Male Goats

Directory of Open Access Journals (Sweden)

Luma Nidhi Pandey

2017-05-01

Full Text Available Bhimal (Grewia optiva is a fodder tree mostly found in mid hills of mid and far western region of Nepal. Bhimal could constitutes one of the main livestock green fodders, especially for goats when fresh green fodder become limited during the winter dry season. However, the feeding value of Bhimal leaves on growth performance of castrated goats probably has not been evaluated so far. Therefore, an experiment was conducted to evaluate the effect of Bhimal leaves feeding on growth performance of castrated male goats for 90 days. Altogether 16 growing castrated male goats of same breed, age and body weight were selected and equally divided into four treatments T1, T2, T3 and T4 with four replications by using Completely Randomized Design (CRD. Four types of experimental diets were prepared having various levels (0 to 100% of Bhimal leaves as fodder. Experimental animals of Treatment 1 were fed with seasonal fodder + 100 g concentrate mixture, Treatment 2 with 100% Bhimal fodder + 100 g concentrate mixture, Treatment 3with 75% Bhimal fodder + 25% seasonal fodder + 100 g concentrate mixture, while Treatment 4 with 50% Bhimal fodder + 50% season fodder + 100 g concentrate mixture. All diets were fed ad-lib and experimental animals had free access to drinking water. The diets offered and refusal was measured daily and weight change was observed fortnightly. The result showed that fodder intake (g/d/animal and total dry matter intake (TDMI g/kg live weight of goats differed significantly (P<0.01, but concentrate intake was not differed significantly (P<0.01 among treatments. The highest dry matter intake per animal /day was in Treatment 2 (52.75 g/kg live weight followed by Treatment 4, Treatment 3 and Treatment 1 (51.7, 48.56 and 32.69 g/kg live weight, respectively.The average daily gain in body weight was observed highest in Treatment 2 (66.66 g/d followed by Treatment 3 (31.66 g/d and Treatment 4 (30.83 g. The growth rate was significantly (P<0

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. 

Infanticide in tree squirrels - a male reproductive strategy?

African Journals Online (AJOL)

1986-07-25

Jul 25, 1986 ... ... of such behaviour. The interpretation of infant killing as a sexually selected male reproductive ... stones of the sexual selection hypothesis of infanticide. The ... of genetically based strain differences in the occurrence of infanticide in ... Aggression plays a prominent role in social behaviour, with both males.

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

Science.gov (United States)

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

2014-12-11

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

Isolation and molecular identification of a Serratia strain from ...

African Journals Online (AJOL)

ONOS

2010-04-05

Apr 5, 2010 ... family Tupaiidae, mainly found in Southern China, India and Southeast Asia. The 17 known species of tree shrews ... for pathogenic coccus cultivation and nutrient agar culture dish and. MacConkey agar for pathogenic rod ...

Phenological adaptations in Ficus tikoua exhibit convergence with unrelated extra-tropical fig trees.

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Ting-Ting Zhao

Full Text Available Flowering phenology is central to the ecology and evolution of most flowering plants. In highly-specific nursery pollination systems, such as that involving fig trees (Ficus species and fig wasps (Agaonidae, any mismatch in timing has serious consequences because the plants must balance seed production with maintenance of their pollinator populations. Most fig trees are found in tropical or subtropical habitats, but the dioecious Chinese Ficus tikoua has a more northerly distribution. We monitored how its fruiting phenology has adapted in response to a highly seasonal environment. Male trees (where fig wasps reproduce had one to three crops annually, whereas many seed-producing female trees produced only one fig crop. The timing of release of Ceratosolen fig wasps from male figs in late May and June was synchronized with the presence of receptive figs on female trees, at a time when there were few receptive figs on male trees, thereby ensuring seed set while allowing remnant pollinator populations to persist. F. tikoua phenology has converged with those of other (unrelated northern Ficus species, but there are differences. Unlike F. carica in Europe, all F. tikoua male figs contain male flowers, and unlike F. pumila in China, but like F. carica, it is the second annual generation of adult wasps that pollinate female figs. The phenologies of all three temperate fig trees generate annual bottlenecks in the size of pollinator populations and for female F. tikoua also a shortage of fig wasps that results in many figs failing to be pollinated.

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

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.

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.

Ergonomics aspects of tree-planting using 'multipot' technology.

Science.gov (United States)

Giguère, D; Bélanger, R; Gauthier, J M; Larue, C

1993-08-01

The highlights of a descriptive study on the ergonomics and occupational health and safety aspects of tree-planting in Québec are presented. The study was planned to consider the most representative geographical sites, planting technologies, and planting organizations. Semi-directed interviews were made with a mixed group of 48 male and female tree-planters and physiological measurements were made on four male planters. Tools and other equipment were also examined. An analysis of the work identified the main elements of the planting cycle, and the high cardiac rate in the working planters was related more to his manual transportation of seedlings and travel on rough paths than to planting per se. A tree-planter will typically travel 2.4 km carrying 16.8 kg of material and equipment in order to plant an average of 1245 seedlings daily. One out of two interviewed planters reported having a work-related accident or incident during his or her lifetime planting career. The body parts reported most frequently injured were the lower extremities (knee, foot, ankle), the skin, the eyes, and the wrist. Recommendations on the development of appropriate tools and footwear for tree-planters and for further research on repetitive strain injury induced by tree-planting have been made.

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

Science.gov (United States)

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

2018-04-01

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

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.

Male Diaphorina citri searching responses to vibrational communication signals

Science.gov (United States)

Prototype devices have been developed that mimic D. citri female replies to male communication signals and lure males to a trap. The objective is to trap a high proportion of males that have landed on a host tree and have begun searching for females. This presentation describes the construction and ...

The Modified Hole Board - Measuring Behavior, Cognition and Social Interaction in Mice and Rats

NARCIS (Netherlands)

Labots, Maaike; Van Lith, Hein A.; Ohl, Frauke; Arndt, Saskia S.

This protocol describes the modified hole board (mHB), which combines features from a traditional hole board and open field and is designed to measure multiple dimensions of unconditioned behavior in small laboratory mammals (e.g., mice, rats, tree shrews and small primates). This paradigm is a

Red-cockaded woodpecker male/female foraging differences in young forest stands.

Energy Technology Data Exchange (ETDEWEB)

Franzreb, Kathleen, E.

2010-07-01

ABSTRACT The Red-cockaded Woodpecker (Picoides borealis) is an endangered species endemic to pine (Pinus spp.) forests of the southeastern United States. I examined Red-cockaded Woodpecker foraging behavior to learn if there were male/female differences at the Savannah River Site, South Carolina. The study was conducted in largely young forest stands (,50 years of age) in contrast to earlier foraging behavior studies that focused on more mature forest. The Redcockaded Woodpecker at the Savannah River site is intensively managed including monitoring, translocation, and installation of artificial cavity inserts for roosting and nesting. Over a 3-year period, 6,407 foraging observations covering seven woodpecker family groups were recorded during all seasons of the year and all times of day. The most striking differences occurred in foraging method (males usually scaled [45% of observations] and females mostly probed [47%]),substrate used (females had a stronger preference [93%] for the trunk than males [79%]), and foraging height from the ground (mean 6 SE foraging height was higher for males [11.1 6 0.5 m] than females [9.8 6 0.5 m]). Niche overlap between males and females was lowest for substrate (85.6%) and foraging height (87.8%), and highest for tree species (99.0%), tree condition (98.3%), and tree height (96.4%). Both males and females preferred to forage in older, large pine trees. The habitat available at the Savannah River Site was considerably younger than at most other locations, but the pattern of male/female habitat partitioning observed was similar to that documented elsewhere within the range attesting to the species’ ability to adjust behaviorally.

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.

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.

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.

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.

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.

Mountain cedar allergens found in nonpollen tree parts.

Science.gov (United States)

Goetz, D W; Goetz, M A; Whisman, B A

1995-09-01

Mountain cedar (Juniperus ashei) pollen is the principal aeroallergen in south central Texas from late December through February. The major mountain cedar allergen is a 40-kD glycoprotein, gp40. To identify allergens in mountain cedar wood, leaves, and berries and to detect mountain cedar allergen in smoke from burning male or female trees. SDS-PAGE plus mountain cedar human sIgE and monoclonal antibody immunoblots identified mountain cedar allergens within pollen and nonpollen tree part extracts. IgE immunoblots identified a single wood allergen at 36 kD and three berry allergens at 36, 26-27, and 21 kD, in addition to known pollen allergens. Mountain cedar monoclonal antibody bound an allergen epitope present not only on 40, 33, and 28-kD pollen allergens, but also on 36 and 32-kD wood allergens, and the 26-27-kD berry allergen. Immunoblot studies detected no mountain cedar allergen in leaves and no allergen in smoke from burning male and female trees. Allergens constituted a much smaller percentage of extractable protein in wood and berries than in pollen. Mountain cedar berry allergen content is too small to give credence to the ingestion of berries as a folk medicine treatment of mountain cedar pollinosis. In addition, while smoke from burning mountain cedar trees may be irritating, it contains no allergens that could cause allergic rhinoconjunctivitis.

Evidence of male attractants for fruit flies in the leaf extract of ...

African Journals Online (AJOL)

Attractiveness of odor from leaves of pepper tree (Schinus molle) to male Ceratitis rosa and C. capitata was evaluated in a wind-tunnel. Odor from the leaves was as attractive to male C. rosa as Trimedlure and more attractive to C. capitata males. Responses of both male and female C. cosyra, C. rosa and C. capitata when ...

Spontaneous ovulation or male effect in alpacas and llamas

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Sumar JB

2016-08-01

Full Text Available New discoveries in ovulation induced mammals, researchers considered the question of whether spontaneous and induced ovulations are distinct entities or individual parts of a single continuum of a “malefacilitated oestrus and ovulation”. This rigid classification should be taken with precaution, because is possible that the various mechanisms involved in the spontaneous ovulation can, under specific conditions coexist in some determined species. It is possible that male hormones can provoke the ovulation by masculine pheromones. The “Ram Effect” can be used to synchronize ewes naturally, for artificial insemination. Pheromones are specialized hormones released by the ram and smelled by the ewes; they are found in the wool and wax, in such a way that synchronized the heat and the advancement of the breeding season Also, using artificial vaginal-cervical stimulation (AVS with a glass rod, ovulation has been induced in the mink, shrews and felids. This form of tactile stimulation (AVS has found no ability for induction of ovulation in SAC. Additional stimuli/cues are often necessary to facilitate the ovulatory response. They include olfactory, visual, auditory or posture, more of them very common in SAC. Few research studies in alpacas and llamas showed a variable number of females ovulating by the sole proximity of the male to the female, by adopting the copulatory position (posture (sitting or prone position, female to female mounting (tactile, males mounting females covered with aprons to avoid penis intromission (tactile and auditory, interrupted matings, sitting close to a male copulating to a female (visual, olfactory?, the guttural sound (orgling made by the copulating male (auditory, and probably other non-identified cues. The rate of spontaneous ovulation in alpacas and llamas, increase up to 50% during the breeding season. These spontaneous ovulation has been diagnosed by sexual behavior (female rejection to the male, by

Potential for the use of male pheromone components in female trapping: a progress report

International Nuclear Information System (INIS)

Howse, P.E.; Underwood, K.L.; Knapp, J.J.; Alemany Ferra, A.; Miranda, M.A.

1999-01-01

Experiments were conducted to determine if reducing the male population using TML traps and pheromone baited traps would enhance female Mediterranean fruit fly capture. Investigations were conducted in citrus plantations in Mallorca. In the first trial (0.36 ha, Son Coll Vey, Palma) Agrisense yellow delta traps were deployed on every third tree in adjacent rows. On each other tree, a TML bait was placed with an insecticide strip containing Dichlorvos. Thus, each of the delta traps was surrounded by a hexagon of TML + insecticide baited trees. The rationale of this experiment was to remove males from the vicinity of pheromone-baited traps and thereby increase the apparency of the female lure. Before the trial, male catches averaged 4.1 per day in TML traps. During the trial, this was reduced to approximately 0.6 males/trap/day. The traps with pheromone (pyrazines in various combinations and ratios) caught around 0.05 females/trap/day. The pheromone traps remained female selective, with a negligible male catch, similar to that in unbaited traps. The most likely cause for the very low female catch may be that insufficient males were removed by the lure and kill devices. In the second trial (0.67 ha, Inca, Mallorca) the proprietor had deployed 83 traps, baited with TML and insecticide, for 18 days prior to the placement of five treatments with six replicates. The delta traps were placed on every third tree, with replicates every third row. The female catch showed a progressive enhancement over a period of 6 weeks, reaching a level about six times that of males in TML traps. (author)

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.

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.

Inferring the chemical form of 137Cs deposited by the Fukushima Dai-ichi Nuclear Power Plant accident by measuring (137)Cs incorporated into needle leaves and male cones of Japanese cedar trees.

Science.gov (United States)

Kanasashi, Tsutomu; Takenaka, Chisato; Sugiura, Yuki

2016-05-15

We hypothesized that the water-soluble (ionic) and water-insoluble (stable) radiocesium from the initial fallout of the Fukushima Dai-ichi Nuclear Power Plant (FDNPP) accident was distributed in various proportions in the surrounding areas and that this distribution was reflected in the trees that suffered deposition from the initial fallout. This study attempted to evaluate local variations in the chemical form of (137)Cs derived from the initial fallout of the FDNPP accident and whether its chemical form affected the radiocesium concentration in the tissues currently growing in trees, even after the initial fallout ceased. For these estimations, the ratio between the (137)Cs concentration in Cryptomeria japonica needle leaves in the tree crown, which existed before the FDNPP accident and subsequently directly exposed to the initial fallout ((137)Cs pre-accident N), and the amount of (137)Cs in the initial fallout itself ((137)Cs fallout) was determined ((137)Cs pre-accident N/(137)Cs fallout) at 66 sites. In addition, the (137)Cs ratios between the male cones produced in 2012 ((137)Cs male cone) and needle leaves that had elongated in the spring of 2011 ((137)Cs 2011N) was determined at 82 sites ((137)Cs male cone/(137) Cs 2011N). Most of the sites with lower (137)Cs pre-accident N /(137)Cs fallout ratios were distributed in eastern Fukushima, relatively close to the Pacific Ocean coastline. Lower (137)Cs pre-accident N/(137)Cs fallout and higher (137)Cs malecone/(137)Cs 2011N were found to be associated with higher proportions of (137)Cs in ionic forms. These observations are consistent with the hypothesis, and likely reflect regional variations in the chemical form of the deposited radiocesium. Copyright © 2016 Elsevier B.V. All rights reserved.

Use of trees by the Texas ratsnake (Elaphe obsoleta) in eastern Texas

Science.gov (United States)

Josh B. Pierce; Robert R. Fleet; Lance McBrayer; D. Craig Rudolph

2008-01-01

We present information on the use of trees by Elaphe obsoleta (Texas Ratsnake) in a mesic pine-hardwood forest in eastern Texas. Using radiotelemetry, seven snakes (3 females, 4 males) were relocated a total of 363 times from April 2004 to May 2005, resulting in 201 unique locations. Snakes selected trees containing cavities and used hardwoods and...

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.

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.

Species collapse via hybridization in Darwin's tree finches.

Science.gov (United States)

Kleindorfer, Sonia; O'Connor, Jody A; Dudaniec, Rachael Y; Myers, Steven A; Robertson, Jeremy; Sulloway, Frank J

2014-03-01

Species hybridization can lead to fitness costs, species collapse, and novel evolutionary trajectories in changing environments. Hybridization is predicted to be more common when environmental conditions change rapidly. Here, we test patterns of hybridization in three sympatric tree finch species (small tree finch Camarhynchus parvulus, medium tree finch Camarhynchus pauper, and large tree finch: Camarhynchus psittacula) that are currently recognized on Floreana Island, Galápagos Archipelago. Genetic analysis of microsatellite data from contemporary samples showed two genetic populations and one hybrid cluster in both 2005 and 2010; hybrid individuals were derived from genetic population 1 (small morph) and genetic population 2 (large morph). Females of the large and rare species were more likely to pair with males of the small common species. Finch populations differed in morphology in 1852-1906 compared with 2005/2010. An unsupervised clustering method showed (a) support for three morphological clusters in the historical tree finch sample (1852-1906), which is consistent with current species recognition; (b) support for two or three morphological clusters in 2005 with some (19%) hybridization; and (c) support for just two morphological clusters in 2010 with frequent (41%) hybridization. We discuss these findings in relation to species demarcations of Camarhynchus tree finches on Floreana Island.

Roost selection by big brown bats in forests of Arkansas: importance of pine snags and open forest habitats to males

Science.gov (United States)

Roger W. Perry; Ronald E. Thill

2008-01-01

Although Eptesicus fuscus (Big Brown Bat) has been widely studied, information on tree-roosting in forests by males is rare, and little information is available on tree roosting in the southeastern United States. Our objectives were to characterize diurnal summer roosts, primarily for male Big Brown Bats, and to determine relationships between forest...

Summer roosting by adult male seminole bats in the Ouachita Mountains, Arkansas

Science.gov (United States)

Roger W. Perry; Ronald E. Thill

2007-01-01

We used radiotelemetry to locate 51 diurnal roosts for 17 male Seminole bats (Lasiurus seminolus) during late spring and early summer, 2000–2005. We quantified characteristics of roost trees and sites surrounding roosts and compared those measurements with random trees and random locations. All but two roosts were located in the foliage of large...

Metabolism and thermoregulation in the tree shrew, Tupaia belangeri

Directory of Open Access Journals (Sweden)

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.

Flowering in the wild olive (Olea europaea L.) tree (oleaster ...

African Journals Online (AJOL)

Yomi

2012-04-19

Apr 19, 2012 ... This study investigates the phenology evolution and the male and female ... ecological niches in oleaster trees. ... The self-pollination may occur, but olive cultivars are ... Plants can ..... The fruit set results from the interaction.

Identification of novel putative causative genes and genetic marker for male sterility in Japanese cedar (Cryptomeria japonica D.Don).

Science.gov (United States)

Mishima, Kentaro; Hirao, Tomonori; Tsubomura, Miyoko; Tamura, Miho; Kurita, Manabu; Nose, Mine; Hanaoka, So; Takahashi, Makoto; Watanabe, Atsushi

2018-04-23

Japanese cedar (Cryptomeria japonica) is an important tree for Japanese forestry. Male-sterile marker development in Japanese cedar would facilitate selection of male-sterile plus trees, addressing the widespread social problem of pollinosis and facilitating the identification of heterozygotes, which are useful for breeding. This study used next-generation sequencing for single-nucleotide polymorphism discovery in libraries constructed from several organs, including male-sterile and male-fertile strobili. The single-nucleotide polymorphisms obtained were used to construct a high-density linkage map, which enabled identification of a locus on linkage group 9 strongly correlated with male-sterile trait. Expressed sequence tags corresponding to 11 marker loci from 5 isotigs were associated with this locus within 33.4-34.5 cM. These marker loci explained 100% of the phenotypic variation. Several homologs of these sequences are associated with male sterility in rice or Arabidopsis, including a pre-mRNA splicing factor, a DEAD-box protein, a glycosyl hydrolase, and a galactosyltransferase. These proteins are thus candidates for the causal male-sterile gene at the ms-1 locus. After we used a SNaPshot assay to develop markers for marker-assisted selection (MAS), we tested F 2 progeny between male-sterile and wild-type plus trees to validate the markers and extrapolated the testing to a larger plus-tree population. We found that two developed from one of the candidates for the causal gene were suitable for MAS. More than half of the ESTs and SNPs we collected were new, enlarging the genomic basis for genetic research on Japanese cedar. We developed two SNP markers aimed at MAS that distinguished individuals carrying the male-sterile trait with 100% accuracy, as well as individuals heterozygous at the male-sterile locus, even outside the mapping population. These markers should enable practical MAS for conifer breeding.

Reproductive features of the eastern mole (Scalopus aquaticus) and star-nose mole (Condylura cristata).

Science.gov (United States)

Bedford, J M; Mock, O B; Nagdas, S K; Winfrey, V P; Olson, G E

1999-11-01

Since moles are closely related to shrews, the gametes and reproductive tracts of the star-nose mole (Condylura cristata) and the eastern mole (Scalopus aquaticus) were examined to gain further insight into unusual reproductive traits of the Soricidae. Moles display many of these soricid traits, but with some important differences. The cumulus oophorus of Scalopus, ovulated about 16 h after hCG injection, was largely dispersed by hyaluronidase and, though quite dense, was nevertheless more similar to that of higher mammals than to the compact 'ball of the soricid cumulus. Within the female tract in these moles, approximately 85% of the length of the oviduct comprises a narrow ampulla with numerous differentiated crypts that, in shrews, house spermatozoa. However, in contrast to shrews, moles produce considerably larger numbers of spermatozoa, which challenges the proposal that, in shrews, oviductal sperm crypts specifically permit lower sperm production by the males. In the sperm head of these two moles, the acrosome displays the long rostrum that is typical of other Insectivora, and the perforatorium has the barbs by which soricid spermatozoa probably bind to the zona pellucida. Perhaps allied to this, immunoblots indicated that the immunoreactive acrosomal matrix of Scalopus spermatozoa is simpler than the polypeptide complex of the bovine and hamster acrosomal matrix.

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.

Flowering in the wild olive ( Olea europaea L.) tree (oleaster ...

African Journals Online (AJOL)

flowers with absence or reduced stamens and flowers with absence of pistil) are frequently observed and may reduce fruit set. This study investigates the phenology evolution and the male and female abortion of the oleaster tree (or the wild olive ...

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.

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...

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...

Identification of microRNAs differentially expressed involved in male flower development.

Science.gov (United States)

Wang, Zhengjia; Huang, Jianqin; Sun, Zhichao; Zheng, Bingsong

2015-03-01

Hickory (Carya cathayensis Sarg.) is one of the most economically important woody trees in eastern China, but its long flowering phase delays yield. Our understanding of the regulatory roles of microRNAs (miRNAs) in male flower development in hickory remains poor. Using high-throughput sequencing technology, we have pyrosequenced two small RNA libraries from two male flower differentiation stages in hickory. Analysis of the sequencing data identified 114 conserved miRNAs that belonged to 23 miRNA families, five novel miRNAs including their corresponding miRNA*s, and 22 plausible miRNA candidates. Differential expression analysis revealed 12 miRNA sequences that were upregulated in the later (reproductive) stage of male flower development. Quantitative real-time PCR showed similar expression trends as that of the deep sequencing. Novel miRNAs and plausible miRNA candidates were predicted using bioinformatic analysis methods. The miRNAs newly identified in this study have increased the number of known miRNAs in hickory, and the identification of differentially expressed miRNAs will provide new avenues for studies into miRNAs involved in the process of male flower development in hickory and other related trees.

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....

Male sterility in chestnuts

International Nuclear Information System (INIS)

Omura, Mitsuo; Akihama, Tomoya

1982-01-01

A tentative plan was proposed for chestnuts based on their pollination system, male sterility and restoration. The studies on the male sterility of 1,063 cultivars and clones suggested that there were three types of male sterility. The first type (S-1) was characterized by antherless florets. In the second type (S-2), the catkins fell before anthesis, and the third type (S-3) appeared to develop normally in gross floral morphology, but the pollen grains were abnormal in shape and did not have germinating power. In an interspecific hybrid clone CS which belonged to S-1, fertility was restored in an open pollinated progeny. The use of CS and CSO-3 with its restored fertility, permitted the planning of breeding the chestnut hybrid cultivars propagated by seeds. The inbred clones with either male sterility or restorer genes are first bred mainly by back crossing with parents with favorable pollen. The clones are selected individually for early bearing, wasp and disease resistance, and restoration. Then, the hybrid seedling lines between male sterile and restorer inbreds are evaluated for homogenity in nut characters and tree habits. Next, the hybrid seedling lines selected will be examined for crop yield, vigor and cross compatibility. The superior seedling lines are finally selected, and the parental inbreds are grafted to be propagated for seed production orchards. (Kaihara, S.)

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.

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.

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.

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.

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.

Distillation time alters essential oil yield, composition, and antioxidant activity of male Juniperus scopulorum trees.

Science.gov (United States)

Zheljazkov, Valtcho D; Astatkie, Tess; Jeliazkova, Ekaterina A; Schlegel, Vicki

2012-01-01

The objective of this study was to evaluate the effect of 15 distillation times (DT), ranging from 1.25 to 960 min, on oil yield, essential oil profiles, and antioxidant capacity of male J. scopulorum trees. Essential oil yields were 0.07% at 1.25 min DT and reached a maximum of 1.48% at 840 min DT. The concentrations of alpha-thujene (1.76-2.75%), alpha-pinene (2.9-8.7%), sabinene (45-74.7%), myrcene (2.4-3.4%), and para-cymene (0.8-3.1%) were highest at the shortest DT (1.5 to 5 min) and decreased with increasing DT. Cis-sabinene hydrate (0.5-0.97%) and linalool plus trans-sabinene (0.56-1.6%) reached maximum levels at 40 min DT. Maximum concentrations of limonene (2.3-2.8%) and pregeijerene-B (0.06-1.4%) were obtained at 360-480 min DT, and 4-terpinenol (0.7-5.7%) at 480 min DT. Alpha-terpinene (0.16-2.9%), gamma-terpinene (0.3-4.9%) and terpinolene (0.3-1.4%) reached maximum at 720 min DT. The concentrations of delta-cadinene (0.06-1.65%), elemol (0-6.0%), and 8-alpha-acetoxyelemol (0-4.4%) reached maximum at 840 min DT. The yield of the essential oil constituents increased with increasing DT. Only linalool/transsabinene hydrate reached a maximum yield at 360 min DT. Maximum yields of the following constituents were obtained at 720 min DT: alpha-thujene, alpha-pinene, camphene, sabinene, myrcene, alpha-terpinene, para-cimene, limonene, gamma-terpinene, terpinolene, and 4-terpinenol. At 840 min DT, cis-sabinene hydrate, prejeijerene-B, gamma muurolene, delta-cadinene, reached maximum. At 960 min DT, maximum yields of beta-pinene, elemol, alphaeudesmol/betaeudesmol, 8-alpha-acetoxyelemol were reached. These changes were adequately modeled by either the Michaelis-Menten or the Power (Convex) nonlinear regression models. Oils from the 480 min DT showed higher antioxidant activity compared to samples collected at 40, 160, or 960 min DT. These results show the potential for obtaining essential oils with various compositions and antioxidant capacity from male J

Spatial requirements of free-ranging Huon tree kangaroos, Dendrolagus matschiei (Macropodidae, in upper montane forest.

Directory of Open Access Journals (Sweden)

Gabriel Porolak

Full Text Available Tree kangaroos (Macropodidae, Dendrolagus are some of Australasia's least known mammals. However, there is sufficient evidence of population decline and local extinctions that all New Guinea tree kangaroos are considered threatened. Understanding spatial requirements is important in conservation and management. Expectations from studies of Australian tree kangaroos and other rainforest macropodids suggest that tree kangaroos should have small discrete home ranges with the potential for high population densities, but there are no published estimates of spatial requirements of any New Guinea tree kangaroo species. Home ranges of 15 Huon tree kangaroos, Dendrolagus matschiei, were measured in upper montane forest on the Huon Peninsula, Papua New Guinea. The home range area was an average of 139.6±26.5 ha (100% MCP; n = 15 or 81.8±28.3 ha (90% harmonic mean; n = 15, and did not differ between males and females. Home ranges of D. matschiei were 40-100 times larger than those of Australian tree kangaroos or other rainforest macropods, possibly due to the impact of hunting reducing density, or low productivity of their high altitude habitat. Huon tree kangaroos had cores of activity within their range at 45% (20.9±4.1 ha and 70% (36.6±7.5 ha harmonic mean isopleths, with little overlap (4.8±2.9%; n = 15 pairs between neighbouring females at the 45% isopleth, but, unlike the Australian species, extensive overlap between females (20.8±5.5%; n = 15 pairs at the complete range (90% harmonic mean. Males overlapped each other and females to a greater extent than did pairs of females. From core areas and overlap, the density of female D. matschiei was one per 19.4 ha. Understanding the cause of this low density is crucial in gaining greater understanding of variations in density of tree kangaroos across the landscape. We consider the potential role of habitat fragmentation, productivity and hunting pressure in limiting tree kangaroo

Inferring the chemical form of {sup 137}Cs deposited by the Fukushima Dai-ichi Nuclear Power Plant accident by measuring {sup 137}Cs incorporated into needle leaves and male cones of Japanese cedar trees

Energy Technology Data Exchange (ETDEWEB)

Kanasashi, Tsutomu, E-mail: kanasashi.tsutomu@g.mbox.nagoya-u.ac.jp [Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601 (Japan); Takenaka, Chisato [Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601 (Japan); Sugiura, Yuki [Japan Atomic Energy Agency, 765-1 Funaishikawa, Tokai-mura, Naka-gun, Ibaraki 319-1184 (Japan)

2016-05-15

We hypothesized that the water-soluble (ionic) and water-insoluble (stable) radiocesium from the initial fallout of the Fukushima Dai-ichi Nuclear Power Plant (FDNPP) accident was distributed in various proportions in the surrounding areas and that this distribution was reflected in the trees that suffered deposition from the initial fallout. This study attempted to evaluate local variations in the chemical form of {sup 137}Cs derived from the initial fallout of the FDNPP accident and whether its chemical form affected the radiocesium concentration in the tissues currently growing in trees, even after the initial fallout ceased. For these estimations, the ratio between the {sup 137}Cs concentration in Cryptomeria japonica needle leaves in the tree crown, which existed before the FDNPP accident and subsequently directly exposed to the initial fallout ({sup 137}Cs{sub pre-accident} {sub N}), and the amount of {sup 137}Cs in the initial fallout itself ({sup 137}Cs{sub fallout}) was determined ({sup 137}Cs{sub pre-accident} {sub N}/{sup 137}Cs{sub fallout}) at 66 sites. In addition, the {sup 137}Cs ratios between the male cones produced in 2012 ({sup 137}Cs{sub male} {sub cone}) and needle leaves that had elongated in the spring of 2011 ({sup 137}Cs{sub 2011N}) was determined at 82 sites ({sup 137}Cs{sub male} {sub cone}/{sup 137} Cs{sub 2011N}). Most of the sites with lower {sup 137}Cs{sub pre-accident} {sub N}/{sup 137}Cs{sub fallout} ratios were distributed in eastern Fukushima, relatively close to the Pacific Ocean coastline. Lower {sup 137}Cs{sub pre-accidentN}/{sup 137}Cs{sub fallout} and higher {sup 137}Cs{sub malecone}/{sup 137}Cs{sub 2011N} were found to be associated with higher proportions of {sup 137}Cs in ionic forms. These observations are consistent with the hypothesis, and likely reflect regional variations in the chemical form of the deposited radiocesium. - Highlights: • Study of spatial variation of ionic and stable {sup 137}Cs in the initial

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.

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.

The risk factors of laryngeal pathology in Korean adults using a decision tree model.

Science.gov (United States)

Byeon, Haewon

2015-01-01

The purpose of this study was to identify risk factors affecting laryngeal pathology in the Korean population and to evaluate the derived prediction model. Cross-sectional study. Data were drawn from the 2008 Korea National Health and Nutritional Examination Survey. The subjects were 3135 persons (1508 male and 2114 female) aged 19 years and older living in the community. The independent variables were age, sex, occupation, smoking, alcohol drinking, and self-reported voice problems. A decision tree analysis was done to identify risk factors for predicting a model of laryngeal pathology. The significant risk factors of laryngeal pathology were age, gender, occupation, smoking, and self-reported voice problem in decision tree model. Four significant paths were identified in the decision tree model for the prediction of laryngeal pathology. Those identified as high risk groups for laryngeal pathology included those who self-reported a voice problem, those who were males in their 50s who did not recognize a voice problem, those who were not economically active males in their 40s, and male workers aged 19 and over and under 50 or 60 and over who currently smoked. The results of this study suggest that individual risk factors, such as age, sex, occupation, health behavior, and self-reported voice problem, affect the onset of laryngeal pathology in a complex manner. Based on the results of this study, early management of the high-risk groups is needed for the prevention of laryngeal pathology. Copyright © 2015 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

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.

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.

A tree branch instead of a ligature: an unusual accidental hanging.

Science.gov (United States)

Vadysinghe, Amal Nishantha; Sivasubramanium, Murugupillai; Jayasooriya, Rankothge Pemasiri

2017-12-01

A unique case of accidental hanging due to compression of the neck of an adult by the branches of a coffee tree is reported. The decedent was a 42-year-old male who was found dead in a semi prone position on a slope. His neck was lodged in a wedge formed by two branches of a coffee tree, with his legs angled downwards on the slope. Autopsy revealed two friction abrasions located horizontally on either side of the front of the neck, just above the larynx. The findings were compatible with compression of the neck by the branches of the tree, with the body weight of the decedent contributing to compression. Subsequent complete autopsy examination confirmed the cause of death as hanging. Following an inquest the death was ruled to be accidental.

Rhinoceros beetles suffer male-biased predation by mammalian and avian predators.

Science.gov (United States)

Kojima, Wataru; Sugiura, Shinji; Makihara, Hiroshi; Ishikawa, Yukio; Takanashi, Takuma

2014-03-01

Male sexually-selected traits often impose an increased risk of predation on their bearers, causing male-biased predation. We investigated whether males of the sap-feeding Japanese rhinoceros beetle Trypoxylus dichotomus were more susceptible to predation than females by comparing the morphology of beetles caught in bait traps with the remains of beetles found on the ground. The males of this species are larger than the females and have a horn on the head. We found that predation pressure was greater for males than for females, and that larger individuals of both sexes were more vulnerable to predation. We identified two predators, the raccoon dog Nyctereutes procyonoides and jungle crow Corvus macrorhynchos, by monitoring sap-site trees with infrared video cameras. Raccoon dogs visited sap-site trees at night, while crows came after daybreak. The highest frequency of visits by both predators was observed in the first half of August, which matches the peak season of T. dichotomus. Raccoon dogs often left bite marks on the remains of prey, whereas crows did not. Bite marks were found on most of the remains collected at two distant localities, which suggested that predation by raccoon dogs is common. Size- and sex-dependent differences in the conspicuousness and active period of T. dichotomus probably explain these biased predation patterns. Our results suggest that having a large horn/body is costly in terms of the increased risk of predation. Predation cost may act as a stabilizing selection pressure against the further exaggeration of male sexual traits.

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 ...

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...

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...

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

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

Roost selection by male and female northern long-eared bats in a pine-dominated landscape

Science.gov (United States)

Roger W. Perry; Ronald E. Thill

2007-01-01

We radiotracked 17 male northern long-eared bats (Myotis septentrionalis) to 43-day roosts and 23 females to 49-day roosts in the Ouachita Mountains of central Arkansas during summers 2000–2005.We compared characteristics of roost trees between males and females, and compared characteristics of sites surrounding roosts with random locations for each...

Ecology and Conservation of the Critically Endangered Tree Species Gymnocladus assamicus in Arunachal Pradesh, India

International Nuclear Information System (INIS)

Choudhury, B.I.; Khan, M.L.; Arunachalam, A.; Das, A.K.

2007-01-01

Gymnocladus assamicus is a critically endangered leguminous tree species endemic to Northeast India. Mature pods of the trees yield soap material and are collected by local people for domestic purposes and religious activities. G. assamicus grows on hill slopes and along banks of streams. Male and hermaphrodite flowers are borne by separate individual trees. Altogether 28 mature trees were documented from nine populations. Of these, very few regenerating trees were found. This species regenerates only through seeds. The major constraints to natural regeneration are over harvesting of mature fruits, habitat destruction, grazing, predation of seeds by scatter-hoarding animals, poor percentage of seed germination due to their hard-waxy seed coats, and the lack of seed dispersal. Effective conservation initiatives should emphasize sustainable harvesting of mature pods, awareness among local people, and preservation of surviving individuals of the species. Nonetheless, reintroduction of the species to suitable ecological habitats is also recommended.

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.

Comparing the use of live trees and deadwood for larval foraging by aye-ayes (Daubentonia madagascariensis) at Kianjavato and Torotorofotsy, Madagascar.

Science.gov (United States)

Sefczek, Timothy M; Randimbiharinirina, Domenico; Raharivololona, Brigitte M; Rabekianja, Joseph D; Louis, Edward E

2017-10-01

Aye-aye (Daubentonia madagascariensis) feeding behavior has become synonymous with deadwood foraging. However, deadwood is not always the most frequently used substrate, as some aye-ayes use live trees more often to access invertebrates. We sought to compare the frequency of aye-aye invertebrate foraging in deadwood and live trees to better understand their feeding behaviors. We followed two male aye-ayes at Kianjavato, a heavily disturbed habitat in southeastern Madagascar, from October 2013 to October 2014, and one male and one female aye-aye at Torotorofotsy, a continuous forest in eastern Madagascar, from July 2014 to December 2015. We collected feeding data by recording the behavior of a focal aye-aye every 5 min for a total of 373 h at Kianjavato and 383 h at Torotorofotsy. Our results showed no difference in the amount of deadwood used between the individuals. However, there was a significant difference in the amount of live tree feeding between the female at Torotorofotsy and one of the males at Kianjavato. We conclude that feeding on invertebrates in live trees is more important to aye-ayes than previously realized and that aye-ayes are exceedingly flexible in their invertebrate feeding behaviors, adjusting to their habitat by using various substrates.

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.

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

Pollen gene flow, male reproductive success, and genetic correlations among offspring in a northern red oak (Quercus rubra L.) seed orchard

Science.gov (United States)

Woeste, Keith

2017-01-01

Northern red oak is a high-value hardwood used for lumber, furniture and veneer. Intensively managed northern red oak seed orchards are required to obtain genetic gain for trait improvement. Data from conifer seed orchards and natural and managed stands of hardwood trees have shed light on the distance over which pollen can move, and underscore the need for managerial attention to seed orchard design, placement, and maintenance. We used eleven microsatellite markers to investigate pollen gene flow, female mate choice, and male reproductive success in a clonal seed orchard of northern red oak based on paternity analysis of seed orchard offspring in progeny tests. Nearly all (93%) offspring were sired by a male parent within the seed orchard. The mean number of male parents per year was 69.5, or 47.6% of all clones in the seed orchard. Female clones in the early phenology group had more offspring sired from extra-orchard pollen (13%) than clones in the intermediate (5%) and late (1%) phenology groups. Distance was the largest influence on pollination success, and pollination occurred most often by male trees in the same subline as the maternal tree. Males in the early phenology group sired more offspring overall in the progeny pool and more offspring per mother tree than males in the intermediate or late phenology groups. Average genetic correlations among all OP progeny ranged between 0.2557 and 0.3529 with a mean of 0.28±0.01. The importance of progeny test genotyping for northern red oak improvement likely is increasing with the demand for improved varieties. The current study demonstrated the feasibility of post hoc assembly of full-sib families for genetic analysis. PMID:28166543

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...

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.

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.

Genetic differentiation for size at first reproduction through male versus female functions in the widespread Mediterranean tree Pinus pinaster

OpenAIRE

Santos-del-Blanco, L.; Climent, J.; González-Martínez, S. C.; Pannell, J. R.

2012-01-01

Background and Aims The study of local adaptation in plant reproductive traits has received substantial attention in short-lived species, but studies conducted on forest trees are scarce. This lack of research on long-lived species represents an important gap in our knowledge, because inferences about selection on the reproduction and life history of short-lived species cannot necessarily be extrapolated to trees. This study considers whether the size for first reproduction is locally adapted...

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.

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

Science.gov (United States)

Vaughan, Timothy G

2017-08-01

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

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.

Innate immunity is not related to the sex of adult Tree Swallows during the nestling period

Science.gov (United States)

Houdek, Bradley J.; Lombardo, Michael P.; Thorpe, Patrick A.; Hahn, D. Caldwell

2011-01-01

Evolutionary theory predicts that exposure to more diverse pathogens will result in the evolution of a more robust immune response. We predicted that during the breeding season the innate immune function of female Tree Swallows (Tachycineta bicolor) should be more effective than that of males because (1) the transmission of sexually transmitted microbes during copulation puts females at greater risk because ejaculates move from males to females, (2) females copulate with multiple males, exposing them to the potentially pathogenic microbes in semen, and (3) females spend more time in the nest than do males so may be more exposed to nest microbes and ectoparasites that can be vectors of bacterial and viral pathogens. In addition, elevated testosterone in males may suppress immune function. We tested our prediction during the 2009 breeding season with microbicidal assays in vitro to assess the ability of the innate immune system to kill Escherichia coli. The sexes did not differ in the ability of their whole blood to kill E. coli. We also found no significant relationships between the ability of whole blood to kill E. coli and the reproductive performance or the physical condition of males or females. These results indicate that during the nestling period there are no sexual differences in this component of the innate immune system. In addition, they suggest that there is little association between this component of innate immunity and the reproductive performance and physical condition during the nestling period of adult Tree Swallows.

The infestation by an exotic ambrosia beetle, Euplatypus parallelus (F. (Coleoptera: Curculionidae: Platypodinae of Angsana trees (Pterocarpus indicus Willd. in southern Thailand

Directory of Open Access Journals (Sweden)

Sara Bumrungsri

2008-07-01

Full Text Available An exotic ambrosia beetle, Euplatypus parallelus (F. was collected from infested Pterocarpus indicus Willd. trees in Prince of Songkla University. Larvae and eggs were found in simple galleries with a single branch. Either a single male or a male and a female were found in each gallery. Half of these infested trees were previously attacked by long-horned beetles probably Aristobia horridula (Hope (Coleoptera: Cerambycidae, while some of them appeared to be healthy. Fusarium oxysporum Schlecht.:Fr. was isolated from frass, sapwood samples and insect larvae, and might be a cause of death of P.indicus.

Digital gene expression analysis of male and female bud transition in Metasequoia reveals high activity of MADS-box transcription factors and hormone-mediated sugar pathways

OpenAIRE

Zhao, Ying; Liang, Haiying; Li, Lan; Tang, Sha; Han, Xiao; Wang, Congpeng; Xia, Xinli; Yin, Weilun

2015-01-01

Metasequoia glyptostroboides is a famous redwood tree of ecological and economic importance, and requires more than 20 years of juvenile-to-adult transition before producing female and male cones. Previously, we induced reproductive buds using a hormone solution in juvenile Metasequoia trees as young as 5-to-7 years old. In the current study, hormone-treated shoots found in female and male buds were used to identify candidate genes involved in reproductive bud transition in Metasequoia. Sampl...

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

Science.gov (United States)

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

2016-01-01

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

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.

Cache-Oblivious Search Trees via Binary Trees of Small Height

DEFF Research Database (Denmark)

Brodal, G.S.; Fagerberg, R.; Jacob, R.

2002-01-01

We propose a version of cache oblivious search trees which is simpler than the previous proposal of Bender, Demaine and Farach-Colton and has the same complexity bounds. In particular, our data structure avoids the use of weight balanced B-trees, and can be implemented as just a single array......, and range queries in worst case O(logB n + k/B) memory transfers, where k is the size of the output.The basic idea of our data structure is to maintain a dynamic binary tree of height log n+O(1) using existing methods, embed this tree in a static binary tree, which in turn is embedded in an array in a cache...... oblivious fashion, using the van Emde Boas layout of Prokop.We also investigate the practicality of cache obliviousness in the area of search trees, by providing an empirical comparison of different methods for laying out a search tree in memory....

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.

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 ...

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.

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

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.

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

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

Science.gov (United States)

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

2016-02-24

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

Trees are good, but…

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...

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.

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

Habitat, food, and small mammal community structure in Namaqualand

Directory of Open Access Journals (Sweden)

M. van Deventer

2006-12-01

Full Text Available The effect of habitat differences and food availability on small mammal (rodent and elephant shrew species richness, diversity, density and biomass was investigated in Namaqualand, South Africa. Species richness in the three habitats sampled, namely Upland Succulent Karoo, Dry Riverine Shrub and North-western Mountain Renosterveld was low, with only 2–4 species per habitat. Rodents trapped were predominantly Gerbillurus paeba and Aethomys namaquensis, with fewer Mus minutoides and Petromyscus sp. The only non-rodent was the elephant shrew Elephantulus edwardii. Ten habitat features, the percentage of total plant cover, tree cover, shrub cover, grass cover, plant litter, total basal cover, sand, gravel or rock cover, and the dominant plant height were recorded at 30 randomly chosen points on five sampling grids in each habitat. Small mammal density and biomass was significantly correlated with food availability (green foliage cover, seeds, and relative density and biomass of insects. Species richness and diversity of small mammals were significantly correlated with shrub cover. Numbers and biomass of specific species correlated significantly with different habitat features in each case.

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

Certainty of paternity and paternal investment in eastern bluebirds and tree swallows

Science.gov (United States)

Kempenaers, Bart; Lanctot, Richard B.; Robertson, Raleigh J.

1998-01-01

Extra-pair paternity is common in many socially monogamous passerine birds with biparental care. Thus, males often invest in offspring to which they are not related. Models of optimal parental investment predict that, under certain assumptions, males should lower their investment in response to reduced certainty of paternity. We attempted to reduce certainty of paternity experimentally in two species, the eastern bluebird, Sialia sialis, and the tree swallow, Tachycineta bicolor, by temporarily removing fertile females on two mornings during egg laying. In both species, experimental males usually attempted to copulate with the female immediately after her reappearance, suggesting that they experienced the absence of their mate as a threat to their paternity. Experimental males copulated at a significantly higher rate than control males. However, contrary to the prediction of the model, experimental males did not invest less than control males in their offspring. There was no difference between experimental and control nests in the proportion of male feeds, male and female feeding rates, nestling growth and nestling condition and size at age 14 days. We argue that females might have restored the males’ confidence in paternity after the experiment by soliciting or accepting copulations. Alternatively, males may not reduce their effort, because the fitness costs to their own offspring may outweigh the benefits for the males, at least in populations where females cannot fully compensate for reduced male investment.

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.

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

MeshTree: A Delay optimised Overlay Multicast Tree Building Protocol

OpenAIRE

Tan, Su-Wei; Waters, A. Gill; Crawford, John

2005-01-01

We study decentralised low delay degree-constrained overlay multicast tree construction for single source real-time applications. This optimisation problem is NP-hard even if computed centrally. We identify two problems in traditional distributed solutions, namely the greedy problem and delay-cost trade-off. By offering solutions to these problems, we propose a new self-organising distributed tree building protocol called MeshTree. The main idea is to embed the delivery tree in a degree-bound...

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.

TreePlus: interactive exploration of networks with enhanced tree layouts.

Science.gov (United States)

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

2006-01-01

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

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.

Development of a diagnostic decision tree for obstructive pulmonary diseases based on real-life data

Directory of Open Access Journals (Sweden)

Esther I. Metting

2016-01-01

Full Text Available The aim of this study was to develop and explore the diagnostic accuracy of a decision tree derived from a large real-life primary care population. Data from 9297 primary care patients (45% male, mean age 53±17 years with suspicion of an obstructive pulmonary disease was derived from an asthma/chronic obstructive pulmonary disease (COPD service where patients were assessed using spirometry, the Asthma Control Questionnaire, the Clinical COPD Questionnaire, history data and medication use. All patients were diagnosed through the Internet by a pulmonologist. The Chi-squared Automatic Interaction Detection method was used to build the decision tree. The tree was externally validated in another real-life primary care population (n=3215. Our tree correctly diagnosed 79% of the asthma patients, 85% of the COPD patients and 32% of the asthma–COPD overlap syndrome (ACOS patients. External validation showed a comparable pattern (correct: asthma 78%, COPD 83%, ACOS 24%. Our decision tree is considered to be promising because it was based on real-life primary care patients with a specialist's diagnosis. In most patients the diagnosis could be correctly predicted. Predicting ACOS, however, remained a challenge. The total decision tree can be implemented in computer-assisted diagnostic systems for individual patients. A simplified version of this tree can be used in daily clinical practice as a desk tool.

Development of a diagnostic decision tree for obstructive pulmonary diseases based on real-life data

Science.gov (United States)

in ’t Veen, Johannes C.C.M.; Dekhuijzen, P.N. Richard; van Heijst, Ellen; Kocks, Janwillem W.H.; Muilwijk-Kroes, Jacqueline B.; Chavannes, Niels H.; van der Molen, Thys

2016-01-01

The aim of this study was to develop and explore the diagnostic accuracy of a decision tree derived from a large real-life primary care population. Data from 9297 primary care patients (45% male, mean age 53±17 years) with suspicion of an obstructive pulmonary disease was derived from an asthma/chronic obstructive pulmonary disease (COPD) service where patients were assessed using spirometry, the Asthma Control Questionnaire, the Clinical COPD Questionnaire, history data and medication use. All patients were diagnosed through the Internet by a pulmonologist. The Chi-squared Automatic Interaction Detection method was used to build the decision tree. The tree was externally validated in another real-life primary care population (n=3215). Our tree correctly diagnosed 79% of the asthma patients, 85% of the COPD patients and 32% of the asthma–COPD overlap syndrome (ACOS) patients. External validation showed a comparable pattern (correct: asthma 78%, COPD 83%, ACOS 24%). Our decision tree is considered to be promising because it was based on real-life primary care patients with a specialist's diagnosis. In most patients the diagnosis could be correctly predicted. Predicting ACOS, however, remained a challenge. The total decision tree can be implemented in computer-assisted diagnostic systems for individual patients. A simplified version of this tree can be used in daily clinical practice as a desk tool. PMID:27730177

Decision tree analysis to stratify risk of de novo non-melanoma skin cancer following liver transplantation.

Science.gov (United States)

Tanaka, Tomohiro; Voigt, Michael D

2018-03-01

Non-melanoma skin cancer (NMSC) is the most common de novo malignancy in liver transplant (LT) recipients; it behaves more aggressively and it increases mortality. We used decision tree analysis to develop a tool to stratify and quantify risk of NMSC in LT recipients. We performed Cox regression analysis to identify which predictive variables to enter into the decision tree analysis. Data were from the Organ Procurement Transplant Network (OPTN) STAR files of September 2016 (n = 102984). NMSC developed in 4556 of the 105984 recipients, a mean of 5.6 years after transplant. The 5/10/20-year rates of NMSC were 2.9/6.3/13.5%, respectively. Cox regression identified male gender, Caucasian race, age, body mass index (BMI) at LT, and sirolimus use as key predictive or protective factors for NMSC. These factors were entered into a decision tree analysis. The final tree stratified non-Caucasians as low risk (0.8%), and Caucasian males > 47 years, BMI decision tree model accurately stratifies the risk of developing NMSC in the long-term after LT.

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...

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...

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...

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.

Terrestrial nest-building by wild chimpanzees (Pan troglodytes): implications for the tree-to-ground sleep transition in early hominins.

Science.gov (United States)

Koops, Kathelijne; McGrew, William C; Matsuzawa, Tetsuro; Knapp, Leslie A

2012-07-01

Nest-building is a great ape universal and arboreal nesting in chimpanzees and bonobos suggests that the common ancestor of Pan and Homo also nested in trees. It has been proposed that arboreal nest-building remained the prevailing pattern until Homo erectus, a fully terrestrial biped, emerged. We investigated the unusual occurrence of ground-nesting in chimpanzees (Pan troglodytes), which may inform on factors influencing the tree-to-ground sleep transition in the hominin lineage. We used a novel genetic approach to examine ground-nesting in unhabituated chimpanzees at Seringbara in the Nimba Mountains, Guinea. Previous research showed that ground-nesting at Seringbara was not ecologically determined. Here, we tested a possible mate-guarding function of ground-nesting by analyzing DNA from shed hairs collected from ground nests and tree nests found in close proximity. We examined whether or not ground-nesting was a group-level behavioral pattern and whether or not it occurred in more than one community. We used multiple genetic markers to identify sex and to examine variation in mitochondrial DNA control region (HV1, HV2) sequences. Ground-nesting was a male-biased behavior and males constructed more elaborate ("night") nests than simple ("day") nests on the ground. The mate-guarding hypothesis was not supported, as ground and associated tree nests were built either by maternally-related males or possibly by the same individuals. Ground-nesting was widespread and likely habitual in two communities. We suggest that terrestrial nest-building may have already occurred in arboreally-adapted early hominins before the emergence of H. erectus. Copyright © 2012 Wiley Periodicals, Inc.

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.

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.

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...

Neural glycoprotein M6a is released in extracellular vesicles and modulated by chronic stressors in blood

OpenAIRE

Monteleone, Melisa C.; Billi, Silvia C.; Brocco, Marcela A.; Frasch, Alberto C.

2017-01-01

Membrane neuronal glycoprotein M6a is highly expressed in the brain and contributes to neural plasticity promoting neurite growth and spine and synapse formation. We have previously showed that chronic stressors alter hippocampal M6a mRNA levels in rodents and tree shrews. We now show that M6a glycoprotein can be detected in mouse blood. M6a is a transmembrane glycoprotein and, as such, unlikely to be free in blood. Here we demonstrate that, in blood, M6a is transported in extracellular vesic...

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...

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.

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

Directory of Open Access Journals (Sweden)

Hughes Joseph

2011-05-01

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

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.

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.

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

The effect of contaminated groundwater on tree growth: A tree-ring analysis

International Nuclear Information System (INIS)

LeBlanc, D.C.; Loehle, C.

1990-10-01

A study was conducted on the effect of contaminated groundwater seepage on tree growth downslope from F- and H-Area seepage basins of the Savannah River Site. Trees in wetlands along Four Mile Creek began to show localized stress and mortality in the late 1970s. Extreme winter temperatures and high rainfall were ruled out as potential causal factors of tree stress. Drought was shown to affect trees in both contaminated and uncontaminated zones, but trees in uncontaminated areas exhibit better recovery after drought than trees in contaminated areas. Pollution-mediated alteration of soil acidity and aluminum, sodium, and heavy metal concentrations likely acted to predispose trees to decline, with severe drought acting as the trigger for decline initiation and tree death. Thus, a moderate pollution loading, not sufficient to cause visible damage of itself, may create conditions in which sudden, severe decline could result from natural stresses. This mechanism of forest decline is common, and should be considered in evaluations of the impact of pollution on wetland forest systems. 28 refs., 4 figs., 6 tabs

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

Science.gov (United States)

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

2017-09-30

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

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...

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

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.

Development of a diagnostic decision tree for obstructive pulmonary diseases based on real-life data

NARCIS (Netherlands)

Metting, Esther I; In 't Veen, Johannes C C M; Dekhuijzen, P N Richard; van Heijst, Ellen; Kocks, Janwillem W H; Muilwijk-Kroes, Jacqueline B; Chavannes, Niels H; van der Molen, Thys

2016-01-01

The aim of this study was to develop and explore the diagnostic accuracy of a decision tree derived from a large real-life primary care population. Data from 9297 primary care patients (45% male, mean age 53±17 years) with suspicion of an obstructive pulmonary disease was derived from an

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.

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.

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

Suppression of leopard moth (Lepidoptera: Cossidae) populations in olive trees in Egypt through mating disruption.

Science.gov (United States)

Hegazi, E M; Khafagi, W E; Konstantopoulou, M A; Schlyter, F; Raptopoulos, D; Shweil, S; Abd El-Rahman, S; Atwa, A; Ali, S E; Tawfik, H

2010-10-01

The leopard moth, Zeuzera pyrina (L.) (Lepidoptera: Cossidae), is a damaging pest for many fruit trees (e.g., apple [Malus spp.], pear [Pyrus spp.] peach [Prunus spp.], and olive [Olea]). Recently, it caused serious yield losses in newly established olive orchards in Egypt, including the death of young trees. Chemical and biological control have shown limited efficiency against this pest. Field tests were conducted in 2005 and 2006 to evaluate mating disruption (MD) for the control of the leopard moth, on heavily infested, densely planted olive plots (336 trees per ha). The binary blend of the pheromone components (E,Z)-2,13-octadecenyl acetate and (E,Z)-3,13-octadecenyl acetate (95:5) was dispensed from polyethylene vials. Efficacy was measured considering reduction of catches in pheromone traps, reduction of active galleries of leopard moth per tree and fruit yield in the pheromone-treated plots (MD) compared with control plots (CO). Male captures in MD plots were reduced by 89.3% in 2005 and 82.9% in 2006, during a trapping period of 14 and 13 wk, respectively. Application of MD over two consecutive years progressively reduced the number of active galleries per tree in the third year where no sex pheromone was applied. In all years, larval galleries outnumbered moth captures. Fruit yield from trees where sex pheromone had been applied in 2005 and 2006 increased significantly in 2006 (98.8 +/- 2.9 kg per tree) and 2007 (23 +/- 1.3 kg per tree) compared with control ones (61.0 +/- 3.9 and 10.0 +/- 0.6 kg per tree, respectively). Mating disruption shows promising for suppressing leopard moth infestation in olives.

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...

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...

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...

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....

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.

Within-population variation in ejaculate characteristics in a prolonged breeder, Peron's tree frog, Litoria peronii

Science.gov (United States)

Sherman, Craig D. H.; Uller, Tobias; Wapstra, Erik; Olsson, Mats

2008-11-01

Sperm number is often a good predictor of success in sperm competition; however, it has become increasingly clear that, for some species, variation in probability of paternity cannot be explained by sperm number alone. Intraspecific variation in ejaculate characteristics, such as the number of viable sperm and sperm longevity, may play an equally important role in determining fertilization success. Here, we assess variation among ejaculates in three factors that may contribute to fertilization success (number of sperm per ejaculate, viability, and longevity), in a population of Peron’s tree frog ( Litoria peronii). We detected large variation among males in the number of sperm per ejaculate and the proportion of viable sperm within ejaculates, which could not be explained by variation in either male size or body condition. However, the proportion of viable sperm released by males increased over the season. Finally, we assessed sperm longevity (proportion viable sperm determined using a dual-fluorochrome vital dye) at two different temperatures. At 23°C, on average, 75% of sperm remained viable after 2 h, but there were significant differences amongst males with the percentage of viable sperm ranging from 43% to 95%. For sperm incubated at 4°C, ejaculates varied fivefold in sperm longevity with some males having 50% viable sperm after 5 days. Our data suggest that ejaculate characteristics (sperm number, viability, and longevity) vary widely in Peron’s tree frog and may therefore play an important role in determining siring success both in the presence and absence of sperm competition. We discuss the results in relation to selection on ejaculate traits via natural and sexual selection in this and other amphibians.

FB-Tree: A B+-Tree for Flash-Based SSDs

DEFF Research Database (Denmark)

Jørgensen, Martin V.; Rasmussen, René B.; Saltenis, Simonas

2011-01-01

Due to their many advantages, flash-based SSDs (Solid-State Drives) have become a mainstream alternative to magnetic disks for database servers. Nevertheless, database systems, designed and optimized for magnetic disks, still do not fully exploit all the benefits of the new technology. We propose....... As a consequence, the FB-tree outperforms a regular B+-tree in all scenarios tested. For instance, the throughput of a random workload of 75% updates increases by a factor of three using only two times the space of the B+-tree....

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...

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)

FTAP, Minimal Cut Sets of Arbitrary Fault Trees. FRTPLT, Fault Tree Structure and Logical Gates Plot for Program FTAP. FRTGEN, Fault Trees by Sub-tree Generator from Parent Tree for Program FTAP

International Nuclear Information System (INIS)

Willie, Randall R.; Rabien, U.

1997-01-01

1 - Description of problem or function: FTAP is a general-purpose program for deriving minimal reliability cut and path set families from the fault tree for a complex system. The program has a number of useful features that make it well-suited to nearly all fault tree applications. An input fault tree may specify the system state as any logical function of subsystem or component state variables or complements of these variables; thus, for instance, 'exclusive-or' type relations may be formed. When fault tree logical relations involve complements of state variables, the analyst may instruct FTAP to produce a family of prime implicants, a generalization of the minimal cut set concept. The program offers the flexibility of several distinct methods of generating cut set families. FTAP can also identify certain subsystems as system modules and provide a collection of minimal cut set families that essentially expresses the system state as a function of these module state variables. Another feature allows a useful subfamily to be obtained when the family of minimal cut sets or prime implicants is too large to be found in its entirety; this subfamily may consist of only those sets not containing more than some fixed number of elements or only those sets 'interesting' to the analyst in some special sense. Finally, the analyst can modify the input fault tree in various ways by declaring state variables identically true or false. 2 - Method of solution: Fault tree methods are based on the observation that the system state, either working or failed, can usually be expressed as a Boolean relation between states of several large, readily identifiable subsystems. The state of each subsystem in turn depends on states of simpler subsystems and components which compose it, so that the state of the system itself is determined by a hierarchy of logical relationships between states of subsystems. A fault tree is a graphical representation of these relationships. 3 - Restrictions on the

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…

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...

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...

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,...

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...

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

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....

Interspecific variation in resistance of two host tree species to spruce budworm

Science.gov (United States)

Fuentealba, Alvaro; Bauce, Éric

2016-01-01

Woody plants regularly sustain biomass losses to herbivorous insects. Consequently, they have developed various resistance mechanisms to cope with insect attack. However, these mechanisms of defense and how they are affected by resource availability are not well understood. The present study aimed at evaluating and comparing the natural resistance (antibiosis and tolerance) of balsam fir (Abies balsamea [L.] Mill.) and white spruce (Picea glauca [Moench) Voss] to spruce budworm, Choristoneura fumiferana (Clem.), and how drainage site quality as a component of resource availability affects the expression of resistance over time (6 years). Our results showed that there are differences in natural resistance between the two tree species to spruce budworm, but it was not significantly affected by drainage quality. Balsam fir exhibited higher foliar toxic secondary compounds concentrations than white spruce in all drainage classes, resulting in lower male pupal mass, survival and longer male developmental time. This, however, did not prevent spruce budworm from consuming more foliage in balsam fir than in white spruce. This response suggests that either natural levels of measured secondary compounds do not provide sufficient toxicity to reduce defoliation, or spruce budworm has developed compensatory mechanisms, which allow it to utilize food resources more efficiently or minimize the toxic effects that are produced by its host's defensive compounds. Larvae exhibited lower pupal mass and higher mortality in rapidly drained and subhygric sites. Drainage class also affected the amount of foliage destroyed but its impact varied over the years and was probably influenced by climatic variables. These results demonstrate the complexity of predicting the effect of resource availability on tree defenses, especially when other confounding environmental factors can affect tree resource allocation and utilization.

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...

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

Science.gov (United States)

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

2015-09-01

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

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.

Biology and Population Dynamics of Mercetaspis halli (Green on Almond and Peach Trees in Saman Region, Chaharmahal and Bakhtiari Province

Directory of Open Access Journals (Sweden)

N. Kianpour

2017-03-01

Full Text Available Introduction: Pest and disease problem with the extension of fruit orchards, becomes a serious and restricted factor for orchard growers. Most of the scale insect of cold region fruit trees in Iran belongto family Diaspididae. One of the most important pests in the fruit orchards of Chaharmahal and Bakhtiari Province are scale insects. Hall scale, Mercetaspis halli (Green (Hemiptera: Diaspididae , which is armoured scale, is known as a primarily pest of stone fruits. They are the most prevalent pests on trees mostly on Almond and Nectarine . In Iran, this pest is reported in the regions such as Khorasan, Marcazi, Semnan on Cherry, Almond and Apricot trees . Rajabi also reported the pest in Tehran, Esfahan, Yazd, Kermanshah, Fars and Kerman province on apricot, peach, cherry trees . Moghaddam in 2004 reported the pest distribution in Fars, Isfahan, Kerman, Sistan and Baluchestan on almond, peach and pistacia. Monthly abundance monitoring of M. halli, which was conducted by Berlinger et al in 1996 , indicated that adult population had three generations per year. From the ecological and biological aspects, no enough information is available in Iran about M. halli scale. Thus, the aim of this research was to investigate aspects of the biology and ecology and seasonal changes of M. halli on Almond and peach trees to clarify the effectiveness of nonchemical management strategy. Materials and Methods: A field study carried out by weekly sampling of different growth stages of M. halli (egg, nymph, male and female on twigs in two the Almond and the Peach orchards in Saman restrict in Chaharmahal and Bakhtiari Province. Different growth stages of armoured scales (egg, nymph, male and female were counted and its population seasonal changes were studied. The population density was determined and compared on different twigs with different ages. The period for ovoviviparously and emergence of 1st and 2nd nymphal instars and matured insects were estimated

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.

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...

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.

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...

Interspecific variation in tree seedlings establishment in canopy gaps in relation to tree density

Energy Technology Data Exchange (ETDEWEB)

Reader, R.J.; Bonser, S.P.; Duralia, T.E.; Bricker, B.D. [Guelph Univ., ON (Canada). Dept. of Botany

1995-10-01

We tested whether interspecific variation in tree seedling establishment in canopy gaps was significantly related to interspecific variation in tree density, for seven deciduous forest tree species (Quercus alba, Hamamelis virginiana, Acer rubrum, Sassafras albidum, Quercus rubra, Prunus serotina, Ostrya virginiana). For each species, seedling establishment was calculated as the difference in seedling density before experimental gap creation versus three years after gap creation. In each of the six experimentally-created gap types (33% or 66% removal of tree basal area from 0.01ha, 0.05ha or 0.20ha patches), differences in seedling establishment among species were significantly related to differences in their density in the tree canopy. A regression model with log{sub e} tree density as the independent variable accounted for between 93% and 98% of interspecific variation in seedling establishment. Our results provide empirical support for models of tree dynamics in gaps that assume seedling establishment depends on canopy tree density. 17 refs, 1 fig, 3 tabs

Proliferation of granule cell precursors in the dentate gyrus of adult monkeys is diminished by stress

Science.gov (United States)

Gould, Elizabeth; Tanapat, Patima; McEwen, Bruce S.; Flügge, Gabriele; Fuchs, Eberhard

1998-01-01

Although granule cells continue to be added to the dentate gyrus of adult rats and tree shrews, this phenomenon has not been demonstrated in the dentate gyrus of adult primates. To determine whether neurons are produced in the dentate gyrus of adult primates, adult marmoset monkeys (Callithrix jacchus) were injected with BrdU and perfused 2 hr or 3 weeks later. BrdU is a thymidine analog that is incorporated into proliferating cells during S phase. A substantial number of cells in the dentate gyrus of adult monkeys incorporated BrdU and ≈80% of these cells had morphological characteristics of granule neurons and expressed a neuronal marker by the 3-week time point. Previous studies suggest that the proliferation of granule cell precursors in the adult dentate gyrus can be inhibited by stress in rats and tree shrews. To test whether an aversive experience has a similar effect on cell proliferation in the primate brain, adult marmoset monkeys were exposed to a resident-intruder model of stress. After 1 hr in this condition, the intruder monkeys were injected with BrdU and perfused 2 hr later. The number of proliferating cells in the dentate gyrus of the intruder monkeys was compared with that of unstressed control monkeys. We found that a single exposure to this stressful experience resulted in a significant reduction in the number of these proliferating cells. Our results suggest that neurons are produced in the dentate gyrus of adult monkeys and that the rate of precursor cell proliferation can be affected by a stressful experience. PMID:9501234

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.

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

OpenAIRE

N. Price, Morgan

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 i...

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...

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.

Prognostic classification index in Iranian colorectal cancer patients: Survival tree analysis

Directory of Open Access Journals (Sweden)

Amal Saki Malehi

2016-01-01

Full Text Available Aims: The aim of this study was to determine the prognostic index for separating homogenous subgroups in colorectal cancer (CRC patients based on clinicopathological characteristics using survival tree analysis. Methods: The current study was conducted at the Research Center of Gastroenterology and Liver Disease, Shahid Beheshti Medical University in Tehran, between January 2004 and January 2009. A total of 739 patients who already have been diagnosed with CRC based on pathologic report were enrolled. The data included demographic and clinical-pathological characteristic of patients. Tree-structured survival analysis based on a recursive partitioning algorithm was implemented to evaluate prognostic factors. The probability curves were calculated according to the Kaplan-Meier method, and the hazard ratio was estimated as an interest effect size. Result: There were 526 males (71.2% of these patients. The mean survival time (from diagnosis time was 42.46± (3.4. Survival tree identified three variables as main prognostic factors and based on their four prognostic subgroups was constructed. The log-rank test showed good separation of survival curves. Patients with Stage I-IIIA and treated with surgery as the first treatment showed low risk (median = 34 months whereas patients with stage IIIB, IV, and more than 68 years have the worse survival outcome (median = 9.5 months. Conclusion: Constructing the prognostic classification index via survival tree can aid the researchers to assess interaction between clinical variables and determining the cumulative effect of these variables on survival outcome.

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.

Field Assessment of 3 Years of Release of sub-sterile males of Ectomyelois ceratoniae (Lepidoptera: Pyralidae)

International Nuclear Information System (INIS)

Jouda, Mediouni; Dhouibi, M.H.

2005-01-01

A weekly long-season release program was conduced in a pomegranate orchard during three years. Irradiation was done using a 60Co source with a dose rate of 46Gy/min. The gamma radiation substerilising dose adopted for this program was 400 Gy. The efficiency of these releases was investigated at the harvest. Releases of the sub-sterile male insects precede the beginning of the wild population activity. The monitoring of the wild pest population was accomplished using a series of Delta traps baited with the sexual pheromone. Traps were kept in the field the whole season. Trapping results and sampling data were used in order to study the insect population's dynamics. We studied reared irradiated male dispersion, their competitiveness into the field and attractiveness of irradiated virgin female. At the harvest, we determined the fruit infestation-rate both in the treated orchard and in the control. Irradiated male dispersion was studied using 24 delta traps. Six levels of male capture were chosen. These levels were 20, 40, 60, 80, 100 and 120 m from the point release. Results showed that irradiation at the substerilising dose 400 Gy don't affect the male's ability of flying. Moreover, we observed that irradiated males are able to reach traps placed at 120 m from the released point. The maximum of insect capture is obtained with levels 40m and 80m. This result is very important and has a practical implementation. In fact, in order to get a homogeneous distribution into the field, distances between 40m and 80 m should be kept between the release-lines. Male's competitiveness was carried out into two cages. The cages were installed on two middle size trees and were covered with a mosquito-net. A delta trap was hung into each cage. The trap was baited with two virgin non- irradiated females. Four ratios of irradiated to normal males were investigated: 1:1, 2.5:1, 5:1 and 10:1. Experimentations were replicated five times for each ratio. Results showed that substeriles

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.

Taxonomic uncertainty and the loss of biodiversity on Christmas Island, Indian Ocean.

Science.gov (United States)

Eldridge, Mark D B; Meek, Paul D; Johnson, Rebecca N

2014-04-01

The taxonomic uniqueness of island populations is often uncertain which hinders effective prioritization for conservation. The Christmas Island shrew (Crocidura attenuata trichura) is the only member of the highly speciose eutherian family Soricidae recorded from Australia. It is currently classified as a subspecies of the Asian gray or long-tailed shrew (C. attenuata), although it was originally described as a subspecies of the southeast Asian white-toothed shrew (C. fuliginosa). The Christmas Island shrew is currently listed as endangered and has not been recorded in the wild since 1984-1985, when 2 specimens were collected after an 80-year absence. We aimed to obtain DNA sequence data for cytochrome b (cytb) from Christmas Island shrew museum specimens to determine their taxonomic affinities and to confirm the identity of the 1980s specimens. The Cytb sequences from 5, 1898 specimens and a 1985 specimen were identical. In addition, the Christmas Island shrew cytb sequence was divergent at the species level from all available Crocidura cytb sequences. Rather than a population of a widespread species, current evidence suggests the Christmas Island shrew is a critically endangered endemic species, C. trichura, and a high priority for conservation. As the decisions typically required to save declining species can be delayed or deferred if the taxonomic status of the population in question is uncertain, it is hoped that the history of the Christmas Island shrew will encourage the clarification of taxonomy to be seen as an important first step in initiating informed and effective conservation action. © 2013 Society for Conservation Biology.

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

Leptopsylla algira costai (Siphonaptera: Leptopsyllidae: New host and new geographical record

Directory of Open Access Journals (Sweden)

Ali Yousefi

2016-11-01

Full Text Available Objective: To access the emerging ectoparasites associated with shrews in Hamedan Province of Iran. Methods: We have captured bicoloured white-toothed shrews [Crocidura leucodon (C. leucodon] using the live traps in April 2014. Ectoparasites collected by brushing the skins were removed and preserved in 70% ethanol containing 5% glycerin, and subsequently they were sent to the parasitology laboratory and processed. The fleas isolated from infested specimen were cleared in 10% aqueous potassium hydroxide, dehydrated in ethanol, cleared in xylene, mounted in Canada balsam and identified using reliable keys. Results: In general, eight fleas (one male, seven females were collected from C. leucodon in Hamedan Province, Western Iran. The fleas were identified as Leptopsylla algira costai Smit, 1955. Conclusions: Fleas are medically important because they transmit a wide variety of diseases to their hosts. In addition, this aricle reports Leptopsylla algira costai for the first time in new host (C. leucodon and new geographical region (Iran.

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

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...

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...

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

Science.gov (United States)

Letunic, Ivica; Bork, Peer

2011-07-01

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

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.

HIPPOCAMPAL ADULT NEUROGENESIS: ITS REGULATION AND POTENTIAL ROLE IN SPATIAL LEARNING AND MEMORY

Science.gov (United States)

Lieberwirth, Claudia; Pan, Yongliang; Liu, Yan; Zhang, Zhibin; Wang, Zuoxin

2016-01-01

Adult neurogenesis, defined here as progenitor cell division generating functionally integrated neurons in the adult brain, occurs within the hippocampus of numerous mammalian species including humans. The present review details various endogenous (e.g., neurotransmitters) and environmental (e.g., physical exercise) factors that have been shown to influence hippocampal adult neurogenesis. In addition, the potential involvement of adult-generated neurons in naturally-occurring spatial learning behavior is discussed by summarizing the literature focusing on traditional animal models (e.g., rats and mice), non-traditional animal models (e.g., tree shrews), as well as natural populations (e.g., chickadees and Siberian chipmunk). PMID:27174001

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…

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 ...

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 ...

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…

ELB-trees an efficient and lock-free B-tree derivative

DEFF Research Database (Denmark)

Bonnichsen, Lars Frydendal; Karlsson, Sven; Probst, Christian W.

2013-01-01

overhead. All lock-free data structures are based on simple atomic operations that, though supported by modern processors, are expensive in execution time. We present a lock-free data structure, ELB-trees, which under certain assumptions can be used as multimaps as well as priority queues. Specifically...... it cannot store duplicate key-value pairs, and it is not linearizable. Compared to existing data structures, ELB-trees require fewer atomic operations leading to improved performance. We measure the parallel performance of ELB-trees using a set of benchmarks and observe that ELB-trees are up to almost 30......As computer systems scale in the number of processors, scalable data structures with good parallel performance become increasingly important. Lock-free data structures promise such improved parallel performance at the expense of higher algorithmic complexity and higher sequential execution time...

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

Science.gov (United States)

2012-01-01

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

A right whale pootree: classification trees of faecal hormones identify reproductive states in North Atlantic right whales (Eubalaena glacialis).

Science.gov (United States)

Corkeron, Peter; Rolland, Rosalind M; Hunt, Kathleen E; Kraus, Scott D

2017-01-01

Immunoassay of hormone metabolites extracted from faecal samples of free-ranging large whales can provide biologically relevant information on reproductive state and stress responses. North Atlantic right whales ( Eubalaena glacialis Müller 1776) are an ideal model for testing the conservation value of faecal metabolites. Almost all North Atlantic right whales are individually identified, most of the population is sighted each year, and systematic survey effort extends back to 1986. North Atlantic right whales number trees as an alternative method of analysing multiple-hormone data sets, building on univariate models that have previously been used to describe hormone profiles of individual North Atlantic right whales of known reproductive state. Our tree correctly classified the age class, sex and reproductive state of 83% of 112 faecal samples from known individual whales. Pregnant females, lactating females and both mature and immature males were classified reliably using our model. Non-reproductive [i.e. 'resting' (not pregnant and not lactating) and immature] females proved the most unreliable to distinguish. There were three individual males that, given their age, would traditionally be considered immature but that our tree classed as mature males, possibly calling for a re-evaluation of their reproductive status. Our analysis reiterates the importance of considering the reproductive state of whales when assessing the relationship between cortisol concentrations and stress. Overall, these results confirm findings from previous univariate statistical analyses, but with a more robust multivariate approach that may prove useful for the multiple-analyte data sets that are increasingly used by conservation physiologists.

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…

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\

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.

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.

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

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

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.

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 ...

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.

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

Reconstructed tree fern Alethopteris zeilleri (Carboniferous, Medullosales)

Energy Technology Data Exchange (ETDEWEB)

Zodrow, Erwin L. [Department of Earth Sciences, University College of Cape Breton, Sydney, Nova, Scotia (Canada B1P 6L2)

2007-01-02

From a smaller open-pit area in the roof shale of the basal Cantabrian coal seam in Sydney Coalfield, Cape Breton Island, Nova Scotia, Canada, large amounts of the pteridosperm foliage Alethopteris zeilleri (Ragot) were found. This foliage is associated with abundant, naked medullosalean axes and dichotomies of varying sizes, up to 0.80-m long, cauline structures 0.90 m and 1.3 m long, detached ovules assigned to Pachytesta incrassata Brongniart, rare male-pollen organs of the type Dolerotheca Halle, rooted tree ferns in life position, and one specimen each of a juvenile medullosalean frond and root mantle. The fossils are compression/impression-preserved, and the foliage yielded thickly cutinized cuticles with unoriented cells (57-103 by 27-57 {mu}m) in intercostal fields. Ultimate rachises, and abaxial surfaces (excluding costal fields) show a mixture of simple and complexly-branched trichomes, and two different structural bases. These, together with fractal dimensionality of curvatures of anticlinal walls in intercostal fields, have taxonomic potential for alethopterids. The finds suggest reconstructing A. zeilleri (Ragot) as a tree, 5-7 m high, that bore both P. incrassata Brongniart and Dolerotheca-type fructifications. Its habitat was low-land coastal plains in the Pennsylvanian coal swamps of ancestral Sydney Coalfield. (author)

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

Science.gov (United States)

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

1997-01-01

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

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....

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

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....

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.

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

Science.gov (United States)

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

2018-04-06

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

Simple Prediction of Type 2 Diabetes Mellitus via Decision Tree Modeling

Directory of Open Access Journals (Sweden)

Mehrab Sayadi

2017-06-01

Full Text Available Background: Type 2 Diabetes Mellitus (T2DM is one of the most important risk factors in cardiovascular disorders considered as a common clinical and public health problem. Early diagnosis can reduce the burden of the disease. Decision tree, as an advanced data mining method, can be used as a reliable tool to predict T2DM. Objectives: This study aimed to present a simple model for predicting T2DM using decision tree modeling. Materials and Methods: This analytical model-based study used a part of the cohort data obtained from a database in Healthy Heart House of Shiraz, Iran. The data included routine information, such as age, gender, Body Mass Index (BMI, family history of diabetes, and systolic and diastolic blood pressure, which were obtained from the individuals referred for gathering baseline data in Shiraz cohort study from 2014 to 2015. Diabetes diagnosis was used as binary datum. Decision tree technique and J48 algorithm were applied using the WEKA software (version 3.7.5, New Zealand. Additionally, Receiver Operator Characteristic (ROC curve and Area Under Curve (AUC were used for checking the goodness of fit. Results: The age of the 11302 cases obtained after data preparation ranged from 18 to 89 years with the mean age of 48.1 ± 11.4 years. Additionally, 51.1% of the cases were male. In the tree structure, blood pressure and age were placed where most information was gained. In our model, however, gender was not important and was placed on the final branch of the tree. Total precision and AUC were 87% and 89%, respectively. This indicated that the model had good accuracy for distinguishing patients from normal individuals. Conclusions: The results showed that T2DM could be predicted via decision tree model without laboratory tests. Thus, this model can be used in pre-clinical and public health screening programs.

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

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)

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

Science.gov (United States)

Wu, Yufeng

2012-03-01

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

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...

Profile of male Brazilian injecting drug users who have sex with men

Directory of Open Access Journals (Sweden)

Ferreira Aline Dayrell

2006-01-01

Full Text Available This study aims to characterize the profile of male injecting drug users who have sex with other men (MSM IDUs recruited through a cross-sectional multi-city survey (AjUDE-Brasil II Project in six Brazilian cities, in 2000-2001. MSM IDUs were compared to other male IDUs using bivariate and multivariate procedures (logistic regression and answer tree analysis with the CHAID algorithm. Among the 709 male IDUs, 187 (26.4% reported ever having had sex with other men, while only 37 reported sex with other men in the previous six months. MSM IDUs were more likely to be unemployed (OR = 2.3, to have injected tranquilizers (OR = 3.6, and to be HIV-seropositive (OR = 2.1, compared to other male IDUs. Male same-sex relations in this subgroup appear to be associated with strategies to finance drug consuming habits, including sex for drugs with occasional female partners or obtaining injection paraphernalia from occasional sex partners. Further studies should focus on this especially vulnerable subgroup of IDUs, due to the bidirectional and complex interrelationships between their drug injecting habits and sexual risk behaviors.

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.

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…

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 ...

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…

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%; ...

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

Science.gov (United States)

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

2012-02-01

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

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...

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

Science.gov (United States)

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

2017-12-01

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

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.

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...

Tree Mortality Undercuts Ability of Tree-Planting Programs to Provide Benefits: Results of a Three-City Study

Directory of Open Access Journals (Sweden)

Sarah Widney

2016-03-01

Full Text Available Trees provide numerous benefits for urban residents, including reduced energy usage, improved air quality, stormwater management, carbon sequestration, and increased property values. Quantifying these benefits can help justify the costs of planting trees. In this paper, we use i-Tree Streets to quantify the benefits of street trees planted by nonprofits in three U.S. cities (Detroit, Michigan; Indianapolis, Indiana, and Philadelphia, Pennsylvania from 2009 to 2011. We also use both measured and modeled survival and growth rates to “grow” the tree populations 5 and 10 years into the future to project the future benefits of the trees under different survival and growth scenarios. The 4059 re-inventoried trees (2864 of which are living currently provide almost $40,000 (USD in estimated annual benefits ($9–$20/tree depending on the city, the majority (75% of which are increased property values. The trees can be expected to provide increasing annual benefits during the 10 years after planting if the annual survival rate is higher than the 93% annual survival measured during the establishment period. However, our projections show that with continued 93% or lower annual survival, the increase in annual benefits from tree growth will not be able to make up for the loss of benefits as trees die. This means that estimated total annual benefits from a cohort of planted trees will decrease between the 5-year projection and the 10-year projection. The results of this study indicate that without early intervention to ensure survival of planted street trees, tree mortality may be significantly undercutting the ability of tree-planting programs to provide benefits to neighborhood residents.

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.

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.

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

OpenAIRE

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

2017-01-01

Background Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the taxonomic framework. Results The SILVA Tree Viewer is a web application designed for visualizing large phylogenetic trees without requiring the download of any software tool or data files. The SILVA T...

Estimation of Tree Cover in an Agricultural Parkland of Senegal Using Rule-Based Regression Tree Modeling

Directory of Open Access Journals (Sweden)

Stefanie M. Herrmann

2013-10-01

Full Text Available Field trees are an integral part of the farmed parkland landscape in West Africa and provide multiple benefits to the local environment and livelihoods. While field trees have received increasing interest in the context of strengthening resilience to climate variability and change, the actual extent of farmed parkland and spatial patterns of tree cover are largely unknown. We used the rule-based predictive modeling tool Cubist® to estimate field tree cover in the west-central agricultural region of Senegal. A collection of rules and associated multiple linear regression models was constructed from (1 a reference dataset of percent tree cover derived from very high spatial resolution data (2 m Orbview as the dependent variable, and (2 ten years of 10-day 250 m Moderate Resolution Imaging Spectrometer (MODIS Normalized Difference Vegetation Index (NDVI composites and derived phenological metrics as independent variables. Correlation coefficients between modeled and reference percent tree cover of 0.88 and 0.77 were achieved for training and validation data respectively, with absolute mean errors of 1.07 and 1.03 percent tree cover. The resulting map shows a west-east gradient from high tree cover in the peri-urban areas of horticulture and arboriculture to low tree cover in the more sparsely populated eastern part of the study area. A comparison of current (2000s tree cover along this gradient with historic cover as seen on Corona images reveals dynamics of change but also areas of remarkable stability of field tree cover since 1968. The proposed modeling approach can help to identify locations of high and low tree cover in dryland environments and guide ground studies and management interventions aimed at promoting the integration of field trees in agricultural systems.

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)

Odour-mediated foraging by yellowjacket wasps (Hymenoptera: Vespidae): predation on leks of pheromone-calling Mediterranean fruit fly males (Diptera: Tephritidae).

Science.gov (United States)

Hendrichs, J; Katsoyannos, B I; Wornoayporn, V; Hendrichs, M A

1994-09-01

Predation is probably the most important male mortality factor in insect species with courtship displays that render males performing them conspicuous targets of predators. Sexually active Mediterranean fruit fly males, Ceratitis capitata (Wied.), aggregate in leks, where they participate in agonistic encounters and engage in visual, acoustic and pheromone-calling displays to attract receptive females. The objective of this study was to assess: a) whether sexually displaying C. capitata males in leks inside host and non-host foliage are subject to predation by the most prominent predators yellow-jacket wasps, Vespula germanica (F.), and if so, b) whether olfactory, visual or auditive stimuli are used by foraging wasps in locating male C. capitata prey. Studies were carried out in a citrus orchard and surroundings on the island of Chios, Greece. Observations were conducted using perforated containers hung within mulberry, fig or citrus foliage. Living C. capitata flies of different sex and either mature or immature were placed inside. Our results show that the yellowjacket wasps have learned to associate the presence of sexually active medfly males aggregated in leks with their prey's pheromone (kairomone). Foraging wasps, flying through the crowns of host trees, responded to the odour source of C. capitata male pheromone by approaching from downwind. Even inside dense citrus tree foliage, wasps keyed in on aggregations of pheromone-calling males using olfactory stimuli. Stimuli of visual and acoustic male signalling were only used at close range, after having followed the pheromone plume close to its source. Visual cues played a greater role in directing wasp foraging under more open and exposed host foliage conditions. Odour-based foraging of wasps inside host foliage in the mid-morning hours, when medfly male lekking activities peak, shifted gradually to a more visual-based host fruit patrolling in the afternoons to capture ovipositing and feeding medfly females

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.

Visual and acoustic signaling in three species of Brazilian nocturnal tree frogs (Anura, Hylidae

Directory of Open Access Journals (Sweden)

Luís Felipe Toledo

2007-06-01

Full Text Available Visual communication seems to be widespread among nocturnal anurans, however, reports of these behaviors in many Neotropical species are lacking. Therefore, we gathered information collected during several sporadic field expeditions in central and southern Brazil with three nocturnal tree frogs: Aplastodiscus perviridis, Hypsiboas albopunctatus and H. bischoffi. These species displayed various aggressive behaviors, both visual and acoustic, towards other males. For A. perviridis we described arm lifting and leg kicking; for H. albopunctatus we described the advertisement and territorial calls, visual signalizations, including a previously unreported behavior (short leg kicking, and male-male combat; and for H. bischoffiwe described the advertisement and fighting calls, toes and fingers trembling, leg lifting, and leg kicking. We speculate about the evolution of some behaviors and concluded that the use of visual signals among Neotropical anurans may be much more common than suggested by the current knowledge.

Arthropod but not bird predation in ethiopian homegardens is higher in tree-poor than in tree-rich landscapes.

Science.gov (United States)

Lemessa, Debissa; Hambäck, Peter A; Hylander, Kristoffer

2015-01-01

Bird and arthropod predation is often associated with natural pest control in agricultural landscapes, but the rates of predation may vary with the amount of tree cover or other environmental factors. We examined bird and arthropod predation in three tree-rich and three tree-poor landscapes across southwestern Ethiopia. Within each landscape we selected three tree-rich and three tree-poor homegardens in which we recorded the number of tree species and tree stems within 100 × 100 m surrounding the central house. To estimate predation rates, we attached plasticine caterpillars on leaves of two coffee and two avocado shrubs in each homegarden, and recorded the number of attacked caterpillars for 7-9 consecutive weeks. The overall mean daily predation rate was 1.45% for birds and 1.60% for arthropods. The rates of arthropod predation varied among landscapes and were higher in tree-poor landscapes. There was no such difference for birds. Within landscapes, predation rates from birds and arthropods did not vary between tree-rich and tree-poor homegardens in either tree-rich or tree-poor landscapes. The most surprising result was the lack of response by birds to tree cover at either spatial scale. Our results suggest that in tree-poor landscapes there are still enough non-crop habitats to support predatory arthropods and birds to deliver strong top-down effect on crop pests.

Arthropod but not bird predation in ethiopian homegardens is higher in tree-poor than in tree-rich landscapes.

Directory of Open Access Journals (Sweden)

Debissa Lemessa

Full Text Available Bird and arthropod predation is often associated with natural pest control in agricultural landscapes, but the rates of predation may vary with the amount of tree cover or other environmental factors. We examined bird and arthropod predation in three tree-rich and three tree-poor landscapes across southwestern Ethiopia. Within each landscape we selected three tree-rich and three tree-poor homegardens in which we recorded the number of tree species and tree stems within 100 × 100 m surrounding the central house. To estimate predation rates, we attached plasticine caterpillars on leaves of two coffee and two avocado shrubs in each homegarden, and recorded the number of attacked caterpillars for 7-9 consecutive weeks. The overall mean daily predation rate was 1.45% for birds and 1.60% for arthropods. The rates of arthropod predation varied among landscapes and were higher in tree-poor landscapes. There was no such difference for birds. Within landscapes, predation rates from birds and arthropods did not vary between tree-rich and tree-poor homegardens in either tree-rich or tree-poor landscapes. The most surprising result was the lack of response by birds to tree cover at either spatial scale. Our results suggest that in tree-poor landscapes there are still enough non-crop habitats to support predatory arthropods and birds to deliver strong top-down effect on crop pests.

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

Science.gov (United States)

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

2017-11-01

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

Shade Trees Spatial Distribution and Its Effect on Grains and Beverage Quality of Shaded Coffee Trees

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Francisco José da Silva Neto

2018-01-01

Full Text Available Shading coffee trees has gained importance, especially among smallholders, as an option to improve the products’ quality, therefore acquiring place at the specialty coffee market, where consumers are willing to give bonus for quality. This work aims to evaluate the influence of shade trees’ spatial distribution among coffee trees’ agronomic characteristics, yield, and beans and cup quality of shaded coffee trees. The experimental design consisted of completely randomized blocks with six repetitions and four treatments: coffee trees on shade trees planting rows, distant one meter from the trunk; coffee trees on shade trees planting row, distant six meters from the trunk; and coffee plants between the rows of shade trees, parallel to the previous treatments. The parameters analyzed were plant height, canopy diameter, plagiotropic branches’ length, yield, coffee fruits’ phenological stage, ripe cherries’ Brix degree, percentage of black, unripe, and insect damaged beans, bean size, and beverage quality. Shade trees quickened coffee fruits’ phenological stage of coffee trees nearest to them. This point also showed the best beverage quality, except for overripe fruits. The remaining parameters evaluated were not affected by shade trees’ spatial distribution.

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.

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.

Edge-Disjoint Fibonacci Trees in Hypercube

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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.

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...

Higher levels of multiple paternities increase seedling survival in the long-lived tree Eucalyptus gracilis.

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Martin F Breed

Full Text Available Studying associations between mating system parameters and fitness in natural populations of trees advances our understanding of how local environments affect seed quality, and thereby helps to predict when inbreeding or multiple paternities should impact on fitness. Indeed, for species that demonstrate inbreeding avoidance, multiple paternities (i.e. the number of male parents per half-sib family should still vary and regulate fitness more than inbreeding--named here as the 'constrained inbreeding hypothesis'. We test this hypothesis in Eucalyptus gracilis, a predominantly insect-pollinated tree. Fifty-eight open-pollinated progeny arrays were collected from trees in three populations. Progeny were planted in a reciprocal transplant trial. Fitness was measured by family establishment rates. We genotyped all trees and their progeny at eight microsatellite loci. Planting site had a strong effect on fitness, but seed provenance and seed provenance × planting site did not. Populations had comparable mating system parameters and were generally outcrossed, experienced low biparental inbreeding and high levels of multiple paternity. As predicted, seed families that had more multiple paternities also had higher fitness, and no fitness-inbreeding correlations were detected. Demonstrating that fitness was most affected by multiple paternities rather than inbreeding, we provide evidence supporting the constrained inbreeding hypothesis; i.e. that multiple paternity may impact on fitness over and above that of inbreeding, particularly for preferentially outcrossing trees at life stages beyond seed development.

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

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....

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

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...

Water, gravity and trees: Relationship of tree-ring widths and total water storage dynamics

Science.gov (United States)

Creutzfeldt, B.; Heinrich, I.; Merz, B.; Blume, T.; Güntner, A.

2012-04-01

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

The longevity of broadleaf deciduous trees in Northern Hemisphere temperate forests: insights from tree-ring series

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Alfredo eDi Filippo

2015-05-01

Full Text Available Understanding the factors controlling the expression of longevity in trees is still an outstanding challenge for tree biologists and forest ecologists. We gathered tree-ring data and literature for broadleaf deciduous (BD temperate trees growing in closed-canopy old-growth forests in the Northern Hemisphere to explore the role of geographic patterns, climate variability, and growth rates on longevity. Our pan-continental analysis, covering 32 species from 12 genera, showed that 300-400 years can be considered a baseline threshold for maximum tree lifespan in many temperate deciduous forests. Maximum age varies greatly in relation to environmental features, even within the same species. Tree longevity is generally promoted by reduced growth rates across large genetic differences and environmental gradients. We argue that slower growth rates, and the associated smaller size, provide trees with an advantage against biotic and abiotic disturbance agents, supporting the idea that size, not age, is the main constraint to tree longevity. The oldest trees were living most of their life in subordinate canopy conditions and/or within primary forests in cool temperate environments and outside major storm tracks. Very old trees are thus characterized by slow growth and often live in forests with harsh site conditions and infrequent disturbance events that kill much of the trees. Temperature inversely controls the expression of longevity in mesophilous species (Fagus spp., but its role in Quercus spp. is more complex and warrants further research in disturbance ecology. Biological, ecological and historical drivers must be considered to understand the constraints imposed to longevity within different forest landscapes.

Up in the tree--the overlooked richness of bryophytes and lichens in tree crowns.

Science.gov (United States)

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

2013-01-01

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

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

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....

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

Science.gov (United States)

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

2014-01-01

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

The Occurrence of the Cicada Cicadatra persica on Apple Trees, Malus domestica, in Erneh, Syria

Science.gov (United States)

Dardar, Marah A.; Belal, Hamzeh M.R.; Basheer, Abedlnabi M.

2013-01-01

An infestation of Cicadatra persica KirKaldy (Hemiptera: Cicadidae) on apple trees, Malus domestica Borkhausen (Rosales: Rosaceae), was reported for the first time in the apple fruit orchards of Erneh, Syria. Nymphs, adults, exuvia, and exit holes in the soil were observed. The species was identified as C. persica based on morphological characters. Some biological observations and an acoustic analysis of the male's songs were also achieved. PMID:23909877

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 ...

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

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, ...

How eco-evolutionary principles can guide tree breeding and tree biotechnology for enhanced productivity.

Science.gov (United States)

Franklin, Oskar; Palmroth, Sari; Näsholm, Torgny

2014-11-01

Tree breeding and biotechnology can enhance forest productivity and help alleviate the rising pressure on forests from climate change and human exploitation. While many physiological processes and genes are targeted in search of genetically improved tree productivity, an overarching principle to guide this search is missing. Here, we propose a method to identify the traits that can be modified to enhance productivity, based on the differences between trees shaped by natural selection and 'improved' trees with traits optimized for productivity. We developed a tractable model of plant growth and survival to explore such potential modifications under a range of environmental conditions, from non-water limited to severely drought-limited sites. We show how key traits are controlled by a trade-off between productivity and survival, and that productivity can be increased at the expense of long-term survival by reducing isohydric behavior (stomatal regulation of leaf water potential) and allocation to defense against pests compared with native trees. In contrast, at dry sites occupied by naturally drought-resistant trees, the model suggests a better strategy may be to select trees with slightly lower wood density than the native trees and to augment isohydric behavior and allocation to defense. Thus, which traits to modify, and in which direction, depend on the original tree species or genotype, the growth environment and wood-quality versus volume production preferences. In contrast to this need for customization of drought and pest resistances, consistent large gains in productivity for all genotypes can be obtained if root traits can be altered to reduce competition for water and nutrients. Our approach illustrates the potential of using eco-evolutionary theory and modeling to guide plant breeding and genetic technology in selecting target traits in the quest for higher forest productivity. © The Author 2014. Published by Oxford University Press. All rights reserved

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

Science.gov (United States)

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

2007-11-01

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

Blarina brevicauda as a biological monitor of polychlorinated biphenyls: evaluation of hepatic cytochrome P450 induction.

Science.gov (United States)

Russell, Julie S; Halbrook, Richard S; Woolf, Alan; French, John B; Melancon, Mark J

2004-08-01

We assessed the value of short-tailed shrews (Blarina brevicauda) as a possible biomonitor for polychlorinated biphenyl pollution through measurement of the induction of hepatic cytochrome P450 and associated enzyme activities. First, we checked the inducibility of four monooxygenases (benzyloxyresorufin-O-dealkylase [BROD], ethoxyresorufin-O-dealkylase [EROD], methoxyresorufin-O-dealkylase [MROD], and pentoxyresorufin-O-dealkylase [PROD]) by measuring the activity of these enzymes in hepatic microsomes prepared from shrews injected with beta-naphthoflavone (betaNF) or phenobarbital (PB), typical inducers of cytochrome P4501A (CYP1A) and CYP2B enzyme families, respectively. Enzyme activity was induced in shrews that received betaNF but not in shrews that received PB; PROD was not induced by either exposure. Later, shrews were exposed to a mixture of polychlorinated biphenyls (PCBs) (Aroclor 1242:1254, in 1:2 ratio) at 0.6, 9.6, and 150 ppm in food, for 31 d. Induction in these shrews was measured by specific enzyme activity (BROD, EROD, and MROD) in hepatic microsomes, by western blotting of solubilized microsomes against antibodies to CYP1A or CYP2B, and by duration of sodium pentobarbital-induced sleep. These three CYP enzymes were induced in shrews by PCBs at similar levels of exposure as in cotton rat (Sigmodon hispidus). Neither sleep time nor the amount of CYP2B family protein were affected by PCB exposure. Blarina brevicauda can be a useful biomonitor of PCBs that induce CYP1A, especially in habitats where they are the abundant small mammal.

Up in the tree--the overlooked richness of bryophytes and lichens in tree crowns.

Directory of Open Access Journals (Sweden)

Steffen Boch

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

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...

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-...

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...

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.

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.

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.

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

Science.gov (United States)

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

2011-09-01

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

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).

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

Directory of Open Access Journals (Sweden)

Annika Wein

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

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

Science.gov (United States)

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

2010-05-01

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

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

Science.gov (United States)

Masson, Josiane; Soille, Pierre; Mueller, Rick

2004-10-01

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

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…

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...

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.

Heterogeneous Compression of Large Collections of Evolutionary Trees.

Science.gov (United States)

Matthews, Suzanne J

2015-01-01

Compressing heterogeneous collections of trees is an open problem in computational phylogenetics. In a heterogeneous tree collection, each tree can contain a unique set of taxa. An ideal compression method would allow for the efficient archival of large tree collections and enable scientists to identify common evolutionary relationships over disparate analyses. In this paper, we extend TreeZip to compress heterogeneous collections of trees. TreeZip is the most efficient algorithm for compressing homogeneous tree collections. To the best of our knowledge, no other domain-based compression algorithm exists for large heterogeneous tree collections or enable their rapid analysis. Our experimental results indicate that TreeZip averages 89.03 percent (72.69 percent) space savings on unweighted (weighted) collections of trees when the level of heterogeneity in a collection is moderate. The organization of the TRZ file allows for efficient computations over heterogeneous data. For example, consensus trees can be computed in mere seconds. Lastly, combining the TreeZip compressed (TRZ) file with general-purpose compression yields average space savings of 97.34 percent (81.43 percent) on unweighted (weighted) collections of trees. Our results lead us to believe that TreeZip will prove invaluable in the efficient archival of tree collections, and enables scientists to develop novel methods for relating heterogeneous collections of trees.

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

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

OpenAIRE

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

2014-01-01

Emamectin benzoate, an insecticide derived from the avermectin family of natural products, has a unique translocation behavior in trees when applied by tree micro injection (TMI), which can result in protection from insect pests (foliar and borers) for several years. Active ingredient imported into leaves was measured at the end of season in the fallen leaves of treated horse chestnut (Aesculus hippocastanum) trees. The dissipation of emamectin benzoate in these leaves seems to be biphasic an...

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...

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

Science.gov (United States)

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

2018-01-01

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

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

Directory of Open Access Journals (Sweden)

Cody A. Freas

2018-01-01

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

Encoding phylogenetic trees in terms of weighted quartets.

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.

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

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

Science.gov (United States)

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

2018-03-05

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

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

Life history dictates fluorosis risk in a small mammal community

International Nuclear Information System (INIS)

Rafferty, D.P.; Faulkner, B.; Lochmiller, R.L.; Qualls, C.W. Jr.; McBee, K.

1995-01-01

Dental lesions, due to fluorosis, previously have been reported in wild, male cotton rats (Sigmodon hispidus) on an abandoned oil refinery located at the Oklahoma Refining Company in Cyril, Oklahoma. This study was expanded to include examinations of the fulvous harvest mouse (Reithrodontomys fulvescens), house mouse (Mus musculus), prairie vole (Microtus ochrogaster), plains pocket gopher (Geomys bursarius), least shrew (Cryptotis parva), shorttailed shrew (Blarina brevicauda), and deer mouse (Peromyscus spp.) at this same site. A sample of each species was collected form the contaminated refining site and a reference site with no known contamination. The authors grossly scored dentition of lower and upper incisors, microscopically examined cellular aberrations in ameloblasts and ondontoblasts, and quantified femur fluoride levels. Alterations in the lower and upper incisors were common in prairie voles, whose incisors possessed striations and erosion of the enamel and appeared chalky white. Incisors of animals taken from the reference site were normal. Patterns in occurrence of fluorosis and degree of enamel erosion was examined relative to the life history characteristics of the species

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

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.

Tree-Based Unrooted Phylogenetic Networks.

Science.gov (United States)

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

2018-02-01

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

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

Science.gov (United States)

David W. MacFarlane; Neil R. Ver Planck

2012-01-01

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

Wood density variation and tree ring distinctness in Gmelina arborea trees by x-ray densitometry

Directory of Open Access Journals (Sweden)

Roger Moya

2009-03-01

Full Text Available Due to its relationship with other properties, wood density is the main wood quality parameter. Modern, accuratemethods such as X-ray densitometry - are applied to determine the spatial distribution of density in wood sections and to evaluatewood quality. The objectives of this study were to determinate the influence of growing conditions on wood density variation andtree ring demarcation of gmelina trees from fast growing plantations in Costa Rica. The wood density was determined by X-raydensitometry method. Wood samples were cut from gmelina trees and were exposed to low X-rays. The radiographic films weredeveloped and scanned using a 256 gray scale with 1000 dpi resolution and the wood density was determined by CRAD and CERDsoftware. The results showed tree-ring boundaries were distinctly delimited in trees growing in site with rainfall lower than 2510 mm/year. It was demonstrated that tree age, climatic conditions and management of plantation affects wood density and its variability. Thespecific effect of variables on wood density was quantified by for multiple regression method. It was determined that tree yearexplained 25.8% of the total variation of density and 19.9% were caused by climatic condition where the tree growing. Wood densitywas less affected by the intensity of forest management with 5.9% of total variation.

Autumn frost hardiness in Norway spruce plus tree progeny and trees of the local and transferred provenances in central Sweden.

Science.gov (United States)

Hannerz, Mats; Westin, Johan

2005-09-01

Reforestation with provenances from locations remote from the planting site (transferred provenances) or the progeny of trees of local provenances selected for superior form and vigor (plus trees) offer alternative means to increase yield over that obtained by the use of seed from unselected trees of the local provenance. Under Swedish conditions, Norway spruce (Picea abies (L.) Karst.) of certain transferred provenances generally has an advantage in productivity relative to the local provenance comparable to that of progeny of plus trees. The aim of this study was to explore the extent to which productivity gains achieved by provenance transfer or the use of plus tree progeny are associated with reductions in autumn frost hardiness, relative to that of trees of the local provenance. In a field trial with 19-year-old trees in central Sweden, bud hardiness was tested on four occasions during the autumn of 2002. Trees of the local provenance were compared with trees of a south Swedish provenance originating 3 degrees of latitude to the south, a Belarusian provenance and the progeny of plus trees of local origin. The Belarusian provenance was the least hardy and the local provenance the most hardy, with plus tree progeny and the south Swedish provenance being intermediate in hardiness. Both the Belarusian provenance and the plus tree progeny were significantly taller than trees of the other populations. Within provenances, tree height was negatively correlated with autumn frost hardiness. Among the plus tree progeny, however, no such correlation between tree height and autumn frost hardiness was found. It is concluded that although the gain in productivity achieved by provenance transfer from Belarus was comparable to that achieved by using the progeny of plus trees of the local provenance, the use of trees of the Belarus provenance involved an increased risk of autumn frost damage because of later hardening.

Inferences from growing trees backwards

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...

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.

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...

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....

着衣と脱衣の詩学 : Shakespeare喜劇における

OpenAIRE

滝川, 睦; TAKIKAWA, Mutsumu

2013-01-01

This paper is intended as an investigation of the poetics of dressing and undressing in Shakespeare's comedies. The focal points are as follows: the undressing and uncrowning of Katherina in The Taming of the Shrew (Shr.); Julia's male clothing in The Two Gentlemen of Verona (TGV); Benedick's dressing and uncrowning in Much Ado about Nothing (Ado). The first chapter, focusing upon Katherina's gesture of throwing off her cap in the final scene, examines the undressing process in Shr.'s taming ...

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.

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.)

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.

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...

A Durable Flash Memory Search Tree

OpenAIRE

Clay III, James; Wortman, Kevin