bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigation of deep levels in nitrogen doped 4H–SiC epitaxial layers grown on 4° and 8° off-axis substrates
Authors: Myers-Ward R. L. , VanMil B. L. , Lew K.-K. , Klein P. B. , Glaser E. R. , Caldwell J. D. , Mastro M. A. , Wang L. , Zhao P. , Eddy C. R. , Gaskill D. K.
Published: September 2010

Intentionally doped n-type 4H–SiC films were grown on 4° and 8° off-axis substrates to investigate the influence of electron concentration on the incorporation of electron traps Z1/2 and EH6/7. No discernible change was seen in the Z1/2 and EH6/7 trap concentrations for films grown on both orientations with electron concentrations in the range of 1×1014 to 1×1016 cm−3, suggesting that the Z1/2 and EH6/7 traps are not associated with isolated carbon vacancies. The defect concentrations did not correlate with the measured carrier lifetimes, which is consistent with a carrier lifetime controlled by other recombination centers. Observed decreases in lifetime were related to increases in doping levels, with similar trends seen for both orientations. Carrier lifetimes in 8° material were slightly longer than in 4° films for similar doping concentrations, most likely being associated with surface recombination and/or extended defects.
Effect of strong gravity on Y1Ba2Cu3O7−x superconductor
Authors: Bagum Rabaya , Yoshiasa Akira , Okayasu Satoru , Iguchi Yusuke , Ono Masao , Okube Maki , Mashimo Tsutomu
Published: September 2010

Beginning with homogeneous samples of the superconducting phase Y1Ba2Cu3O7−x (Y123), we examined changes in structure and composition under a strong gravitational field and temperatures remarkably lower than the Y123 melting point. We observed essentially two-layers with different compositions caused by sedimentation of atoms. The layer exposed to the stronger gravitational field is composed of an Y123 phase that has a smaller unit cell volume compared with the initial sample, green, transparent, large single crystals of Y211, and a BaCuO2 phase. Despite the remarkably lower temperature, compositional and structural changes in addition to decomposition were found. The unit cell volume of the Y211 phase was larger than previously indicated by synchrotron x-ray diffraction (XRD) analysis. Refinement of the Y211 structure from the XRD data also showed that these crystals are very perfect due to a very high extinction coefficient 0.7(9)×10−6 and symmetrical arrangement compared with the superconducting phase Y123 crystal structure. The study provides evidence that strong gravitational fields can be applied to produce new materials at temperatures much below their melting points.
Contact superconductivity in In–PbTe junctions
Authors: Grabecki G. , Kolwas K. A. , Wróbel J. , Kapcia K. , Puźniak R. , Jakieła R. , Aleszkiewicz M. , Dietl T. , Springholz G. , Bauer G.
Published: September 2010

We report on electron transport studies on superconductor/semiconductor hybrid structures of indium and n-type PbTe quantum wells embedded between Pb0.92Eu0.08Te barriers. In/PbTe contacts form by spontaneous alloying, which occurs already at room temperature. The alloyed phase penetrates deeply into the semiconductor and forms metallic contacts even in the presence of depletion layers at the semiconductor’s surface. Although the detailed structure of this phase is unknown, we observe that it exhibits a superconducting transition at temperatures below 7 K. This causes such substantial reduction in the contact resistances that they even become comparable to those predicted for ideal superconductor-normal conductor contacts. Our findings suggest that the new superconducting phase is result of Josephson coupling arising between tiny superconducting precipitates randomly distributed in the interface region. In analogy to the granular superconducting systems, the coupling would lead to the occurrence of the global superconductivity only when the Coulomb charging energies of the precipitates are sufficiently small. This condition is exceptionally well fulfilled in PbTe because of a huge static dielectric constant of this material, ε>1000.
Energy transfer mechanism and Auger effect in Er3+ coupled silicon nanoparticle samples
Authors: Pitanti A. , Navarro-Urrios D. , Prtljaga N. , Daldosso N. , Gourbilleau F. , Rizk R. , Garrido B. , Pavesi L.
Published: September 2010

We report a spectroscopic study about the energy transfer mechanism among silicon nanoparticles (Si-np), both amorphous and crystalline, and Er ions in a silicon dioxide matrix. From infrared spectroscopic analysis, we have determined that the physics of the transfer mechanism does not depend on the Si-np nature, finding a fast (<200 ns) energy transfer in both cases, while the amorphous nanoclusters reveal a larger transfer efficiency than the nanocrystals. Moreover, the detailed spectroscopic results in the visible range here reported are essential to understand the physics behind the sensitization effect, whose knowledge assumes a crucial role to enhance the transfer rate and possibly employing the material in optical amplifier devices. Joining the experimental data, performed with pulsed and continuous-wave excitation, we develop a model in which the internal intraband recombination within Si-np is competitive with the transfer process via an Auger electron-“recycling” effect. Posing a different light on some detrimental mechanism such as Auger processes, our findings clearly recast the role of Si-np in the sensitization scheme, where they are able to excite very efficiently ions in close proximity to their surface.
Thermodynamics with friction. I. The Clausius inequality revisited
Authors: Bizarro João P. S.
Published: September 2010

The different forms of the Clausius inequality are generalized to explicitly include frictional work, which can be partly dissipated as heat in the surroundings and thus contribute to increase its entropy so, in a cyclic process, the net entropy leaving the surroundings with the heat directly exchanged with the system is no longer constrained by the second law to be nonpositive. Likewise, the lower bound for the system’s entropy change in an arbitrary transformation is not now determined solely by the heat transferred from the surroundings but can be smaller by a term given by frictional dissipation in the latter. A wide range of applications is discussed, from thermal engines to mesoscopic devices, including the efficiency of dithermal engines and the problem of information erasure. Moreover, it is verified that the macroscopic approach utilized to extend standard macroscopic equilibrium theory in such a manner as to incorporate friction can be cast as well in the continuous, fieldlike formulation of nonequilibrium thermodynamics.
Nanoductility induced brittle fracture in shocked high performance ceramics
Authors: Branicio Paulo S. , Kalia Rajiv K. , Nakano Aiichiro , Vashishta Priya
Published: September 2010

Nanoductility induced crack nucleation mechanism mediated by a single dislocation core is revealed in a 300 million-atom molecular dynamics simulation of shocked silicon carbide ceramic. The atomistic damage mechanism involves dynamic transitions between clearly delineated regimes—from shock-induced structural transformation to plastic deformation to brittle fracture. Such atomistic understanding may help in the design of nanocrack suppression strategies to realize predictive modeling of complex damage processes in high-performance ceramics.
Enhanced sensing performance by the plasmonic analog of electromagnetically induced transparency in active metamaterials
Authors: Dong Zheng-Gao , Liu Hui , Cao Jing-Xiao , Li Tao , Wang Shu-Ming , Zhu Shi-Ning , Zhang X.
Published: September 2010

The gain-assisted plasmonic analog of electromagnetically induced transparency (EIT) in a metallic metamaterial is investigated for the purpose to enhance the sensing performance of the EIT-like plasmonic structure. The structure is composed of three bars in one unit, two of which are parallel to each other (dark quadrupolar element) but perpendicular to the third bar (bright dipolar element), The results show that, in addition to the high sensitivity to the refractive-index fluctuation of the surrounding medium, the figure of merit for such active EIT-like metamaterials can be greatly enhanced, which is attributed to the amplified narrow transparency peak.
Current-voltage characteristics of zinc-blende (cubic) Al0.3Ga0.7N/GaN double barrier resonant tunneling diodes
Authors: Zainal N. , Novikov S. V. , Mellor C. J. , Foxon C. T. , Kent A. J.
Published: September 2010

Measurements of the current-voltage characteristics of zinc-blende (cubic) Al0.3Ga0.7N/GaN, double barrier resonant tunneling diodes are presented. Clear and reproducible negative differential resistance effects are observed, with room temperature peak-to-valley ratios up to 4 and peak currents up to about 1000 A cm−2.
Subterahertz characterization of ethanol hydration layers by microfluidic system
Authors: Laurette S. , Treizebre A. , Affouard F. , Bocquet B.
Published: September 2010

Characterizations of ethanol hydration layers are examined through subterahertz spectroscopy of water/ethanol mixtures by using a microfluidic system. A three-component model is used to explain measurements discrepancies with the Lambert–Beer law and to determine ethanol hydration shell absorption. Moreover, the hydration shell distribution is compared with molecular dynamics simulations with a good agreement. Ethanol hydration number is then computed and it can quickly characterize only the first water hydration layer or the whole hydration shell, depending on the chosen extraction model.
Inheritance of Resistance to Foliar Infection by Xanthomonas axonopodis pv. dieffenbachiae in Anthurium
Authors: Elibox W. , Umaharan P.
Published: September 2010

The inheritance of resistance to the foliar phase of bacterial blight disease, caused by Xanthomonas axonopodis pv. dieffenbachiae, in Anthurium andraeanum was studied using parent-offspring regression analysis. In all, 14 parental cultivars, each represented by 3 plants per replicate, and 12 biparental progenies derived from the parents, each represented by 20 plants per replicate, were evaluated for foliar resistance using a leaf-disc, vacuum infiltration method in a randomized complete block design with three replications over two seasons. Three to five leaf discs (5.6 cm2; stage-2 leaves) obtained from each plant were vacuum infiltrated (15 psi; 10 s) with 108 CFU/ml of inoculum and incubated (30°C) in trays. The time taken for the lesion to cover the entire disc was recorded for each disc. The progeny distributions were normally distributed with considerable transgressive segregation. Midparent/offspring regression analysis showed a high narrow sense heritability of 0.89 ± 0.13. These results indicate that inheritance of foliar resistance to blight is quantitative, with a major role for additive genetic effects. A breeding strategy to combine resistance to bacterial blight at both the foliar and systemic levels is discussed.
A Method to Induce Stem Cankers by Inoculating Nonwounded Populus Clones with Septoria musiva Spore Suspensions
Authors: LeBoldus Jared M. , Blenis Peter V. , Thomas Barb R.
Published: September 2010

Most artificial inoculations of Populus spp. stems with Septoria musiva have required host wounding to induce canker development; in the absence of wounds, frequencies of cankers have been low. Three greenhouse inoculation experiments were conducted to demonstrate the reliability and repeatability of an inoculation method that did not require wounding. In the first, 16 clones of hybrid poplar were inoculated with three isolates of S. musiva to compare responses following wounding and inoculation with mycelium (wound inoculation) with responses following inoculation of nonwounded trees by spraying with a conidial suspension (spray inoculation). Stem disease severity among clones following spray inoculation was correlated with stem disease severity following wound inoculation. A significant clone–isolate interaction was detected with spray inoculation but not wound inoculation. In the other two greenhouse experiments, 29 clones of hybrid poplar and 69 clones of Populus balsamifera were inoculated with a spore suspension mixture of three isolates. In both cases, the experimental error was similar to that obtained in previous experiments, in which trees were wound inoculated, and was adequately small to permit detection of differences in responses among clones. Ultimately, field studies will be needed to determine the best inoculation method for predicting stem responses to this pathogen under field conditions. However, relative to wound inoculation, spray inoculation of nonwounded trees has the advantage of yielding faster results, permitting inoculation with a mixture of isolates, and not circumventing potential mechanisms for resisting penetration. The ability to infect stems without wounding creates opportunities for numerous types of epidemiological and disease control studies that are difficult to conduct with wound inoculation.
First Report of Hiemalis begonias Wilt Disease Caused by Fusarium foetens in Canada
Authors: Tian X. L. , Dixon M. , Zheng Y.
Published: September 2010

Hiemalis begonias Fotsch (Begonia × hiemalis), a member of the family Begoniaceae, is a commercially important potted flowering plant in Europe and North America. In the spring of 2010, stunted growth and dull green leaves of H. begonias were observed in a commercial greenhouse in southern Ontario, Canada. Symptoms began with dull green foliage, followed by wilted leaves, then the stem base became water soaked with vascular discoloration, and finally, large macroconidial masses of a fungus developed on the collapsed stems and veins. A fungus was consistently isolated from the leaves, stems, and roots of symptomatic plants. Single conidia were isolated from sporodochia and cultured on potato dextrose agar (PDA) and oatmeal agar (OA) for 7 days. Isolates exhibited strong pungent odors on PDA and OA and a brownish orange colony on OA and a light orange colony on PDA. Masses of light orange and hemispherical-shaped conidia and stromata formed on OA. Conidiophores formed from aerial mycelium producing ellipsoidal microconidia without septation. Sporodochia formed on agar surface producing three-septate, slightly curved macroconidia. The cultural and conidial characteristics of the isolates were similar to those of Fusarium foetens Schroers (4). Partial translation elongation factor 1-α (TEF) gene was amplified and sequenced with primers ef1 and ef2. A comparison of a partial sequence has been deposited in GenBank (Accession No. HM748968) and showed a 100% match with F. foetens (2). Inoculations with F. foetens isolates were performed by injecting a 100-μl suspension of 1 × 106 conidia/ml into stems of five healthy plants near the ground or soaking the soil of five healthy 6-week-old H. begonias cv. Golden Edith with 50 ml of suspension. Control plants were similarly injected with sterile water or sown in sterile soil. After 4 weeks, all inoculated plants developed dark, wilting leaves and collapsed stems and veins similar to those observed in the commercial greenhouse. F. foetens was reisolated from diseased plants, and identification was reconfirmed by conidial characteristics and TEF 1-α sequence. Control plants were healthy and symptom free. F. foetens has recently been described in association with a new disease of H. begonias in Europe (3) and the United States (1). F. foetens can cause major economic losses to farmers and marketers of H. begonias in Europe and the United States. To our knowledge, this is the first report of F. foetens causing wilt disease of H. begonias in Canada.

References: (1) W.-H. Elmer et al. Plant Dis. 88:1287, 2004. (2) D.-M. Geiser et al. Eur. J. Plant Pathol. 110:473, 2004. (3) R. Schrage. Phytomed. Ges. 33:68, 2003. (4) H.-J. Schroers et al. Mycologia 96:393, 2004.
Bioethics: An African Perspective
Authors: Tangwa Godfrey B.
Published: September 2010

In this paper I have attempted to open a window on an African approach to Bioethics — that of the Nso' of the Bamenda Highlands of Kamerun — from the vantage position of someone who has familiarity with both African and Western cultures. Because of its scientific‐cum‐technological sophistication and its proselytising character, Western culture, as well as Western systems of thought and practice, have greatly affected and influenced other cultures, particularly African culture. But Western culture, systems of thought and practice, have been highly impervious and immune to influences from other cultures, philosophies, systems of thought and practice, even where these might have been salutary and enriching to Western culture and systems. What I have here termed Nso' eco‐bio‐cummunitarianism clearly indicates a viable alternative world‐view within which some of the bioethical perplexities and controversies of today might be more satisfactorily resolved than within a Western framework. I have further attempted to show, by way of example, how within such a world‐view, abortion and suicide, for instance, would be disapproved of while euthanasia, in its etymological purity, is approved of.
‘Bioethics’ is Subordinate to Morality in Japan
Authors: Tanida Noritoshi
Published: September 2010

Disputes over brain death and euthanasia are used to illuminate the question whether there really is a Japanese way of thinking in bioethics. In Japanese thought, a person does not exist as an individual but as a member of the family, community or society. I describe these features of Japanese society as ‘mutual dependency’. In this society, an act is ‘good’ and ‘right’ when it is commonly done, and it is ‘bad’ and ‘wrong’ when nobody else does it. Thus, outsiders to this ring of mutual dependency encounter ostracism. One feature of this society is a lack of open discussion which leads to the existence of multiple standards. This Japanese morality even prevails over written laws. In Japan, there is a public stance that euthanasia does not exist. On the other hand, there are certain decisions which have permitted euthanasia. Similarly, organ transplants were performed from brain dead donors, while that procedure was not accepted officially by the medical profession. In this situation, there is a danger that human rights will be neglected. So far bioethical approaches have not helped to work out these problems. This may be because Japanese think that bioethics is subordinate to morality. The current dispute over brain death involves a struggle for the establishment of a rational society in Japan. Overcoming mutual dependency and ostracism is essential to resolve this struggle and to lead Japan into a society of mutual respect where all individuals, families and communities are esteemed.
Community and Justice: The Challenges of Bicultural Partnership to Policy on Assisted Reproductive Technology
Authors: Nicholas Barbara
Published: September 2010

Listening to other cultures offers challenges to our fundamental assumptions and world views. In New Zealand public policy on Assisted Reproductive Technology (ART) is being worked out in a society committed to the development of bicultural partnership honouring the Treaty of Waitangi, a treaty with the indigenous people.

Strong claims to the cultural significance of genetic heritage by Maori have made apparent to non‐Maori (Pakeha) their own assumptions. These claims also resist reductive understandings of genetics.

In this paper I review, as a Pakeha ethicist, initiatives taken in New Zealand, and the impact of bicultural development on public policy on ART. I also discuss some of the issues this raises for western bioethics as it relates to non‐western approaches and include reference to the significance of genetic heritage as it is affecting guidelines for donor insemination and surrogacy.
Experiences and Attitudes Towards End‐of‐Life Decisions Amongst Danish Physicians
Authors: Folker Anna P. , Holtug Nils , Jensen Annette B. , Kappel Klemens , Nielsen Jesper K. , Norup Michael
Published: September 2010

In this survey we have investigated the experiences and attitudes of Danish physicians regarding end‐of‐life decisions. Most respondents have made decisions that involve hastening the death of a patient, and almost all find it acceptable to do so. Such decisions are made more often, and considered ethically more acceptable, with the informed consent of the patient than without. But both non‐resuscitation decisions, and decisions to provide pain relief in doses that will shorten the patient's life, have been made and found acceptable by at least 50% of the respondents, even when there is no informed consent. Furthermore, 12% have doubled morphine dosages with fixed intervals, thus providing doses substantially higher than that necessary to control pain, without the informed consent of the patient. Two per cent have helped in assisted suicide, and 5% have administered a lethal injection at the patient's request. Respectively 37% and 34% find these last two practices ethically acceptable. Amongst those that do not find them acceptable, the most important reasons to be opposed are, the doctrine of double effect, the doctrine of doing and allowing, and the view that human life is sacred. Amongst supporters, the most important reasons mentioned are, that the patient's right to self‐determination should be respected, the view that a patient should not be forced to suffer, and the view that the patient has a right to be helped to a dignified death.
Choosing the Best: Against Paternalistic Practice Guidelines
Authors: Savulescu Julian
Published: September 2010

Isobel Ross rightly points out that providing information is not enough to guarantee that patients will choose the best course of action. She argues that to adequately protect patients' interests, we need practice guidelines to ‘ensure that dangerous and unnecessarily risky procedures are excluded from practice’. What constitutes an ‘unnecessarily risky procedure’ is to be determined by a group of reasonable doctors. At one point, Ross suggests that such guidelines are ‘presumptive’ rather than ‘absolute’. But this is really a concession to patient variability. She intends that certain procedures are ruled out on paternalistic grounds.

I will argue that practice guidelines are desirable but should not determine practice. We should not rule out procedures on paternalistic grounds.
Maternal Correlates of Growth in Toddler Vocabulary Production in Low‐Income Families
Authors: Pan Barbara Alexander , Rowe Meredith L. , Singer Judith D. , Snow Catherine E.
Published: September 2010

This study investigated predictors of growth in toddlers' vocabulary production between the ages of 1 and 3 years by analyzing mother–child communication in 108 low‐income families. Individual growth modeling was used to describe patterns of growth in children's observed vocabulary production and predictors of initial status and between‐person change. Results indicate large variation in growth across children. Observed variation was positively related to diversity of maternal lexical input and maternal language and literacy skills, and negatively related to maternal depression. Maternal talkativeness was not related to growth in children's vocabulary production in this sample. Implications of the examination of longitudinal data from this relatively large sample of low‐income families are discussed.
Tunnel‐Free Supercover 3D Polygons and Polyhedra
Authors: Andrès Eric , Nehlig Philippe , Françon Jean
Published: September 2010

A new discrete 3D line and 3D polygon, called Supercover 3D line and Supercover 3D polygon, are introduced. Analytical definitions are provided. The Supercover 3D polygon is a tunnel free plane segment defined by vertices and edges. An edge is a Supercover 3D line segment. Two different polygons can share a common edge and if they do, the union of both polygons is tunnel free. This definition of discrete polygons has the “most” properties in common with the continuous polygons. It is particularly interesting for modeling of discrete scenes, especially using tunnel‐free discrete polyhedra. Algorithms for computing Supercover 3D Lines and Polygons are given and illustrated.
Computing Volumes of Solids Enclosed by Recursive Subdivision Surfaces
Authors: Peters Jörg , Nasri Ahmad
Published: September 2010

The volume of a solid enclosed by a recursive subdivision surface can be approximated based on the closed‐form representation of regular parts of the subdivision surface and a tight estimate of the local convex hull near extraordinary points. The approach presented is efficient, i.e. non‐exponential, and robust in that it yields rapidly contracting error bounding boxes. An extension to measuring higher‐order moments is sketched.
Automatic Hierarchical Level of Detail Optimization in Computer Animation
Authors: Mason Ashton E.W. , Blake Edwin H.
Published: September 2010

We show that the hierarchical level of detail optimization problem is equivalent to a constrained version of the Multiple Choice Knapsack Problem, and present a new algorithm whose solution to it is at least half as good as the optimal one. The advantage of the hierarchical algorithm is that it allows the use of hierarchical level of detail descriptions in which shared representations may be provided for groups of objects. Rendering cost may then be saved to afford better renderings of more important objects, and the algorithm is capable of providing a complete representation of the visible scene even when the visible scene complexity is very high. Our algorithm has a worst case time complexity of O(nlogn), and is incremental so that it typically completes in only a few iterations. We introduce the use of perceptual evaluation to demonstrate the effectiveness of the use of representations for groups of objects that our algorithm allows.
An Analysis of Quasi‐Monte Carlo Integration Applied to the Transillumination Radiosity Method
Authors: Szirmay‐Kalos László , Fóris Tibor , Neumann László , Csébfalvi Balázs
Published: September 2010

This paper presents an enhanced transillumination radiosity method that can provide accurate solutions at relatively low computational cost. The proposed algorithm breaks down the double integral of the gathered power to an area integral that is computed analytically and to a directional integral that is evaluated by quasi‐Monte Carlo techniques. Since the analytical integration results in a continuous function of finite variation, the quasi‐Monte Carlo integration that follows the analytical integration will be efficient and its error can be bounded by the Koksma‐Hlawka inequality. The paper also analyses the requirements of the convergence, presents theoretical error bounds and proposes error reduction techniques. The theoretical bounds are compared with simulation results.
Normal Computation for Discrete Surfaces in 3D Space
Authors: Thürmer Grit , Wüthrich Charles A.
Published: September 2010

Associating normal vectors to surfaces is essential for many rendering algorithms. We introduce a new method to compute normals on discrete surfaces in object space. Assuming that the surface separates space locally into two disjoint subsets, each of these subsets contains implicitly information about the surface inclination. Considering one of these subsets in a small neighbourhood of a surface point enables us to derive the surface normal from this set. We show that this leads to exact results for C1 continuous surfaces in R3. Furthermore, we show that good approximations can be obtained numerically by sampling the considered area. Finally, we derive a method for normal computation on surfaces in discrete space.
The Personal Interaction Panel – a Two‐Handed Interface for Augmented Reality
Authors: Szalavári Zsolt , Gervautz Michael
Published: September 2010

This paper describes the introduction of a new interaction paradigm to augmented reality applications. The everyday tool handling experience of working with pen and notebooks is extended to create a three dimensional two‐handed interface, that supports easy‐to‐understand manipulation tasks in augmented and virtual environments. In the design step we take advantage from the freedom, given by our very low demands on hardware and augment form and functionality to this device. On the basis of examples from object manipulation, augmented research environments and scientific visualization we show the generality of applicability. Although being in the first stages implementation, we consider the wide spectrum of suitability for different purposes.
Orthogonal Decomposition of Non‐Uniform Bspline Spaces using Wavelets
Authors: Kazinnik Roman , Elber Gershon
Published: September 2010

We take advantage of ideas of an orthogonal wavelet complement to produce multiresolution orthogonal decomposition of nonuniform Bspline (NUB) spaces. The editing of NUB curves and surfaces can be handled at different levels of resolutions.

Applying Multiresolution decomposition to possibly C1 discontinuous surfaces, one can preserve the general shape on one hand and local features on the other of the free‐form models, including geometric discontinuities. The Multiresolution decomposition of the NUB tensor product surface is computed via the symbolic computation of inner products of Bspline basis functions. To find a closed form representation for the inner product of the Bspline basis functions, an equivalent interpolation problem is solved.

As an example for the strength of the Multiresolution decomposition, a tool demonstrating the Multiresolution editing capabilities of NUB surfaces was developed and is presented as part of this work, allowing interactive 3D editing of NUB free‐form surfaces.
Interactive Boundary Computation of Boolean Combinations of Sculptured Solids
Authors: Krishnan S. , Gopi M. , Manocha D. , Mine M.
Published: September 2010

We present algorithms and systems for interactive boundary computation of Boolean combinations of sculptured solids. The algorithm is applicable to all spline solids and computes an accurate boundary representation. To speed up the computation, the algorithm exploits parallelism at all stages. It has been implemented on a multi‐processor SGI and takes one second on average per boolean operation to compute the boundary of high degree primitives. The system has also been integrated with an immersive design and manipulation environment. The resulting system is able to interactively evaluate boundaries of the models, display them for model validation and place them at appropriate position using collision detection algorithms.
Optimization of Cardiac Resynchronization Devices Using Acoustic Cardiography: A Comparison to Echocardiography
Authors: Hasan Ayesha , Abraham William T. , Quinn‐Tate Lori , Brown Lei , Amkieh Ali
Published: September 2010

Optimization of pacemaker settings for cardiac resynchronization therapy (CRT) remains challenging and problematic. Several noninvasive methods are offered to customize the programmed parameters for individual patients, but so far only echocardiographic imaging has established itself as an accepted method. The authors examined the value of acoustic cardiography as a fast and more cost‐efficient alternative to established echocardiographic imaging techniques for the optimization of CRT devices. The atrioventricular delay in 22 subjects with implanted CRT devices was independently optimized using echocardiography (Doppler transmitral flow) as well as acoustic cardiography, and the recommended settings from each method were later compared. Doppler echocardiography and acoustic cardiography recommendations matched within a mean value ± SD of 17±16 milliseconds and gave a correlation coefficient of r=0.90 (p<0.001). In 17 of the 22 cases (77.3%), the difference between echocardiographic and acoustic cardiogram CRT optimization results was ≤20 milliseconds. Furthermore, the echocardiographic transmitral flow pattern was not significantly different for the setting independently chosen by the echocardiographic expert and the acoustic cardiographer for the cases with a difference of >20 milliseconds (22.7%). In addition, it took less time for the acoustic cardiogram to collect sufficient information to make a recommendation, and it was found that the acoustic cardiogram data trend is easier to interpret.
Biases in Maximum Likelihood and Parsimony: A Simulation Approach to a 10‐Taxon Case
Authors: Pol Diego , Siddall Mark E.
Published: September 2010

Biases present in maximum likelihood and parsimony are investigated through a simulation study in a 10‐taxon case in which several long branches coexist with short branches in the modeled topology. The performance of these methods is explored while increasing the length of the long branches with different amounts of data. Also, simulations with different taxonomic sampling schemes are examined through this study. The presence of a strong bias in parsimony is corroborated: the well‐known long‐branch attraction. Likelihood performance is found to be sensitive to the mere presence extreme of branch length disparity, retrieving topologies compatible with long‐branch attraction and long‐branch repulsion, irrespective of the correctness of the model used.
Phylogenetic algorithms and the evolution of species communities in forest fragments
Authors: Pellens Roseli , Grandcolas Philippe , Guilbert Eric
Published: September 2010

In forest fragmentation studies, low specific richness in small fragments and community nestedness are usually considered to result from species loss. However, except in the case of fragmentation experiments, these studies cannot distinguish between original low richness and secondary species loss, or between original high richness and secondary colonizations in fragments. To distinguish between these possibilities is a matter of historical inference for which phylogenetic algorithms are designed. The methods of phylogenetic analysis, and especially parsimony analysis, can be used to find a tree of relationships between communities from different forest fragments, taking the presence or absence of species among different communities as characters. Parsimony analysis searches if species subsets can be classified in a nested hierarchy, and also establishes how the communities evolved, polarizing species changes into either extinctions or colonizations. By re‐analyzing two classical studies in this new and powerful way, we demonstrate that the differences between fragments and large continuous forests cannot be attributed to species loss in all cases, contrary to expectations from models.

© The Willi Hennig Society 2005.
A case study of apparent conflict between molecular phylogenies: the interrelationships of African elephants
Authors: Debruyne Régis
Published: September 2010

Recent molecular phylogenies of the African elephants suggest that there is an evolutionary structure withinLoxodonta africana. Some nuclear results (Roca et al., 2001) support the separation of the forest African elephant subspeciesL. a. cyclotisas a species distinct from the savannah elephantL. a. africana, on the basis of the recognition of both forming highly divergent (reciprocally monophyletic) clades. Conversely, a mitochondrial survey (Eggert et al., 2002), while admitting a geographic partitioning of the genetic structure within African elephants, suggests retaining the status quo. They recognize three diagnosible entities (western, central and south‐eastern Africa) with non‐overlapping ranges withinL. africana sensu lato.In order to address these conflicting views (historical fragmentation and speciation or isolation by distance, respectively), we have sequenced two datasets of 1961 bp (for 50 elephants) and about 3700 bp, respectively (for 20 elephants) of the mitochondrial DNA for both forms of elephants (cyclotisandafricana). They span the cytochromebgene, the control region and several RNAs. When compared with former mtDNA data, they provide the most comprehensive view of the African elephant phylogeny (78 mtDNA haplotypes, of which 44 are new) and provide the first insight into populations from the Democratic Republic of Congo. The genetic diversity of mtDNA was appraised and the stability of alternative phylogenetic trees was investigated. Our results are inconsistent with both those prior studies. They revealed two highly divergent molecular clades referred to as F and S, that do not conform to the morphological delineations ofcyclotisandafricana.A non‐negligible proportion of specimens ofL. a. africanadisplay haplotypes prevailing in forest elephant populations (clade F). The geographic distribution of clades and areas of their co‐occurrence support the hypothesis of incomplete isolation between forest and savannah African elephant populations, followed by recurrent interbreeding between the two forms. We state that the conclusions of prior studies resulted from insufficient character and/or geographic sampling. We conclude that there is no satisfying argument which can recognize two or more species of African elephants. We briefly comment on the meaning of such an attitude in a conservation viewpoint.

© The Willi Hennig Society 2005.
The molecular phylogeny of the Miarus campanulae (Coleoptera: Curculionidae) species group inferred from CO1 and ITS2 sequences
Authors: Vahtera Varpu , Muona Jyrki
Published: September 2010

Miarus is a Holarctic weevil genus with morphologically very similar species, all breeding on Campanula plants or their close relatives. Two European members of this genus, Miarus campanulae (L.), the type species, and Miarus graminis (Bohemann) have recently been split into several new species on the basis of slight external variations. The separation of these new forms has proved impossible and new data was needed. Molecular data were gathered from specimens from a number of locations in Finland, Estonia, Denmark and Sweden. The regions sequenced were mitochondrial CO1 and nuclear ITS2. Both combined and separate datasets were analyzed using the optimization alignment program POY, with parsimony as the optimality criterion. The recently separated Miarus species was found to be indistinguishable from the traditionally recognized form on the basis of this sequence data. On the other hand, the traditionally recognized species were characterized by numerous synapomorphies. Our data suggest that recent studies have underestimated the morphological variation in this genus. We propose that this may also be true for many taxonomically problematic beetle complexes in well‐studied European regions. The idea that molecular evidence will inevitably reveal unnoticed cryptic variation may only apply to poorly known regions. Miarus fennicusKangas, 1978 is placed as a junior synonym of Miarus campanulae (Linnaeus, 1767) syn. nov.

© The Willi Hennig Society 2006.
High selectivity in symbiotic associations of lichenized ascomycetes and cyanobacteria
Authors: Stenroos Soili , Högnabba Filip , Myllys Leena , Hyvönen Jaakko , Thell Arne
Published: September 2010

The selectivity of mycobionts and cyanobionts in lichen symbioses were examined. We analyzed symbiotic cyanobionts, collected from different sample sites, and compared them to free‐living cyanobacteria Nostoc. Cyanobionts were obtained from lichens assigned to the genera Pseudocyphellaria and Sticta, in particular. Multiple gene loci were screened and direct optimization was used in the phylogenetic analyses. We show that many lichen fungi are strongly selective towards their cyanobionts. Lichenized ascomycetes seem to be able to identify and choose a specific strain, species or a species group of Nostoc with which to associate. The present analyses also suggest that some of the Nostoc taxa may be specialized in symbiotic life with only lichenized ascomycetes. Despite the selectivity observed in fungi, there appears to be no coevolution between the partners. We have also discussed the problems of using the tRNALeu intron as a marker in phylogenetic analyses.

© The Willi Hennig Society 2006.
Photosystem II gene sequences ofpsbBandpsbCclarify the phylogenetic position ofVanilla(Vanilloideae, Orchidaceae)
Authors: Cameron Kenneth M. , Carmen Molina M.
Published: September 2010

Nucleotide sequences of the plastid genespsbBandpsbCwere obtained for 34 taxa to represent most genera currently classified within Vanilloideae (Orchidaceae). These genes code for two of the subunits that make up the Photosystem II protein P680, and have only rarely been used for reconstructing phylogenetic relationships among plants. We failed to amplifypsbBfrom the achlorophyllous generaCyrtosiaandLecanorchis, but were able to align full length copies ofpsbCsequences from two species ofCyrtosiawith the other taxa. This was not the case for an anomalouspsbCsequence obtained forLecanorchis. Nucleotide variation within each of these genes is sufficient to resolve the major relationships among Vanilloideae, and the combined two‐gene tree is fully resolved at the genus level and highly supported. These gene trees demonstrate with a high degree of confidence (95% jackknife support) that a clade of mostly achlorophyllous tropical vines includingPseudovanillaandErythrorchisare the sister group toVanilla. The two New Caledonian endemic genera of Vanilloideae are sister to this pair, andEpistephiumis sister to all remaining Vanillieae.

© The Willi Hennig Society 2006.
Quantification of the success of phylogenetic inference in simulations
Authors: Simmons Mark P. , Webb Colleen T.
Published: September 2010

For phylogenetic simulation studies, the accuracy of topological reconstruction obtained from different data matrices or different methods of phylogenetic inference generally needs to be quantified. Two components of performance within this context are: (1) how the inferred tree topology matches or conflicts with the correct tree topology, and (2) the branch support assigned to both correctly and incorrectly resolved clades. We present a method (averaged overall success of resolution) that incorporates both of these components. Branch support is incorporated in the averaged overall success of resolution by linearly scaling the observed support relative to that conferred by uncontradicted synapomorphies. We believe that this method represents an improvement relative to the commonly used approaches of quantifying the percentage of clades that are correctly resolved in the inferred trees or presenting the Robinson–Foulds distance between the inferred trees and the correct tree. In contrast to Bremer support, the averaged overall success of resolution may be applied equally well to distance, likelihood and parsimony analyses.

© The Willi Hennig Society 2006.
A Prospective Study of Stomach Cancer among a Rural Japanese Population: A 6‐Year Survey
Authors: Kato Ikuko , Tominaga Suketami , Matsumoto Kazutoshi
Published: September 2010

Stomach cancer mortality was prospectively studied among 9753 Japanese men and women who first responded to a mailed questionnaire in 1985 and were then followed through May 31, 1991. During this follow‐up period, 57 stomach cancer deaths were identified. Current smokers had an increased risk of deaths from stomach cancer compared with never smokers (relative risk (RR) = 2.29, 95% confidence interval (CI): 1.15–4.56), but there was no dose‐response to amount of cigarettes smoked. Daily alcohol drinkers who consumed 50 ml or more of alcohol per day also had a greater risk than nondrinkers (RR = 3.05, 95% CI: 1.35–6.91). There was no association between stomach cancer mortality and individual food consumption except a positive association with fruit intake. However, frequent use (≤3–4/week) of broiling of meats and traditional style Japanese salad preparation in their cooking procedures were positively associated with stomach cacer mortality. The RR values compared with infrequent use (≥1–2/month) were 2.27 (95% CI: 1–06–4.85) and 3.10 (95% CI: 1.40–6.85), respectively. A positive family history of cancer, especially stomach cancer, significantly increased the risk of stomach cancer deaths (RR=2.01, 95% CI: 1.12–3.63). The effects of these variables remained after adjustment for other variables.
Modulatory Influence of Oral Contraceptive Pills Ovral and Noracycline on 3‐Methylcholanthrene‐induced Carcinogenesis in the Uterine Cervix of Mouse
Authors: Hussain S. Perwez , Rao A. Ramesha
Published: September 2010

The present study reports the modulatory influences of combined oral contraceptive formulations, Ovral (0.05 mg ethinylestradiol plus 0.5 mg norgestrel per pill) and Noracycline (0.05 mg ethinylestradiol plus 0.1 mg lynestrenol per pill), on methylcholanthrene (MCA)‐induced carcinogenesis in the uterine cervix of Swiss albino mouse. Placement of cotton thread impregnated with beeswax containing ∼ 300 μg of MCA yielded cervical tumors in 0.0%, 8.6% and 26% animals, respectively, in 30, 60 and 90 days. Concomitant treatments with doses D1 (1/2000th of a pill), D2 (1/ 200th of a pill) and D3 (1/20th of a pill) of Ovral yielded cervical tumors in 0.0%, 0.0% and 4.5% mice at 30 days, 0.0%, 6.2% and 10% mice at 60 days and in 3.3% (P<0.05), 3.4% (P<0.05) and 47% mice at 90 days, respectively. Likewise, concomitant treatments with doses D1 (1/2000th of a pill), D2 (1/200th of a pill) and D3 (1/20th of a pill) of Noracycline yielded cervical tumors in 0.0%, 0.0%, 16.6% mice at 30 days, 4%, 3.7% and 54% (P<0.05) mice at 60 days and 3.2% (P<0.05), 20% and 63% (P<0.05) of mice at 90 days, respectively. Both Ovral and Noracycline displayed biphasic action on MCA‐induced cervical carcinogenesis in mice. At lower dose levels (D1 and D2), they were inhibitory while at the higher dose level (D3) they were augmentatory in their actions. Both pills also significantly enhanced the incidence of cervical hyperplasia.
Inhibition of Heat Inactivation of Reverse Transcriptase of Human Immunodeficiency Virus Type 1 by Seropositive Sera
Authors: Nagumo Toshiyuki , Takeuchi Yasuhiro , Hoshino Hiroo
Published: September 2010

The reverse transcriptase (RT) activity of a lysate of human immunodeficiency virus type 1 (HIV) was almost completely inactivated by incubation at 56°C for 20—‐30 min. The heat‐inactivation of RT in the virus lysate or purified RT was partially inhibited in the presence of some human sera or plasma containing antibodies against HIV. The IgG fraction purified from the seropositive sera was responsible for stabilization of RT upon heat inactivation. This is a new assay system for detection of antibodies against RT.
Novel Complications with HTLV‐1‐associated Myelopathy/Tropical Spastic Paraparesis: Interstitial Cystitis and Persistent Prostatitis
Authors: Nomata Koichiro , Nakamura Tatsufumi , Suzu Hiroshi , Yushita Yoshiaki , Kanetake Hiroshi , Sawada Takashi , Ikeda Shuichi , Hino Shigeo , Nagataki Shigenobu , Saito Yutaka
Published: September 2010

Lower urinary symptoms associated with HTLV‐1‐associated myelopathy/tropical spastic paraparesis (HAM/TSF) are common, but have been regarded as ‘neurogenic’ due to spinal involvements. However, in some cases, these symptoms are persistent, progressive, and not directly correlated with the severity of other neurologic symptoms of the lower spinal cord. These findings prompted us to locate organic lesions in the lower urinary tract and to correlate them with HTLV‐1 infection. Among 35 HAM patients with lower urinary symptoms, we found 4 cases with the symptoms persistent and progressive: 3 with contracted bladder and another with persistent prostatitis. Histological or cytological examinations indicated local lymphocytic infiltrations in the lower urinary tract in all cases: 3 by the infiltration in the bladder and the other by a high concentration of lymphocytes in expressed prostatic secretions. Of 3 cases whose urinary samples were available, 2 showed significant increase in the concentration of urinary anti‐HTLV‐1 antibody of IgA class. The urinary IgA antibody of the third case was not elevated, but the sample had been obtained after resection of the affected bladder. None of the control cases showed significant anti‐HTLV‐1 IgA antibody in urine except for a case of gross hematuria due to chemotherapy directed against adult T‐cell leukemia. We suggest inclusion of these processes into the spectrum of complications for HAM/TSP. The elevated excretion of anti‐HTLV‐1 of IgA class in urine may be an indicator of these complications.