bluuebunny/crossref_metadata_2025 huggingface dataset:
COMPARATIVE TREATMENT OF ACNE VULGARIS USING PALOMAR LUX APPLIQUÉ TECHNIQUE AND DIRECT INTRALESIONAL INJECTION
Authors: GENINA ELINA A. , BASHKATOV ALEXEY N. , TUCHIN VALERY V. , SIMONENKO GEORGY V. , SHERSTNEVA VERA N. , YAROSLAVSKY ILYA V. , ALTSHULER GREGORY B.
Published: September 2009

Intralesional injection of triamcinolone (TMC) preparations is an effective therapy for cystic acne lesions. However, invasive delivery techniques limit the use of this modality to a relatively narrow class of cases. Skin permeability can be enhanced through creating a lattice of micro-zones (islets) of light-induced limited thermal damage in the upper layers of epidermis. In this paper, we directly compared safety and efficacy of delivering TMC acetonide with this novel technique versus conventional intralesional injection for treatment of inflammatory acne lesions. A combination of an intense pulsed light system and a specially designed appliqué with a pattern of absorbing centers has been used to create the lattice of islets of damage (LID). Quantitative analysis has included estimation of the following parameters: redness, diameter, and height of acne lesions. Clinical photography has been used to document dynamics of lesion development at successive visits (two hours, 24 hours and one week post-treatment). Seven subjects have participated in the study. No difference in lesion dynamics between the treatment and control groups was observed at two-hours follow-up. At 24-hours/one-week follow-ups, TMC-injected and TMC-LID-delivered groups have demonstrated 82%/93% and 80%/89% improvement in height of lesions in comparison to control (60%/68%). Delivery of TMC with the newly proposed LID technique is at least as effective as intralesional injection for treating inflammatory acne lesions. Enhancement of skin permeability using LID approach is a promising technique for accelerating delivery of various compounds to their target areas in the skin.
LIGHT-INDUCED FLUORESCENCE SPECTROSCOPY AND OPTICAL COHERENCE TOMOGRAPHY OF BASAL CELL CARCINOMA
Authors: BORISOVA EKATERINA , CARSTEA ELFRIDA , CRISTESCU LUMINITA , PAVLOVA ELMIRA , HADJIOLOV NIKOLAY , TROYANOVA PETRANKA , AVRAMOV LATCHEZAR
Published: September 2009

Many up-to-date optical techniques have been developed and applied recently in clinical practice for obtaining qualitatively and quantitatively new data from the investigated lesions. Due to their high sensitivity in detection of small changes, these techniques are widely used for detection of early changes in biological tissues. Light-induced fluorescence spectroscopy (LIFS) is one of the most promising techniques for early detection of cutaneous neoplasia. Increasing number of recent publications have suggested that optical coherence tomography (OCT) also has potential for non-invasive diagnosis of skin cancer. This recent work is a part of clinical trial procedure for introduction of LIFS technique into the common medical practice in National Oncological Medical Center in Bulgaria for diagnosis of non-melanoma skin cancer. We focus our attention here on basal cell carcinoma lesions and their specific features revealed by LIFS and OCT analysis. In this paper we prove the efficiency of using the combined LIFS-OCT method in skin lesions studies by integrating the complimentary qualities of each particular technique. For LIFS measurements several excitation sources, each emitting at 365, 385 and 405 nm maxima are applied. An associated microspectrometer detects in vivo the fluorescence signals from human skin. The main spectral features of the lesions and normal skin are discussed and their possible origins are indicated. OCT images are used to evaluate the lesion thickness, structure and severity stage, when possible. The obtained results could be used to develop a more complete picture of optical properties of these widely spread skin disorders. At the same time, our studies show that the combined LIFS-OCT method could be introduced in clinical algorithms for early tumor detection and differentiation between normal/benign/malignant skin lesions.
LIVE IMAGING OF EARLY DEVELOPMENTAL PROCESSES IN MAMMALIAN EMBRYOS WITH OPTICAL COHERENCE TOMOGRAPHY
Authors: LARIN KIRILL V. , LARINA IRINA V. , LIEBLING MICHAEL , DICKINSON MARY E.
Published: September 2009

Early embryonic imaging of cardiovascular development in mammalian models requires a method that can penetrate through and distinguish the many tissue layers with high spatial and temporal resolution. In this paper we evaluate the capability of Optical Coherence Tomography (OCT) technique for structural 3D embryonic imaging in mouse embryos at different stages of the developmental process ranging from 7.5 dpc up to 10.5 dpc. Obtained results suggest that the collected data is suitable for quantitative and qualitative measurements to assess cardiovascular function in mouse models, which is likely to expand our knowledge of the complexity of the embryonic heart, and its development into an adult heart.
IN VIVO TRANS-RECTAL ULTRASOUND-COUPLED NEAR-INFRARED OPTICAL TOMOGRAPHY OF INTACT NORMAL CANINE PROSTATE
Authors: PIAO DAQING , JIANG ZHEN , BARTELS KENNETH E. , REED HOLYOAK G. , RITCHEY JERRY W. , XU GUAN , BUNTING CHARLES F. , SLOBODOV GENNADY
Published: September 2009

This is the first tomography-presentation of the optical properties of a normal canine prostate, in vivo, in its native intact environment in the pelvic canal. The imaging was performed by trans-rectal near-infrared (NIR) optical tomography in steady-state measurement at 840 nm on three sagittal planes across the right lobe, middle-line, and left lobe, respectively, of the prostate gland. The NIR imaging planes were position-correlated with concurrently applied trans-rectal ultrasound, albeit there was no spatial prior employed in the NIR tomography reconstruction. The reconstructed peak absorption coefficients of the prostate on the three planes were 0.014, 0.012, and 0.014 mm-1. The peak reduced scattering coefficients were 5.28, 5.56, and 6.53 mm-1. The peak effective attenuation coefficients were 0.45, 0.43, and 0.50 mm-1. The absorption and effective attenuation coefficients were within the ranges predictable at 840 nm by literature values which clustered sparsely from 355 nm to 1064 nm, none of which were performed on a canine prostate with similar conditions. The effective attenuation coefficients of the gland were shown to be generally higher in the internal aspects than in the peripheral aspects, which is consistent with the previous findings that the urethral regions were statistically more attenuating than the capsular regions.
EARLY CATARACT DETECTION BY DYNAMIC LIGHT SCATTERING WITH SPARSE BAYESIAN LEARNING
Authors: NYEO SU-LONG , ANSARI RAFAT R.
Published: September 2009

Dynamic light scattering (DLS) is a promising technique for early cataract detection and for studying cataractogenesis. A novel probabilistic analysis tool, the sparse Bayesian learning (SBL) algorithm, is described for reconstructing the most-probable size distribution of α-crystallin and their aggregates in an ocular lens from the DLS data. The performance of the algorithm is evaluated by analyzing simulated correlation data from known distributions and DLS data from the ocular lenses of a fetal calf, a Rhesus monkey, and a man, so as to establish the required efficiency of the SBL algorithm for clinical studies.
Divided by a Common Language
Authors: Little Bob
Published: September 2009

Many U.S. companies -- especially those in the learning technologies sector -- view the U.K. as America "writ small." They believe the U.K., with a land mass roughly equivalent to the state of Oregon, speaks the same language, buys for the same reasons, and is susceptible to the same marketing techniques. These companies have discovered, often at considerable cost, that these assumptions are false.
Subtle gaze direction
Authors: Bailey Reynold , McNamara Ann , Sudarsanam Nisha , Grimm Cindy
Published: September 2009

This article presents a novel technique that combines eye-tracking with subtle image-space modulation to direct a viewer's gaze about a digital image. We call this paradigm
subtle gaze direction
. Subtle gaze direction exploits the fact that our peripheral vision has very poor acuity compared to our foveal vision. By presenting brief, subtle modulations to the peripheral regions of the field of view, the technique presented here draws the viewer's foveal vision to the modulated region. Additionally, by monitoring saccadic velocity and exploiting the visual phenomenon of saccadic masking, modulation is automatically terminated before the viewer's foveal vision enters the modulated region. Hence, the viewer is never actually allowed to scrutinize the stimuli that attracted her gaze. This new subtle gaze directing technique has potential application in many areas including large scale display systems, perceptually adaptive rendering, and complex visual search tasks.
Improving Chen and Han's algorithm on the discrete geodesic problem
Authors: Xin Shi-Qing , Wang Guo-Jin
Published: September 2009

The computation of geodesic distances or paths between two points on triangulated meshes is a common operation in many computer graphics applications. In this article, we present an exact algorithm for the single-source all-vertices shortest path problem.

Mitchell et al. [1987] proposed an
O
(
n
2
log
n
) method (MMP), based on Dijkstra's algorithm, where
n
is the complexity of the polyhedral surface. Then, Chen and Han [1990] (CH) improved the running time to
O
(
n
2
). Interestingly Surazhsky et al. [2005] provided experimental evidence demonstrating that the MMP algorithm runs many times faster, in practice, than the CH algorithm.

The CH algorithm encodes the structure of the set of shortest paths using a set of windows on the edges of the polyhedron. Our experiments showed that in many examples over 99% of the windows created by the CH algorithm are of no use to define a shortest path. So this article proposes to improve the CH algorithm by two separate techniques. One is to filter out useless windows using the current estimates of the distances to the vertices, the other is to maintain a priority queue like that achieved in Dijkstra's algorithm. Our experimental results suggest that the improved CH algorithm, in spite of an
O
(
n
2
log
n
) asymptotic time complexity, greatly outperforms the original CH algorithm in both time and space. Furthermore, it generally runs faster than the MMP algorithm and uses considerably less space.
A simple approach to nonlinear tensile stiffness for accurate cloth simulation
Authors: Volino Pascal , Magnenat-Thalmann Nadia , Faure Francois
Published: September 2009

Recent mechanical models for cloth simulation have evolved toward accurate representation of elastic stiffness based on continuum mechanics, converging to formulations that are largely analogous to fast finite element methods. In the context of tensile deformations, these formulations usually involve the linearization of tensors, so as to express linear elasticity in a simple way. However, this approach needs significant adaptations and approximations for dealing with the nonlinearities resulting from large cloth deformations. Toward our objective of accurately simulating the nonlinear properties of cloth, we show that this linearization can indeed be avoided and replaced by adapted strain-stress laws that precisely describe the nonlinear behavior of the material. This leads to highly streamlined computations that are particularly efficient for simulating the nonlinear anisotropic tensile elasticity of highly deformable surfaces. We demonstrate the efficiency of this method with examples related to accurate garment simulation from experimental tensile curves measured on actual materials.
Photorealistic models for pupil light reflex and iridal pattern deformation
Authors: Pamplona Vitor F. , Oliveira Manuel M. , Baranoski Gladimir V. G.
Published: September 2009

We introduce a physiologically-based model for pupil light reflex (PLR) and an image-based model for iridal pattern deformation. Our PLR model expresses the pupil diameter as a function of the lighting of the environment, and is described by a delay-differential equation, naturally adapting the pupil diameter even to abrupt changes in light conditions. Since the parameters of our PLR model were derived from measured data, it correctly simulates the actual behavior of the human pupil. Another contribution of our work is a model for realistic deformation of the iris pattern as a function of pupil dilation and constriction. Our models produce high-fidelity appearance effects and can be used to produce real-time predictive animations of the pupil and iris under variable lighting conditions. We assess the predictability and quality of our simulations through comparisons of modeled results against measured data derived from experiments also described in this work. Combined, our models can bring facial animation to new photorealistic standards.
Generalized hypertree decompositions: NP-hardness and tractable variants
Authors: Gottlob Georg , Miklós Zoltán , Schwentick Thomas
Published: September 2009

The generalized hypertree width GHW(
H
) of a hypergraph
H
is a measure of its cyclicity. Classes of conjunctive queries or constraint satisfaction problems whose associated hypergraphs have bounded GHW are known to be solvable in polynomial time. However, it has been an open problem for several years if for a fixed constant
k
and input hypergraph
H
it can be determined in polynomial time whether GHW(
H
) ≤
k
. Here, this problem is settled by proving that even for
k
= 3 the problem is already NP-hard. On the way to this result, another long standing open problem, originally raised by Goodman and Shmueli [1984] in the context of join optimization is solved. It is proven that determining whether a hypergraph
H
admits a tree projection with respect to a hypergraph
G
is NP-complete. Our intractability results on generalized hypertree width motivate further research on more restrictive tractable hypergraph decomposition methods that approximate generalized hypertree decomposition (GHD). We show that each such method is dominated by a tractable decomposition method definable through a function that associates a set of partial edges to a hypergraph. By using one particular such function, we define the new Component Hypertree Decomposition method, which is tractable and strictly more general than other approximations to GHD published so far.
The complexity of query containment in expressive fragments of XPath 2.0
Authors: Cate Balder ten , Lutz Carsten
Published: September 2009

XPath is a prominent W3C standard for navigating XML documents that has stimulated a lot of research into query answering and static analysis. In particular, query containment has been studied extensively for fragments of the 1.0 version of this standard, whereas little is known about query containment in (fragments of) the richer language XPath 2.0. In this article, we consider extensions of CoreXPath, the navigational core of XPath 1.0, with operators that are part of or inspired by XPath 2.0: path intersection, path equality, path complementation, for-loops, and transitive closure. For each combination of these operators, we determine the complexity of query containment, both with and without DTDs. It turns out to range from ExpTime (for extensions with path equality) and 2-ExpTime (for extensions with path intersection) to non-elementary (for extensions with path complementation or for-loops). In almost all cases, adding transitive closure on top has no further impact on the complexity. We also investigate the effect of dropping the upward and/or sibling axes, and show that this sometimes leads to a reduction in complexity. Since the languages we study include negation and conjunction in filters, our complexity results can equivalently be stated in terms of satisfiability. We also analyze the above languages in terms of succinctness.
A property of quantum relative entropy with an application to privacy in quantum communication
Authors: Jain Rahul , Radhakrishnan Jaikumar , Sen Pranab
Published: September 2009

We prove the following information-theoretic property about quantum states.

Substate theorem:
Let ρ and σ be quantum states in the same Hilbert space with relative entropy
S
(ρ ‖ σ) ≔ Tr ρ (log ρ - log σ) =
c
. Then for all ϵ > 0, there is a state ρ′ such that the trace distance ‖ρ′ - ρ‖
tr
: Tr √(ρ′ - ρ)
2
≤ ϵ, and ρ′/2

O
(
c
/ϵ
2
)

≤ σ.

It states that if the relative entropy of ρ and σ is small, then there is a state ρ′ close to ρ, i.e. with small trace distance ‖ρ′ - ρ‖
tr
, that when scaled down by a factor 2

O
(
c
)

‘sits inside’, or becomes a ‘substate’ of, σ. This result has several applications in quantum communication complexity and cryptography. Using the substate theorem, we derive a privacy trade-off for the
set membership problem
in the two-party quantum communication model. Here Alice is given a subset
A
⊆ [
n
], Bob an input
i
∈ [
n
], and they need to determine if
i
∈
A
.

Privacy trade-off for set membership:
In any two-party quantum communication protocol for the set membership problem, if Bob reveals only
k
bits of information about his input, then Alice must reveal at least
n
/2

O(
k
)

bits of information about her input.

We also discuss relationships between various information theoretic quantities that arise naturally in the context of the substate theorem.
Capture the Backchannel
Authors: Rowell Laurie
Published: September 2009

When you look out over the sea of faces in your lecture classes, are some students focusing on laptop screens while others are working their thumbs on their cell phone pads? Imagine you could harness all that clicking as a backchannel stream tied into the lecture. In principle establishing a backchannel sounds easy. You can either set up a separate Twitter account or use a specialty application like Live Question Tool, which requires no registration and takes about a minute for the instructor to create an instance. The real question is whether a secondary stream would be a learning advantage to your students.
Promoting Interaction in Distance Education
Authors: Anderson Richard , Linnell Natalie
Published: September 2009

The Center for Collaborative Technologies at the University of Washington is dedicated to creating software tools that encourage interaction in the classroom. These include Classroom Presenter, a Tablet PC-based presentation and interaction system, and ConferenceXP, a video conferencing application for distributed courses, co-developed with Microsoft Research. In this article, we describe the use of Classroom Presenter in a pair of international distance learning courses. The two classes used different technologies: one was a synchronous class that used internet-based video conferencing and the other was an asynchronous class that used Tutored Video
Must e-Learning Be 'Cool?'
Authors: Schank Roger C.
Published: September 2009

Upon taking a tour of some training applications in the virtual world Second Life, Roger C. Shank wonders why organizations push for their elearning solutions to be 'cool' over being effective.
Learn From Rogue Tweeters
Authors: Gualtieri Lisa
Published: September 2009

Many organizations are struggling with social media, trying to determine exactly how to use it in a formalized way. But while they strategize about how to push messages or disseminate information, they're being preempted by rogue individuals who, in the true spirit of social media, stake a claim and represent their organization with nothing more than permission.
Five Questions for Marjee Chmiel
Authors: Gualtieri Lisa
Published: September 2009

Marjee Chmiel is the director of digital media for National Geographic's The JASON Project where she designs and produces a variety of video games and other interactive online applications that support The Jason Project's award winning online science curriculum. Chmiel spoke to eLearnMag.org editor-in-chief Lisa Gualtieri about The Jason Project and her insights on making education engaging for children, teachers, and adult learners.
Evolution of Plant Defenses in Nonindigenous Environments
Authors: Orians Colin M. , Ward David
Published: September 2009

Exotic plants provide a unique opportunity to explore the evolution of defense allocation in plants. Many studies have focused on whether enemy release leads to a change in defense allocation. Little research has focused on induced defenses and on how resource availability in the nonindigenous range might cause evolutionary shifts in defense trait allocation. We examine (a) the major evolutionary hypotheses predicting defense expression in plants, (b) the hypotheses explaining defense evolution of exotic species, and (c) the importance of geographic variation in ecological interactions to defense evolution (geographic mosaics). In addition, we review the strengths and weaknesses of experimental approaches, present case studies, and suggest areas that deserve further attention.
Landscape Epidemiology of Vector-Borne Diseases
Authors: Reisen William K.
Published: September 2009

Landscape epidemiology describes how the temporal dynamics of host, vector, and pathogen populations interact spatially within a permissive environment to enable transmission. The spatially defined focus, or nidus, of transmission may be characterized by vegetation as well as by climate, latitude, elevation, and geology. The ecological complexity, dimensions, and temporal stability of the nidus are determined largely by pathogen natural history and vector bionomics. Host populations, transmission efficiency, and therefore pathogen amplification vary spatially, thereby creating a heterogeneous surface that may be defined by remote sensing and statistical tools. The current review describes the evolution of landscape epidemiology as a science and exemplifies selected aspects by contrasting the ecology of two different recent disease outbreaks in North America caused by West Nile virus, an explosive, highly virulent mosquito-borne virus producing ephemeral nidi, and Borrelia burgdorferi, a slowly amplifying chronic pathogen producing semipermanent nidi.
Integrative Taxonomy: A Multisource Approach to Exploring Biodiversity
Authors: Schlick-Steiner Birgit C. , Steiner Florian M. , Seifert Bernhard , Stauffer Christian , Christian Erhard , Crozier Ross H.
Published: September 2009

Good alpha taxonomy is central to biology. On the basis of a survey of arthropod studies that used multiple disciplines for species delimitation, we evaluated the performance of single disciplines. All included disciplines had a considerable failure rate. Rigor in species delimitation can thus be increased when several disciplines chosen for complementarity are used. We present a flexible procedure and stopping rule for integrative taxonomy that uses the information from different disciplines separately. Disagreement among disciplines over the number and demarcation of species is resolved by elucidating and invoking evolutionary explanations for disagreement. With the identification of further promising study organisms and of new questions for in-depth analysis, evolutionary biology should profit from integrative taxonomy. An important rationale is clarity in researcher bias in the decision-making process. The success of integrative taxonomy will further increase through methodological progress, taxonomic training of evolutionary biologists, and balanced resource allocation.
Parallel Olfactory Systems in Insects: Anatomy and Function
Authors: Galizia C. Giovanni , Rössler Wolfgang
Published: September 2009

A striking commonality across insects and vertebrates is the recurring presence of parallel olfactory subsystems, suggesting that such an organization has a highly adaptive value. Conceptually, two different categories of parallel systems must be distinguished. In one, specific sensory organs or processing streams analyze different chemical stimuli (segregate parallel systems). In the other, similar odor stimuli are processed but analyzed with respect to different features (dual parallel systems). Insects offer many examples for both categories. For example, segregate parallel systems for different chemical stimuli are realized in specialized neuronal streams for processing sex pheromones and CO2. Dual parallel streams related to similar or overlapping odor stimuli are prominent in Hymenoptera. Here, a clear separation of sensory tracts to higher-order brain centers is present despite no apparent differences regarding the classes or categories of olfactory stimuli being processed. In this paper, we review the situation across insect species and offer hypotheses for the function and evolution of parallel olfactory systems.
The Pathobiology of Glioma Tumors
Authors: Gladson Candece L. , Prayson Richard A. , Liu Wei Michael
Published: September 2009

The ongoing characterization of the genetic and epigenetic alterations in the gliomas has already improved the classification of these heterogeneous tumors and enabled the development of rodent models for analysis of the molecular pathways underlying their proliferative and invasive behavior. Effective application of the targeted therapies that are now in development will depend on pathologists’ ability to provide accurate information regarding the genetic alterations and the expression of key receptors and ligands in the tumors. Here we review the mechanisms that have been implicated in the pathogenesis of the gliomas and provide examples of the cooperative nature of the pathways involved, which may influence the initial therapeutic response and the potential for development of resistance.
Molecular Pathogenesis of Necrotizing Fasciitis
Authors: Olsen Randall J. , Musser James M.
Published: September 2009

Necrotizing fasciitis, also known as the flesh-eating disease, is a severe invasive infection associated with very high rates of human morbidity and mortality. It is most commonly caused by group A Streptococcus(GAS), a versatile human pathogen that causes diseases ranging in severity from uncomplicated pharyngitis (or strep throat) to life-threatening infections such as necrotizing fasciitis. Herein, we review recent discoveries bearing on the molecular pathogenesis of GAS necrotizing fasciitis. Importantly, the integration of new technologies and the development of human-relevant animal models have markedly expanded our understanding of the key pathogen-host interactions underlying GAS necrotizing fasciitis. For example, we now know that GAS organisms secrete a variety of proteases that disrupt host tissue and that these proteolytic enzymes are regulated by multiple transcriptional and posttranslational processes. This pathogenesis knowledge will be crucial to supporting downstream efforts that seek to develop novel vaccines and therapeutic agents for this serious human infection.
Biorational Approaches to Managing Stored-Product Insects
Authors: Phillips Thomas W. , Throne James E.
Published: September 2009

Stored-product insects can cause postharvest losses, estimated from up to 9% in developed countries to 20% or more in developing countries. There is much interest in alternatives to conventional insecticides for controlling stored-product insects because of insecticide loss due to regulatory action and insect resistance, and because of increasing consumer demand for product that is free of insects and insecticide residues. Sanitation is perhaps the first line of defense for grain stored at farms or elevators and for food-processing and warehouse facilities. Some of the most promising biorational management tools for farm-stored grain are temperature management and use of natural enemies. New tools for computer-assisted decision-making and insect sampling at grain elevators appear most promising. Processing facilities and warehouses usually rely on trap captures for decision-making, a process that needs further research to optimize.
Sociobiology of the Myxobacteria
Authors: Velicer Gregory J. , Vos Michiel
Published: September 2009

Cooperation is integral to much of biological life but can be threatened by selfish evolutionary strategies. Diverse cooperative traits have evolved among microbes, but particularly sophisticated forms of sociality have arisen in the myxobacteria, including group motility and multicellular fruiting body development. Myxobacterial cooperation has succeeded against socially destructive cheaters and can readily re-evolve from some socially defective genotypes. However, social harmony does not extend far. Spatially structured natural populations of the model species Myxococcus xanthus have fragmented into a large number of socially incompatible genotypes that exclude, exploit, and/or antagonize one another, including genetically similar neighbors. Here, we briefly review basic social evolution concepts as they pertain to microbes, discuss potential benefits of myxobacterial social traits, highlight recent empirical studies of social evolution in M. xanthus, and consider their implications for how myxobacterial cooperation and conflict evolve in the wild.
Gene Transfer and Diversification of Microbial Eukaryotes
Authors: Andersson Jan O.
Published: September 2009

The importance of lateral gene transfer in genome evolution of microbial eukaryotes is slowly being appreciated. Acquisitions of genes have led to metabolic adaptation in diverse eukaryotic lineages. In most cases the metabolic genes have originated from prokaryotes, often followed by sequential transfers between eukaryotes. However, the knowledge of gene transfer in eukaryotes is still mainly based on anecdotal evidence. Some of the observed patterns may be biases in experimental approaches and sequence databases rather than evolutionary trends. Rigorous systematic studies of gene acquisitions that allow for the possibility of exchanges of all categories of genes from all sources are needed to get a more objective view of gene transfer in eukaryote evolution. It may be that the role of gene transfer in the diversification process of microbial eukaryotes currently is underestimated.
Biological Insights from Structures of Two-Component Proteins
Authors: Gao Rong , Stock Ann M.
Published: September 2009

Two-component signal transduction based on phosphotransfer from a histidine protein kinase to a response regulator protein is a prevalent strategy for coupling environmental stimuli to adaptive responses in bacteria. In both histidine kinases and response regulators, modular domains with conserved structures and biochemical activities adopt different conformational states in the presence of stimuli or upon phosphorylation, enabling a diverse array of regulatory mechanisms based on inhibitory and/or activating protein-protein interactions imparted by different domain arrangements. This review summarizes some of the recent structural work that has provided insight into the functioning of bacterial histidine kinases and response regulators. Particular emphasis is placed on identifying features that are expected to be conserved among different two-component proteins from those that are expected to differ, with the goal of defining the extent to which knowledge of previously characterized two-component proteins can be applied to newly discovered systems.
Predatory Lifestyle of Bdellovibrio bacteriovorus
Authors: Sockett Renee Elizabeth
Published: September 2009

Bdellovibrio species are naturally predatory, small, motile, Deltaproteobacteria that invade the periplasm of other larger gram-negative bacteria, killing and digesting them. Bdellovibrio grows and divides inside the prey cell, in a structure called a bdelloplast, which then lyses, releasing the Bdellovibrio to prey upon more bacteria. This capability makes Bdellovibrio a potential therapeutic agent, but since its discovery in the 1960s it has not been applied in this way. This review considers what is known postgenomically about Bdellovibrio and its predatory lifestyle, drawing also from what was learned by the excellent microbial physiology work of the early Bdellovibrio researchers. Recent work on the diversity and evolution of predatory bdellovibrios, the role of surface structures in predation, and the ongoing questions about how Bdellovibrio switches between axenic and predatory growth and how its predatory activities may be tempered in the wild, as well as suggestions for future research priorities, are discussed.
Microbiology of the Atmosphere-Rock Interface: How Biological Interactions and Physical Stresses Modulate a Sophisticated Microbial Ecosystem
Authors: Gorbushina Anna A. , Broughton William J.
Published: September 2009

Life at the atmosphere-lithosphere boundary is an ancient terrestrial niche that is sparsely covered by thin subaerial biofilms. The microbial inhabitants of these biofilms (a) have adapted to all types of terrestrial/subaerial stresses (e.g., desiccation, extreme temperatures, low nutrient availability, intense solar radiation), (b) interact with minerals that serve as both a dwelling and a source of mineral nutrients, and (c) provoke weathering of rocks and soil formation. Subaerial communities comprise heterotrophic and phototrophic microorganisms that support each other's lifestyle. Major lineages of eubacteria associated with the early colonization of land (e.g., Actinobacteria, Cyanobacteria) are present in these habitats along with eukaryotes such as microscopic green algae and ascomycetous fungi. The subaerial biofilm inhabitants have adapted to desiccation, solar radiation, and other environmental challenges by developing protective, melanized cell walls, assuming microcolonial architectures and symbiotic lifestyles. How these changes occurred, their significance in soil formation, and their potential as markers of climate change are discussed below.
The Trypanosoma brucei Flagellum: Moving Parasites in New Directions
Authors: Ralston Katherine S. , Kabututu Zakayi P. , Melehani Jason H. , Oberholzer Michael , Hill Kent L.
Published: September 2009

African trypanosomes are devastating human and animal pathogens. Trypanosoma brucei rhodesiense and T. b. gambiense subspecies cause the fatal human disease known as African sleeping sickness. It is estimated that several hundred thousand new infections occur annually and the disease is fatal if untreated. T. brucei is transmitted by the tsetse fly and alternates between bloodstream-form and insect-form life cycle stages that are adapted to survive in the mammalian host and the insect vector, respectively. The importance of the flagellum for parasite motility and attachment to the tsetse fly salivary gland epithelium has been appreciated for many years. Recent studies have revealed both conserved and novel features of T. brucei flagellum structure and composition, as well as surprising new functions that are outlined here. These discoveries are important from the standpoint of understanding trypanosome biology and identifying novel drug targets, as well as for advancing our understanding of fundamental aspects of eukaryotic flagellum structure and function.
Malaria Parasite Development in the Mosquito and Infection of the Mammalian Host
Authors: Aly Ahmed S.I. , Vaughan Ashley M. , Kappe Stefan H.I.
Published: September 2009

Plasmodium sporozoites are the product of a complex developmental process in the mosquito vector and are destined to infect the mammalian liver. Attention has been drawn to the mosquito stages and pre-erythrocytic stages owing to recognition that these are bottlenecks in the parasite life cycle and that intervention at these stages can block transmission and prevent infection. Parasite progression in the Anopheles mosquito, sporozoite transmission to the mammalian host by mosquito bite, and subsequent infection of the liver are characterized by extensive migration of invasive stages, cell invasion, and developmental changes. Preparation for the liver phase in the mammalian host begins in the mosquito with an extensive reprogramming of the sporozoite to support efficient infection and survival. Here, we discuss what is known about the molecular and cellular basis of the developmental progression of parasites and their interactions with host tissues in the mosquito and during the early phase of mammalian infection.
A Life with Acetogens, Thermophiles, and Cellulolytic Anaerobes
Authors: Ljungdahl Lars G.
Published: September 2009

Frankly, I was surprised to receive an invitation to write a prefatory chapter for the Annual Review of Microbiology. I have read several such chapters written by outstanding researchers, many of whom I know and admire. I did not think I belonged to such a preeminent group. In my view, my contributions to the physiology and biochemistry of anaerobic thermophilic bacteria and, more lately, to anaerobic fungi are modest compared to the contribution made by other authors of prefatory chapters. I am honored to write about my life and my work, and I hope that those who read this chapter will sense how exciting and rewarding they have been.
Anaerobic Oxidation of Methane: Progress with an Unknown Process
Authors: Knittel Katrin , Boetius Antje
Published: September 2009

Methane is the most abundant hydrocarbon in the atmosphere, and it is an important greenhouse gas, which has so far contributed an estimated 20% of postindustrial global warming. A great deal of biogeochemical research has focused on the causes and effects of the variation in global fluxes of methane throughout earth's history, but the underlying microbial processes and their key agents remain poorly understood. This is a disturbing knowledge gap because 85% of the annual global methane production and about 60% of its consumption are based on microbial processes. Only three key functional groups of microorganisms of limited diversity regulate the fluxes of methane on earth, namely the aerobic methanotrophic bacteria, the methanogenic archaea, and their close relatives, the anaerobic methanotrophic archaea (ANME). The ANME represent special lines of descent within the Euryarchaeota and appear to gain energy exclusively from the anaerobic oxidation of methane (AOM), with sulfate as the final electron acceptor according to the net reaction:

[Formula: see text]

This review summarizes what is known and unknown about AOM on earth and its key catalysts, the ANME clades and their bacterial partners.
Composite Electronic Materials for Supercapacitor Applications
Authors: Rosario-Canales Mariem , Deria Pravas , Gopu Preethi , Therien Michael , Santiago-Avilés Jorge
Published: September 2009

The polyanionic, poly(aryleneethynylene) polymer PNES that helically wraps single-walled carbon nanotubes (SWNTs) was used in a variety of novel electrically active composites, combined with the electroactive polymer poly(3,4-propylenedioxythiophene) PProDOT, to function as supercapacitor charge storage media. PNES provides solubility and dispersion characteristics for SWNTs in water and in organic solvents like methanol (MeOH). PNES/SWNT samples were prepared by drop casting PNES/SWNT/MeOH suspensions on Pt button electrodes; high stability PProDOT/PNES/SWNT composites were then prepared by electrochemical polymerization in ionic liquid/propylene carbonate electrolyte solution. These composites enhanced key redox capacitors rubrics compared to those of PProDOT-based terminals. The PNES-wrapped SWNTs were characterized by transmission electron microscopy and Vis-NIR absorption spectroscopy. PProDOT- and PProDOT/PNES/SWNT-based devices were interrogated by cyclic voltammetry (CV) to different cell voltages. Electronic transport properties of the PNES/SWNT composite samples were measured from 2K to room temperature.
Sensitivity Analysis of Pd-MOS Structure for Hydrogenated Gases by Scanning Light Pulse Technique
Authors: Braga Mauro S. , Maciel de Matos Keth R. , Santos Daniela S. , Ramirez-Fernandez Francisco J. , Salcedo Walter J.
Published: September 2009

This paper presents an analysis of the performance of a Pd-MOS structure with respect to their sensitivity to hydrogenated gases. Assays using an experimental arrangement of the scanning light pulse technique (SLPT) were carried out. This arrangement allowed the chemical images patterns generation that show the sensitivity of the device to different gas composition, which the sensor was exposed.
Structural Characterization of Arsenic Implanted SOI
Authors: De Oliveira Roana , Dalponte Mateus , Boudinov Henri
Published: September 2009

Solid phase epitaxy re-growth of arsenic implanted in silicon on insulator (SOI) was studied by Rutherford Backscattering Spectrometry and Transmission Electron Microscopy. Two SOI structures with different Si overlayer and buried oxide thicknesses were used. The As+ implantations were performed with a single energy of 20 keV to a dose of 5x1014 cm-2 in both substrates. A plateau-like profile was achieved in an additional set of SOI samples by triple energy implantation. Rapid thermal annealing and conventional furnace annealing were applied for re-crystallization and dopant activation. The results are discussed considering the amorphization depth reached by dopant implantation and the crystal recovery process via thermal treatment.
Three-Dimensional Plasma Etching Simulation using Advanced Ray Tracing and Level Set Techniques
Authors: Ertl Otmar , Selberherr Siegfried
Published: September 2009

We present three-dimensional simulation techniques for plasma etching processes. Models based on Langmuir-type adsorption and on ballistic particle transport at feature scale can be efficiently solved in three dimensions. Surface coverages are self-consistently calculated. The local sputter rates of ions and the fluxes of neutrals are computed using modern ray tracing algorithms. In this way angle and energy dependent sputter yields or specular reflections of ions can be incorporated in a natural manner. For the time evolution of the surface we apply a recently developed fast multi-level-set framework. Our simulation techniques are demonstrated using a SF6/O2 plasma etching process model.
Characterization of Gold-Formaldehyde Baths for Electrochemical Deposition
Authors: Cardoso Juliana L. , Dos Santos Filho Sebastião G.
Published: September 2009

Cyanide-based gold baths have been widely used for gold plating; however they are recently avoided due to their toxicity. Non-cyanide baths have been developed to overcome those problems, most of them based on Au(I)-sulfide complex, but they are usually unstable. A stable Au(I)-sulfide containing formaldehyde was developed and its behavior has been investigated. The possible electrochemical reactions were analyzed with the aid of Cyclic Voltammetry (CV). In addition, Rutherford Backscattering Spectrometry (RBS) was used to obtain the deposits composition and thickness.
Electrodeposition of p-Cu2O Layers on Co/p-Si Planar Structures
Authors: Delatorre Rafael G. , Stenger Vagner , Zoldan Vinicius C. , Da Silva Douglas L. , Dos Santos Sebastiao G. , Viegas Alexandre D. , Pasa Andre A.
Published: September 2009

The electrodeposition of p-Cu2O layers on Co/p-Si planar structures for potential application as p/metal/p metal base transistors were investigated. The deposits were prepared from electrolytes containing lactic acid and copper sulphate and characterized by Rutherford Backscattering Spectrometry (RBS), X - Ray Diffraction (XRD), and Transmission Electron Microscopy (TEM). The formation of Cu2O/Co Schottky interfaces was confirmed by electrical measurements.
Customized Polynomial Contact Lenses via Wet Etching
Authors: De Oliveira Costa Rodolfo F. , Barçante Thiago , Souza Jardim Marco A. , De Souza Beijamim R. , De Lima Monteiro Davies William
Published: September 2009

Customized polynomial contact lenses are meant to correct high-order optical distortions in the human vision, beyond focus and astigmatism, but they are not yet a commercial solution mainly due to reproducibility and cost issues. Aiming at circumventing these obstacles to market, this paper investigates the possibility of fabrication of such lenses by wet etching of a silicon mould and subsequent casting of the lens polymer. The proposed technique to obtain the mould is based on ordinary anisotropic etching of c-Si with an aqueous KOH solution, where a subtle step ensures the achievement of an arbitrary smooth topology.
Study of TiOxNy MOS Capacitors
Authors: Albertin Katia F. , Niwa Takuya , Nobaro Bruno A. , Souza Denise C. , Zuñiga Alejandro , Pereyra Inés
Published: September 2009

A set of TiOxNy films was deposited by reactive RF magnetron sputtering varying the nitrogen partial pressure in a Ar/N2 gaseous mixture. Utilizing these films as gate dielectric layer MOS capacitors were fabricated and characterized. The TiOxNy films were characterized by Fourier Transform Infrared Spectroscopy (FTIR), Rutherford Backscattering (RBS), optical absorption, and High Resolution Transmission Electron Microscopy (HRTEM). Capacitance-voltage (1MHz) and current-voltage measurements were used to obtain the effective dielectric constant, the effective oxide thickness (EOT), the leakage current density, and the interface quality. MOS capacitors results show that the TiOxNy films present a dielectric constant varying from 28 to 80, good interface quality with silicon, and a leakage current density of approximately 0.25 mA/cm2 for VG = -1V, which is acceptable for high performance logic circuits and low power circuits fabrication. The leakage current density is reduced in 3 orders of magnitude with an increase in nitrogen concentration.
CdS-Decorated Multi-Walled Carbon Nanotubes as a Material for New Devices
Authors: Silva Marcos Flávio O. , Rodrigues Wagner N. , Miquita Douglas R. , Ladeira Luiz O. , Pinheiro Carlos B.
Published: September 2009

Cadmium Sulfide (CdS) nanoparticles were successfully grown on Multi-Walled Carbon Nanotubes (MWNTs) via a simple chemical reaction. The CdS-MWNTs sample was afterwards characterized with Scanning and Transmission Electron Microscopies (SEM/TEM) and X-ray diffraction (XRD). The obtained images show clearly the decoration of the MWNTs by the CdS nanoparticles, and the XRD measurements indicate the CdS structure as Zinc Blend type.
Deposition of Carbon Nanotubes on Silicon for Field Emission Application
Authors: Dantas Michel O. , Galeazzo Elisabete , Peres Henrique E. , Ramirez-Fernandez Francisco J. , Diniz Eric , Castro Ricardo H.
Published: September 2009

This paper discusses some results about Single-Walled Carbon Nanotubes electrophoretically deposited on silicon in order to fabricate Field Emission devices. Field emission characterization was executed into a high vacuum chamber. Emission characteristics from distinct samples were compared by extracting the macroscopic electric field from V-d curves and applying it as a quality parameter. It was demonstrated that carbon nanotubes on the Si surface could improve approximately 8 times the field emission properties of devices.
Influence of Electronegative Gas on the Efficiency of Conventional and Hollow Cathode Magnetron Sputtering Systems
Authors: Duarte Diego A. , Massi Marcos , Da Silva Sobrinho Argemiro S. , Tezani Leandro L. , Fontana Luis C. , Maciel Homero S.
Published: September 2009

The aim of this work is to study the influence of electronegative gas (oxygen at different concentrations) on the electrical characteristics of two configurations of magnetron sputtering systems, namely Hollow Cathode Magnetron Sputtering (HCMS) and Conventional Magnetron Sputtering (CMS). A comparison of the plasma impedances and magnetron efficiency of these systems were carried out through the current-voltage characteristics of the discharges operating at the same pressure and different oxygen concentration on O2/Ar mixtures. The results showed significant variations in the plasma impedance and magnetron efficiency, indicating that HCMS system presents better electrical characteristics than CMS system, i.e., low plasma impedance and high magnetron efficiency. The results indicate that HCMS system is a very interesting technique to be used as deposition system in micro and nanoelectronic processes.