bluuebunny/crossref_metadata_2025 huggingface dataset:
On the Manifold
Property of the Set of Singularities of Kinematic Mappings: Modeling, Classification, and
Genericity
Authors: Müller Andreas
Published: November 2010

It is commonly assumed that the singularities of kinematic mappings constitute generically smooth manifolds but this has not yet been proven. Moreover, before this assumption can be verified, the concept of genericity needs to be clarified. In this paper, two different notions of generic properties of kinematic mappings are discussed. One accounts for the stability of the manifold property with respect to small changes in the geometry of a mechanism while the other concerns the likelihood that a mechanism possesses smooth manifolds of singularities. Singularities forming smooth manifolds is the condition for singularity-free motion of overconstrained mechanisms but also has consequences for reliable control of serial manipulators. As basis for establishing genericity, a formulation of the kinematic mapping is presented that takes into account the type of joints and feasible link geometries. The continuous transition between link geometries defines a deformation of a kinematic mapping. All mappings obtained in this way constitute a class of kinematic mappings. A basic characteristic of a kinematic chain is its motion space. An explicit expression for the motion spaces of individual as well as classes of kinematic mappings is given. The actual conditions for genericity will be addressed in a forthcoming publication.
FSI Analysis of a Healthy and a Stenotic Human Trachea Under Impedance-Based Boundary Conditions
Authors: Malvè M. , Pérez del Palomar A. , Chandra S. , López-Villalobos J. L. , Mena A. , Finol E. A. , Ginel A. , Doblaré M.
Published: November 2010

In this work, a fluid-solid interaction (FSI) analysis of a healthy and a stenotic human trachea was studied to evaluate flow patterns, wall stresses, and deformations under physiological and pathological conditions. The two analyzed tracheal geometries, which include the first bifurcation after the carina, were obtained from computed tomography images of healthy and diseased patients, respectively. A finite element-based commercial software code was used to perform the simulations. The tracheal wall was modeled as a fiber reinforced hyperelastic solid material in which the anisotropy due to the orientation of the fibers was introduced. Impedance-based pressure waveforms were computed using a method developed for the cardiovascular system, where the resistance of the respiratory system was calculated taking into account the entire bronchial tree, modeled as binary fractal network. Intratracheal flow patterns and tracheal wall deformation were analyzed under different scenarios. The simulations show the possibility of predicting, with FSI computations, flow and wall behavior for healthy and pathological tracheas. The computational modeling procedure presented herein can be a useful tool capable of evaluating quantities that cannot be assessed in vivo, such as wall stresses, pressure drop, and flow patterns, and to derive parameters that could help clinical decisions and improve surgical outcomes.
The Role of Mass Balance Equations in Growth Mechanics Illustrated in Surface and Volume Dissolutions
Authors: Ateshian Gerard A.
Published: November 2010

Growth mechanics problems require the solution of mass balance equations that include supply terms and account for mass exchanges among constituents of a mixture. Though growth may often be accompanied by a variety of concomitant phenomena that increase modeling complexity, such as solid matrix deformation, evolving traction-free configurations, cell division, and active cell contraction, it is important to distinguish these accompanying phenomena from the fundamental growth process that consists of deposition or removal of mass from the solid matrix. Therefore, the objective of this study is to present a canonical problem of growth, namely, dissolution of a rigid solid matrix in a solvent. This problem illustrates a case of negative growth (loss of mass) of the solid in a mixture framework that includes three species, a solid, a solvent, and a solute, where the solute is the product of the solid dissolution. By analyzing both volumetric and surface dissolutions, the two fundamental modes of growth are investigated within the unified framework of mixture theory.
Fabrication of mesas with micro- and nanopatterned surface relief used as working stamps for step and stamp imprint lithography
Authors: Schleunitz Arne , Spreu Christian , Haatainen Tomi , Klukowska Anna , Schift Helmut
Published: November 2010

A manufacturing concept to fabricate working stamps with defined mesa structures using combined nanoimprint and photolithography is presented. OrmoStamp, an UV-curable organic-inorganic hybrid polymer, was used as mold material. 30 μm high large mesa structures (4×4 mm2) with sharp borders and almost vertical sidewalls were manufactured. On top they featured nanograting patterns with 200 nm height and lateral size as a surface relief. The good thermal decoupling of stamp body and imprinted substrate and the high planarity (divergence <50 nm) make the stamp very suitable for thermal step and repeat nanoimprint lithography of confined patterns with low stitching errors. Up to 210 imprints were performed with a single mesa into a 325 nm thin layer of mr-I 7030E.
Rotation speed control of Janus particles by dielectrophoresis in a microfluidic channel
Authors: Honegger T. , Lecarme O. , Berton K. , Peyrade D.
Published: November 2010

In this work, Janus particles (Au/fluorescent polystyrene) are fabricated and their flip/flop rotational effect is studied in a microfluidic channel thanks to dielectrophoresis, providing a new type of local light switch. A method for producing large amounts (more than 106 particles/ml) of Janus particles is first presented. Those particles were then injected in an electromicrofluidic chip and stabilized in the fluid by a dielectrophoretic trap. The spanning frequency of this trap allowed performing a “flip-flop” effect of the Janus particles by recording their fluorescent intensities. Flip (Au top side) and flop (PS top side) frequencies are identified. Finally, experiments were performed on the time triggered commutations between flip and flop frequencies to define the capability of each Janus particle to sustain speed control of their flip-flop.
Photopatternable inorganic hardmask
Authors: Telecky Alan , Xie Peng , Stowers Jason , Grenville Andrew , Smith Bruce , Keszler Douglas A.
Published: November 2010

The authors present a directly photopatternable inorganic hardmask for 193 nm lithography based on the solution-deposited dielectric metal oxide sulfate (MSOx) system. To demonstrate pattern fidelity, 18 nm half-pitch features were written at a dose near 240 μC/cm2 (30 keV) with line width roughness values between 1.6 and 1.8 nm. Well-resolved and uniform 30 nm contact holes were fabricated via a litho-freeze-litho-etch process employing electron beam exposure and a simple thermal freeze. ZircSOx has a high index of refraction approaching 1.9 at 193 nm, and the extinction coefficient, k, can be varied by an order of magnitude by substituting Zr with Hf. Optical interference lithography at 193 nm was used to realize 60 nm half-pitch lines in MSOx at a dose of 25 mJ/cm2.
Comparison of positive tone versus negative tone resist pattern collapse behavior
Authors: Yeh Wei-Ming , Noga David E. , Lawson Richard A. , Tolbert Laren M. , Henderson Clifford L.
Published: November 2010

In this work, e-beam lithography patterns have been specifically designed and fabricated which provide the opportunity to probe the collapse behavior of both positive and negative tone systems. The pattern layout includes adjacent parallel line structures that both vary in the line size and also in the distance by which they are separated by the space between them. This type of structure allows for the control and modulation of the capillary forces, and ultimately the stresses, experienced by the photoresist line pairs during the final rinse and drying steps of the development process. Using such structures, it is possible to determine the critical stress, i.e., the maximum stress experienced by the photoresist lines before collapse, as a function of a variety of parameters including: material type, substrate preparation conditions, resist film thickness, and resist feature width. In this article, such a modular approach has been used to compare the pattern collapse behavior of a prototypical positive tone resist formulated using a protected hydroxystyrene-based copolymer and a prototypical negative tone epoxide-based molecular photoresist (4-EP). It was found that the critical stress at the point of pattern collapse decreased both as the thickness and the feature width of the resist lines decreased, though this trend was observed to a much lesser extent in the negative tone 4-EP material. It is observed that the negative tone resist, whose imaging mechanism involves cross-linking, shows far superior pattern collapse performance as compared to the positive tone deprotection based resist and is in general able to achieve significantly higher aspect ratio patterning at equivalent feature linewidths.
Carotenoid-Related Alteration of Cell Membrane Fluidity Impacts
Staphylococcus aureus
Susceptibility to Host Defense Peptides
Authors: Mishra Nagendra N. , Liu George Y. , Yeaman Michael R. , Nast Cynthia C. , Proctor Richard A. , McKinnell James , Bayer Arnold S.
Published: November 2010

Carotenoid pigments of
Staphylococcus aureus
provide integrity to its cell membrane (CM) and limit oxidative host defense mechanisms. However, the role of carotenoids in staphylococcal resistance to nonoxidative host defenses has not been characterized. The current study examined the relationship among CM carotenoid content, membrane order, and
in vitro
susceptibility to daptomycin or to prototypic neutrophil-derived, platelet-derived, or bacterium-derived cationic antimicrobial peptides (human neutrophil defensin-1 [hNP-1], platelet microbicidal proteins [PMPs], or polymyxin B, respectively). A previously characterized methicillin-susceptible
Staphylococcus aureus
(MSSA) isogenic clinical strain set was used, including a parental isolate with an intact carotenoid biosynthetic operon (
crtOPQMN
) containing the
crtM
gene encoding early steps in staphyloxanthin biosynthesis, a
crtM
deletion mutant, and a
crtMN
multicopy plasmid-complemented variant. Compared to the parental and
crtM
knockout strains, the
crtMN
-complemented strain exhibited (i) increased carotenoid production, (ii) increased CM rigidity (
P
< 0.001), and (iii) uniformly reduced susceptibility to killing by the above-mentioned range of cationic peptides (statistically significant for hNP-1 [20 μg/ml];
P
= 0.0037). There were no significant differences in phospholipid composition and asymmetry, fatty acid profiles, surface charge, or cell wall thickness among the strain set. Collectively, these data support the concept that carotenoid biosynthesis can contribute to the ability of
S. aureus
to subvert nonoxidative host defenses mediated by cationic peptides, potentially by increasing target membrane rigidity.
Detection of NDM-1-Producing
Klebsiella pneumoniae
in Kenya
Authors: Poirel Laurent , Revathi Gunturu , Bernabeu Sandrine , Nordmann Patrice
Published: November 2010

Seven carbapenem-resistant NDM-1-positive
Klebsiella pneumoniae
isolates were recovered from patients hospitalized between 2007 and 2009 in different wards at a referral and tertiary care center in Nairobi. Most of the isolates were obtained from urine. All isolates carried the
bla
NDM-1
carbapenemase gene previously reported from India, Pakistan, and the United Kingdom. These isolates were clonally related and expressed many other resistance determinants, including β-lactamases CTX-M-15, OXA-1, OXA-9, CMY-6, and aminoglycoside resistance methylase RmtC. This work corresponds to the first report of NDM-1 producers in Africa.
Exploring the Links between Natural Products and Bacterial Assemblages in the SpongeAplysina aerophoba
Authors: Sacristán-Soriano Oriol , Banaigs Bernard , Casamayor Emilio O. , Becerro Mikel A.
Published: November 2010

The spongeAplysina aerophobaproduces a large diversity of brominated alkaloids (BAs) and hosts a complex microbial assemblage. Although BAs are located within sponge cells, the enzymes that bind halogen elements to organic compounds have been exclusively described in algae, fungi, and bacteria. Bacterial communities withinA. aerophobacould therefore be involved in the biosynthesis of these compounds. This study investigates whether changes in both the concentration of BAs and the bacterial assemblages are correlated inA. aerophoba. To do so, we quantified major natural products using high-performance liquid chromatography and analyzed bacterial assemblages using denaturing gradient gel electrophoresis on the 16S rRNA gene. We identified multiple associations between bacteria and natural products, including a strong relationship between aChloroflexiphylotype and aplysinamisin-1 and between an unidentified bacterium and aerophobin-2 and isofistularin-3. Our results suggest that these bacteria could either be involved in the production of BAs or be directly affected by them. To our knowledge, this is one of the first reports that find a significant correlation between natural products and bacterial populations in any benthic organism. Further investigating these associations will shed light on the organization and functioning of host-endobiont systems such asAplysina aerophoba.
Global Phylogeography of Chitinase Genes in Aquatic Metagenomes
Authors: Beier Sara , Jones Christopher M. , Mohit Vani , Hallin Sara , Bertilsson Stefan
Published: November 2010

Phylogeny-based analysis of chitinase and 16S rRNA genes from metagenomic data suggests that salinity is a major driver for the distribution of both chitinolytic and total bacterial communities in aquatic systems. Additionally, more acidic chitinase proteins were observed with increasing salinity. Congruent habitat separation was further observed for both genes according to latitude and proximity to the coastline. However, comparison of chitinase and 16S rRNA genes extracted from different geographic locations showed little congruence in distribution. There was no indication that dispersal limited the global distribution of either gene.
Adjacent Gene Pairing Plays a Role in the Coordinated Expression of Ribosome Biogenesis Genes
MPP10
and
YJR003C
in Saccharomyces cerevisiae
Authors: Arnone James T. , McAlear Michael A.
Published: November 2010

The rRNA and ribosome biogenesis (RRB) regulon from
Saccharomyces cerevisiae
contains some 200 genes, the expression of which is tightly regulated under changing cellular conditions. RRB gene promoters are enriched for the RRPE and PAC consensus motifs, and a significant fraction of RRB genes are found as adjacent gene pairs. A genetic analysis of the
MPP10
promoter revealed that both the RRPE and PAC motifs are important for coordinated expression of
MPP10
following heat shock, osmotic stress, and glucose replenishment. The association of the RRPE binding factor Stb3 with the
MPP10
promoter was found to increase after glucose replenishment and to decrease following heat shock. Similarly, bulk histone H3 clearing and histone H4K12 acetylation levels at the
MPP10
promoter were found to increase or decrease following glucose replenishment or heat shock, respectively. Interestingly, substitutions in the PAC and RRPE sequences at the
MPP10
promoter were also found to impact the regulated expression of the adjacent RRB gene
YJR003
, whose promoter lies in the opposite orientation and some 3.8 kb away. Furthermore, the regulated expression of
YJR003C
could be disrupted by inserting a reporter cassette that increased its distance from
MPP10
. Given that a high incidence of gene pairing was also found within the ribosomal protein (RP) and RRB regulons across different yeast species, our results indicate that immediately adjacent positioning of genes can be functionally significant for their coregulated expression.
Candida albicans Als3, a Multifunctional Adhesin and Invasin
Authors: Liu Yaoping , Filler Scott G.
Published: November 2010

Candida albicans
is part of the normal human flora, and it grows on mucosal surfaces in healthy individuals. In susceptible hosts, this organism can cause both mucosal and hematogenously disseminated disease. For
C. albicans
to persist in the host and induce disease, it must be able to adhere to biotic and abiotic surfaces, invade host cells, and obtain iron. The
C. albicans
hypha-specific surface protein Als3 is a member of the agglutinin-like sequence (Als) family of proteins and is important in all of these processes. Functioning as an adhesin, Als3 mediates attachment to epithelial cells, endothelial cells, and extracellular matrix proteins. It also plays an important role in biofilm formation on prosthetic surfaces, both alone and in mixed infection with
Streptococcus gordonii
. Als3 is one of two known
C. albicans
invasins. It binds to host cell receptors such as E-cadherin and N-cadherin and thereby induces host cells to endocytose the organism. Als3 also binds to host cell ferritin and enables
C. albicans
to utilize this protein as a source of iron. Because of its multiple functions and its high expression level
in vivo
, Als3 is a promising target for vaccines that induce protective cell-mediated and antibody responses. This review will summarize the multiple functions of this interesting and multifunctional protein.
Role of Defensins in Corneal Epithelial Barrier Function against
Pseudomonas aeruginosa
Traversal
Authors: Augustin Danielle K. , Heimer Susan R. , Tam Connie , Li Wing Y. , Le Due Jeff M. , Evans David J. , Fleiszig Suzanne M. J.
Published: November 2010

Studies have shown that epithelium-expressed antimicrobial peptides (AMPs), e.g., β-defensins, play a role in clearing bacteria from mouse corneas already infected with
Pseudomonas aeruginosa
. Less is known about the role of AMPs in allowing the cornea to resist infection when healthy. We previously reported that contact lens exposure, a major cause of
P. aeruginosa
keratitis, can inhibit the upregulation of human β-defensin 2 (hBD-2) by corneal epithelial cells in response to
P. aeruginosa
antigens
in vitro
. Here, we studied the role of AMPs in maintaining the corneal epithelial barrier to
P. aeruginosa
penetration using both
in vitro
(human) and
in vivo
(mouse) experiments. Results showed that preexposing human corneal epithelial multilayers to bacterial antigens in a culture supernatant (known to upregulate AMP expression) reduced epithelial susceptibility to
P. aeruginosa
traversal up to 6-fold (
P
< 0.001). Accordingly, small interfering RNA (siRNA) knockdown of any one of four AMPs expressed by human epithelia promoted
P. aeruginosa
traversal by more than 3-fold (
P
< 0.001). The combination knockdown of AMPs further enhanced susceptibility to bacterial traversal by ∼8-fold (
P
< 0.001).
In vivo
experiments showed that the loss of murine β-defensin 3 (mBD-3), a murine ortholog of hBD-2, enhanced corneal susceptibility to
P. aeruginosa
. The uninjured ocular surface of mBD-3
−/−
mice showed a reduced capacity to clear
P. aeruginosa
, and their corneal epithelia were more susceptible to bacterial colonization, even when inoculated
ex vivo
to exclude tear fluid effects. Together, these
in vitro
and
in vivo
data show functional roles for AMPs in normal corneal epithelial cell barrier function against
P. aeruginosa
.
Burkholderia thailandensis oacA
Mutants Facilitate the Expression of
Burkholderia mallei
-Like O Polysaccharides
Authors: Brett Paul J. , Burtnick Mary N. , Heiss Christian , Azadi Parastoo , DeShazer David , Woods Donald E. , Gherardini Frank C.
Published: November 2010

Previous studies have shown that the O polysaccharides (OPS) expressed by
Burkholderia mallei
are similar to those produced by
Burkholderia thailandensis
except that they lack the 4-
O
-acetyl modifications on their 6-deoxy-α-
l
-talopyranosyl residues. In the present study, we describe the identification and characterization of an open reading frame, designated
oacA
, expressed by
B. thailandensis
that accounts for this phenomenon. Utilizing the
B. thailandensis
and
B. mallei
lipopolysaccharide (LPS)-specific monoclonal antibodies Pp-PS-W and 3D11, Western immunoblot analyses demonstrated that the LPS antigens expressed by the
oacA
mutant,
B. thailandensis
ZT0715, were antigenically similar to those produced by
B. mallei
ATCC 23344. In addition, immunoblot analyses demonstrated that when
B. mallei
ATCC 23344 was complemented in
trans
with
oacA
, it synthesized
B. thailandensis
-like LPS antigens. To elucidate the structure of the OPS moieties expressed by ZT0715, purified samples were analyzed via nuclear magnetic resonance spectroscopy. As predicted, these studies demonstrated that the loss of OacA activity influenced the O acetylation phenotype of the OPS moieties. Unexpectedly, however, the results indicated that the O methylation status of the OPS antigens was also affected by the loss of OacA activity. Nonetheless, it was revealed that the LPS moieties expressed by the
oacA
mutant reacted strongly with the
B. mallei
LPS-specific protective monoclonal antibody 9C1-2. Based on these findings, it appears that OacA is required for the 4-
O
acetylation and 2-
O
methylation of
B. thailandensis
OPS antigens and that ZT0715 may provide a safe and cost-effective source of
B. mallei
-like OPS to facilitate the synthesis of glanders subunit vaccine candidates.
Nasal Immunization with a Fusion Protein Consisting of the Hemagglutinin A Antigenic Region and the Maltose-Binding Protein Elicits CD11c+CD8+Dendritic Cells for Induced Long-Term Protective Immunity
Authors: Du Yuan , Hashizume Tomomi , Kurita-Ochiai Tomoko , Yuzawa Satoshi , Abiko Yoshimitsu , Yamamoto Masafumi
Published: November 2010

We assessed the efficacy of a fusion protein consisting of the 25-kDa antigenic region ofPorphyromonas gingivalishemagglutinin A and theEscherichia colimaltose-binding protein (25k-hagA-MBP) as a nasal vaccine for the prevention of oral infection withP. gingivalis. Nasal immunization with 25k-hagA-MBP induced high levels of 25k-hagA-specific serum IgG, serum IgA, and salivary IgA antibodies in a Toll-like receptor 4 (TLR4)-dependent manner. These antibody responses were maintained for at least 1 year after immunization. Analysis of cytokine responses showed that nasal administration of 25k-hagA-MBP induced antigen-specific CD4+T cells producing interleukin 4 (IL-4) and IL-5, but not gamma interferon (IFN-γ), in the spleen and cervical lymph nodes (CLNs). Furthermore, increased numbers of CD11c+CD8α+, but not CD11c+CD11b+or CD11c+B220+, dendritic cells with upregulated expression of CD80, CD86, CD40, and major histocompatibility complex class II (MHC II) molecules were noted in the spleen, CLNs, and nasopharynx-associated lymphoreticular tissues (NALT). Interestingly, when 25k-hagA-MBP or cholera toxin (CT) was given intranasally to enable examination of their presence in neuronal tissues, the amounts of 25k-hagA-MBP were significantly lower than those of CT. Importantly, mice given 25k-hagA-MBP nasally showed a significant reduction in alveolar bone loss caused by oral infection withP. gingivalis, even 1 year after the immunization. These results suggest that 25k-hagA-MBP administered nasally would be an effective and safe mucosal vaccine againstP. gingivalisinfection and may be an important tool for the prevention of chronic periodontitis in humans.
Interbacterial Macromolecular Transfer by the
Campylobacter fetus
subsp.
venerealis
Type IV Secretion System
Authors: Kienesberger Sabine , Trummler Caroline Schober , Fauster Astrid , Lang Silvia , Sprenger Hanna , Gorkiewicz Gregor , Zechner Ellen L.
Published: November 2010

We report here the first demonstration of intra- and interspecies conjugative plasmid DNA transfer for
Campylobacter fetus
. Gene regions carried by a
Campylobacter coli
plasmid were identified that are sufficient for conjugative mobilization to
Escherichia coli
and
C. fetus
recipients. A broader functional range is predicted. Efficient DNA transfer involves the
virB9
and
virD4
genes of the type IV bacterial secretion system encoded by a pathogenicity island of
C. fetus
subsp.
venerealis
. Complementation of these phenotypes from expression constructions based on the promoter of the
C. fetus
surface antigen protein (
sap
) locus was temperature dependent, and a temperature regulation of the
sap
promoter was subsequently confirmed under laboratory conditions. Gene transfer was sensitive to surface or entry exclusion functions in potential recipient cells carrying IncPα plasmid RP4 implying functional relatedness to
C. fetus
proteins. The
virB
/
virD4
locus is also known to be involved in bacterial invasion and killing of cultured human cells
in vitro
. Whether specifically secreted effector proteins contribute to host colonization and infection activities is currently unknown. Two putative effector proteins carrying an FIC domain conserved in a few bacterial type III and type IV secreted proteins of pathogens were analyzed for secretion by the
C. fetus
or heterologous conjugative systems. No evidence for interbacterial translocation of the Fic proteins was found.
Citrate Uptake in Exchange with Intermediates in the Citrate Metabolic Pathway in
Lactococcus lactis
IL1403
Authors: Pudlik Agata M. , Lolkema Juke S.
Published: November 2010

Carbohydrate/citrate cometabolism in
Lactococcus lactis
results in the formation of the flavor compound acetoin. Resting cells of strain IL1403(pFL3) rapidly consumed citrate while producing acetoin when substoichiometric concentrations of glucose or
l
-lactate were present. A proton motive force was generated by electrogenic exchange of citrate and lactate catalyzed by the citrate transporter CitP and proton consumption in decarboxylation reactions in the pathway. In the absence of glucose or
l
-lactate, citrate consumption was biphasic. During the first phase, hardly any citrate was consumed. In the second phase, citrate was converted rapidly, but without the formation of acetoin. Instead, significant amounts of the intermediates pyruvate and α-acetolactate, and the end product acetate, were excreted from the cells. It is shown that the intermediates and acetate are excreted in exchange with the uptake of citrate catalyzed by CitP. The availability of exchangeable substrates in the cytoplasm determines both the rate of citrate consumption and the end product profile. It follows that citrate metabolism in
L. lactis
IL1403(pFL3) splits up in two routes after the formation of pyruvate, one the well-characterized route yielding acetoin and the other a new route yielding acetate. The flux distribution between the two branches changes from 85:15 in the presence of
l
-lactate to 30:70 in the presence of pyruvate. The proton motive force generated was greatest in the presence of
l
-lactate and zero in the presence of pyruvate, suggesting that the pathway to acetate does not generate proton motive force.
Leprosy and the Human Genome
Authors: Misch Elizabeth A. , Berrington William R. , Vary James C. , Hawn Thomas R.
Published: November 2010

Despite the availability of effective treatment for several decades, leprosy remains an important medical problem in many regions of the world. Infection withMycobacterium lepraecan produce paucibacillary disease, characterized by well-formed granulomas and a Th1 T-cell response, or multibacillary disease, characterized by poorly organized cellular infiltrates and Th2 cytokines. These diametric immune responses confer states of relative resistance or susceptibility to leprosy, respectively, and have well-defined clinical manifestations. As a result, leprosy provides a unique opportunity to dissect the genetic basis of humanin vivoimmunity. A series of studies over the past 40 years suggests that host genes influence the risk of leprosy acquisition and the predilection for different clinical forms of the disease. However, a comprehensive, cellular, and molecular view of the genes and variants involved is still being assembled. In this article, we review several decades of human genetic studies of leprosy, including a number of recent investigations. We emphasize genetic analyses that are validated by the replication of the same phenotype in independent studies or supported by functional experiments demonstrating biological mechanisms of action for specific polymorphisms. Identifying and functionally exploring the genetic and immunological factors that underlie human susceptibility to leprosy have yielded important insights intoM. lepraepathogenesis and are likely to advance our understanding of the immune response to other pathogenic mycobacteria. This knowledge may inform new treatment or vaccine strategies for leprosy or tuberculosis.
Folded DNA in Action: Hairpin Formation and Biological Functions in Prokaryotes
Authors: Bikard David , Loot Céline , Baharoglu Zeynep , Mazel Didier
Published: November 2010

Structured forms of DNA with intrastrand pairing are generated in several cellular processes and are involved in biological functions. These structures may arise on single-stranded DNA (ssDNA) produced during replication, bacterial conjugation, natural transformation, or viral infections. Furthermore, negatively supercoiled DNA can extrude inverted repeats as hairpins in structures called cruciforms. Whether they are on ssDNA or as cruciforms, hairpins can modify the access of proteins to DNA, and in some cases, they can be directly recognized by proteins. Folded DNAs have been found to play an important role in replication, transcription regulation, and recognition of the origins of transfer in conjugative elements. More recently, they were shown to be used as recombination sites. Many of these functions are found on mobile genetic elements likely to be single stranded, including viruses, plasmids, transposons, and integrons, thus giving some clues as to the manner in which they might have evolved. We review here, with special focus on prokaryotes, the functions in which DNA secondary structures play a role and the cellular processes giving rise to them. Finally, we attempt to shed light on the selective pressures leading to the acquisition of functions for DNA secondary structures.
Nitrogen Fixation and Hydrogen Metabolism in Cyanobacteria
Authors: Bothe Hermann , Schmitz Oliver , Yates M. Geoffrey , Newton William E.
Published: November 2010

This review summarizes recent aspects of (di)nitrogen fixation and (di)hydrogen metabolism, with emphasis on cyanobacteria. These organisms possess several types of the enzyme complexes catalyzing N2fixation and/or H2formation or oxidation, namely, two Mo nitrogenases, a V nitrogenase, and two hydrogenases. The two cyanobacterial Ni hydrogenases are differentiated as either uptake or bidirectional hydrogenases. The different forms of both the nitrogenases and hydrogenases are encoded by different sets of genes, and their organization on the chromosome can vary from one cyanobacterium to another. Factors regulating the expression of these genes are emerging from recent studies. New ideas on the potential physiological and ecological roles of nitrogenases and hydrogenases are presented. There is a renewed interest in exploiting cyanobacteria in solar energy conversion programs to generate H2as a source of combustible energy. To enhance the rates of H2production, the emphasis perhaps needs not to be on more efficient hydrogenases and nitrogenases or on the transfer of foreign enzymes into cyanobacteria. A likely better strategy is to exploit the use of radiant solar energy by the photosynthetic electron transport system to enhance the rates of H2formation and so improve the chances of utilizing cyanobacteria as a source for the generation of clean energy.
GENETIC ALGORITHMS AND OPTIMIZATION PROBLEMS IN QUANTUM COMPUTING
Authors: HARDY Y. , STEEB W.-H.
Published: November 2010

We solve a number of problems in quantum computing by applying genetic algorithms. We use the bitset class of C ++ to represent any data type for genetic algorithms. Thus we have a flexible way to solve any optimization problem. The Bell-CHSH inequality and entanglement measures are studied using genetic algorithms. Entangled states form the backbone for teleportation. The C ++ code is also provided.
NUMERICAL STUDY OF BÉNARD CONVECTION WITH TEMPERATURE-DEPENDENT VISCOSITY IN A POROUS CAVITY VIA LATTICE BOLTZMANN METHOD
Authors: RONG FUMEI , GUO ZHAOLI , ZHANG TING , SHI BAOCHANG
Published: November 2010

In this paper, the heat transfer characteristics of a two-dimensional steady Bénard convection flow with a temperature-dependent viscosity are studied numerically by the lattice Boltzmann method (LBM). The double-distribution model for LBM is proposed, one is to simulate incompressible flow in porous media and the other is to solve the volume averaged energy equation. The method is validated by comparing the numerical results with those existing literature. The effect of viscosity dependent on temperature is investigated. The average Nusselt numbers for the cases of exponential form of viscosity-temperature and effective Rayleigh number based on average temperature (T ref = 0.5 (Th +Tc)) are compared. A new formula of reference temperature (T ref = Tc +f (b) (Th -Tc)) is proposed and the numerical results show that the average Nusselt numbers predicted by this method have higher precision than those obtained by average temperature.
HAWKING RADIATION VIA TUNNELING OF MASSIVE PARTICLES FROM A GRAVITY'S RAINBOW
Authors: LIU CHENG-ZHOU
Published: November 2010

In the tunneling framework of Hawking radiation, the quantum tunneling of massive particles in the modified Schwarzschild black holes from gravity's rainbow is investigated. While the massive particle tunneling from the event horizon, the metric fluctuation is taken into account, not only due to energy conservation but also to the Planck scale effect of spacetime. The obtained results show that, the emission rate is related to changes of the black hole's quantum corrected entropies before and after the emission. This implies that, considering the quantum effect of spacetime, information conservation of black holes is probable. Meanwhile, the quantum corrected entropy of the modified black hole is obtained and the leading correction behave as log-area type. And that, the emission spectrum with Planck scale correction is obtained and it deviates from the thermal spectrum.
CHARGED PARTICLES' TUNNELING FROM A NONCOMMUTATIVE CHARGED BLACK HOLE
Authors: MEHDIPOUR S. HAMID
Published: November 2010

We apply the tunneling process of charged massive particles through the quantum horizon of a Reissner–Nordström black hole in a new noncommutative gravity scenario. In this model, the tunneling amplitude on account of noncommutativity influences in the context of coordinate coherent states is modified. Our calculation points out that the emission rate satisfies the first law of black hole thermodynamics and is consistent with an underlying unitary theory.
A NOTE ON HOMEOMORPHISM FOR BACKWARD DOUBLY SDEs AND APPLICATIONS
Authors: AMAN A. , N'ZI M. , OWO J. M.
Published: November 2010

In this note, we study the class of backward doubly stochastic differential equations (BDSDEs). In our framework, the terminal values depend on a real parameter. Under suitable assumptions and by the help of strict comparison theorem, we show homeomorphism property for the solution. This result is used to study homeomorphism property for quasi-linear stochastic partial differential equations.
ASYMPTOTIC COMPACTNESS OF STOCHASTIC COMPLEX GINZBURG–LANDAU EQUATION ON AN UNBOUNDED DOMAIN
Authors: BLÖMKER DIRK , HAN YONGQIAN
Published: November 2010

The Ginzburg–Landau-type complex equations are simplified mathematical models for various pattern formation systems in mechanics, physics and chemistry. In this paper, we consider the complex Ginzburg–Landau (CGL) equations on the whole real line perturbed by an additive spacetime white noise. Our main result shows that it generates an asymptotically compact stochastic or random dynamical system. This is a crucial property for the existence of a stochastic attractor for such CGL equations. We rely on suitable spaces with weights, due to the regularity properties of spacetime white noise, which gives rise to solutions that are unbounded in space.
Fold–thrust belts: overlooked provinces or justifiably avoided?
Authors: Goffey Graham P. , Craig Jonathan , Needham Tim , Scott Robert
Published: November 2010

This volume results from a conference intended to assess the exploration and exploitation primarily of onshore fold–thrust belts. These are commonly perceived as ‘difficult’ places to explore and therefore are often avoided by companies. However, fold–thrust belts host large oil and gas fields and barriers to effective exploration mean that substantial resources may remain.

This volume shows how evaluation techniques have developed over time. It is possible in certain circumstances to achieve good 3D seismic data. Structural restoration techniques have moved into the 3D domain and simple thermal constraints can be enhanced by using more sophisticated palaeo-thermal indicators to more accurately model burial and uplift evolution of source and reservoirs. Awareness of the influence of pre-thrust structure and stratigraphy and of hybrid thick and thin-skinned deformation styles is supplementing the simplistic thin-skinned fault-bend and fault propagation models employed in earlier exploration.

The ‘learning curve’ in fold–thrust belt exploration has not been steep and further improvement seems likely to be a slow, expensive and iterative process with information from outcrop, well penetration and slowly improving seismic data. Industry and academia need together to develop and continually improve the necessary understanding of subsurface geometries, reservoir and charge evolution and timing.
Spontaneous fluid emissions in the Northern Apennines: geochemistry, structures and implications for the petroleum system
Authors: Capozzi Rossella , Picotti Vincenzo
Published: November 2010

Natural seeps in the Northern Apennines document a variability of fluids and reservoirs in terms of origin, age and evolution. Their spatial distribution appears controlled by the presence or absence of the tectonic overburden provided by the Ligurian nappe. The general trend of deepening of the Mesozoic basement toward the internal part of the thrust belt is reflected by the nature of the seeps, characterized by thermogenic methane and oil at the foothills, whereas the innermost seeps show occurrence of dry thermogenic gas suggesting overcooking of the residual oil. At the front of the Ligurian nappe, or in places never covered by it, the seepages are associated with biogenic methane related to bacterial degradation of the organic-rich intervals occurring in the Pliocene and Pleistocene marine succession. The coupling of geochemical and structural analysis allows reconstructing the tectono-thermal evolution of the belt, improving our knowledge on the processes acting within the reservoir and controlling important parameters of the petroleum system, such as the reservoir porosity and its modifications, and the migration patterns.
Deepwater folding and thrusting offshore NW Borneo, SE Asia
Authors: Hesse S. , Back S. , Franke D.
Published: November 2010

The slope and deepwater portion of the offshore NW Borneo continental margin hosts a number of proven hydrocarbon accumulations. Reprocessed and post-stack depth-migrated regional 2D seismic data reveal the occurrence of an extensive series of deepwater folds located at the leading edges of imbricate thrusts. Typical thrust-top folds include (1) anticlines characterized by large interlimb angles that lack a sea-floor expression; (2) anticlines with medium interlimb angles that show a clear sea-floor expression and normal faulting in the crest; and (3) anticlines with small to medium interlimb angles, a clear sea-floor expression and intensive crestal faulting associated with partial crestal failure. The different fold types occur at specific locations within the fold–thrust system, the widest and youngest anticlines near the present-day thrust front, and the narrowest and oldest folds in the most landward parts of the fold–thrust belt. Geometric restoration of the deepwater fold–thrust system along six regional shelf-to-basin cross sections provides incremental measurements of fault- and fold-related shortening for the time between the Miocene and present day in deepwater NW Borneo. Across the study area, the main thrust and fold activity appears to be largely of Pliocene–Holocene age. An apparent maximum of both incremental and total shortening is located in the central part of the study area. This location coincides with the maximum width of the fold–thrust belt and the preferential location for the development of the most recent deepwater anticlines.
Business process modeling languages
Authors: Mili Hafedh , Tremblay Guy , Jaoude Guitta Bou , Lefebvre Éric , Elabed Lamia , Boussaidi Ghizlane El
Published: November 2010

Requirements capture is arguably the most important step in software engineering, and yet the most difficult and the least formalized one [Phalp and Shepperd 2000]. Enterprises build information systems to support their
business processes
. Software engineering research has typically focused on the development process, starting with user requirements—if that—with business modeling often confused with software system modeling [Isoda 2001]. Researchers and practitioners in management information systems have long recognized that understanding the business processes that an information system must support is key to eliciting the needs of its users (see e.g., Eriksson and Penker 2000]), but lacked the tools to model such business processes or to relate such models to software requirements. Researchers and practitioners in business administration have long been interested in modeling the processes of organizations for the purposes of understanding, analyzing, and improving such processes [Hammer and Champy 1993], but their models were often too coarse to be of use to software engineers. The advent of ecommerce and workflow management systems, among other things, has led to a convergence of interests and tools, within the broad IT community, for modeling and enabling business processes. In this article we present an overview of business process modeling languages. We first propose a categorization of the various languages and then describe representative languages from each family.
Usability of a Multimodal Video Game to Improve Navigation Skills for Blind Children
Authors: Sánchez Jaime , Saenz Mauricio , Garrido Jose Miguel
Published: November 2010

This work presents an evaluative study on the usability of a haptic device together with a sound-based video game for the development and use of orientation and mobility (O&M) skills in closed, unfamiliar spaces by blind, school-aged children. A usability evaluation was implemented for a haptic device especially designed for this study (Digital Clock Carpet) and a 3D video game (MOVA3D) in order to determine the degree to which the user accepted the device, and the level of the user’s satisfaction regarding her interaction with these products for O&M purposes. In addition, a cognitive evaluation was administered. The results show that both the haptic device and the video game are usable, accepted and considered to be pleasant for use by blind children. The results also show that they are ready to be used for cognitive learning purposes. Results from a cognitive study demonstrated significant gains in tempo-spatial orientation skills of blind children when navigating in unfamiliar spaces.
Multimodal Presentation of Two-Dimensional Charts
Authors: Abu Doush Iyad , Pontelli Enrico , Son Tran Cao , Simon Dominic , Ma Ou
Published: November 2010

Several solutions, based on aural and haptic feedback, have been developed to enable access to complex on-line and digital information contents for people with visual impairment. Nevertheless, there are several components of widely used software applications that are still beyond the reach of traditional screen readers and Braille displays. This article investigates the nonvisual accessibility issues associated with the graphing component of Microsoft Excel and proposes a novel approach and system. The goal is to provide flexible multi-modal presentation schemes which can help visually impaired users in comprehending the most commonly used two dimensional business charts, demonstrated within the familiar context of Excel charts. The methodology identifies the need for three distinct strategies used in the user interaction with a chart:
exploratory, guided
, and
summarization
. These methodologies have been implemented using a multimodal approach, which combines aural cues, speech commentaries, and 3-dimensional haptic feedback. The prototype implementation and the preliminary studies suggest that the multimodality can be effectively realized and users denote preferences in intertwining these methodologies to gain understanding of the content of charts. These methodologies have been implemented in a system, which makes use of the Novint Falcon haptic device and integrated as a plug-in in Microsoft Excel.
Hypertext 2010 conference review
Authors: Chin Alvin
Published: November 2010

The Hypertext conference is SIGWEB's flagship conference every year on hypertext and hypermedia. This year's Hypertext 2010 was the 21st ACM Conference on Hypertext and Hypermedia and was held at the University of Toronto campus in Toronto, Canada from June 13--16, 2010. Everyone enjoyed the hospitality of the local conference committee and student volunteers, which made the conference run smoothly and efficiently. The General Chair for Hypertext 2010 was Mark Chignell from the University of Toronto, and the Program Chair was Elaine Toms from Dalhousie University in Halifax, Nova Scotia, Canada.
On the Exact Solution of a Generalized Polya Process
Authors: Konno Hidetoshi
Published: November 2010

There are two types of master equations in describing nonequilibrium phenomena with memory effect: (i) the memory function type and (ii) the nonstationary type. A generalized Polya process is studied within the framework of a non‐stationary type master equation approach. For a transition‐rate with an arbitrary time‐dependent relaxation function, the exact solution of a generalized Polya process is obtained. The characteristic features of temporal variation of the solution are displayed for some typical time‐dependent relaxation functions reflecting memory in the systems.
Community-Based Screening for Infantile Anemia in an Okinawan Village, Japan
Authors: Hokama Tomiko , Yogi Chiemi , Binns Colin W. , Lee Andy H.
Published: November 2010

Infancy is a vulnerable age group for anemia throughout the world. However, community-based screening for infantile anemia is seldom reported. This study determined the prevalence of anemia among infants in an Okinawan village from 2003 to 2008, in relation to secondary prevention of the condition. The prevalence among infants aged 3–5, 6–12 and 16–23 months was 12.3%, 15.8%, and 4.2%, respectively, based on cross-sectional surveys (n=3070), and was 11.0%, 17.2%, and 3.9% according to another retrospective cohort study (n=511). The relatively low prevalence of anemia at early childhood suggested that previous detection and treatment through early and late infantile screening had been successful.