bluuebunny/crossref_metadata_2025 huggingface dataset:
Magnetic resonance studies of the low-dimensional magnet NaFe(WO4)2
Authors: Dergachev K. G. , Kobets M. I. , Khatsko E. N.
Published: May 2005

Magnetic resonance studies of the low-dimensional monoclinic compound NaFe(WO4)2 are carried out in the frequency range 25–142 GHz and temperature range 1.8–300 K. The EPR data near the phase transition attest to the two-dimensionality of the magnetic structure of NaFe(WO4)2. The frequency-field relation of the AFMR spectrum shows that this compound is a biaxial antiferromagnet. The characteristic parameters of the AFMR energy spectrum are determined: the values of the energy gaps ν1=141 GHz and ν2=168.7 GHz, the anisotropy fields Ha1=10.5 kOe and Ha2=15 kOe, and the exchange field He=121 kOe. The ratio of the intralayer to the interlayer exchange is estimated. Additional absorption is observed due to local modes caused by destruction of the translational order of the magnetic structure.
Elastic aspects of domain quadruplets in ferroics
Authors: Mokrý P. , Fousek J.
Published: May 2005

Coexistence of ferroelectric ferroelastic domains in some materials plays an important role in practical area of domain engineering. Here the problem is discussed theoretically from the point of view of elastic aspects. Domain quadruplets are considered, i.e., systems of four ferroelastic domains coinciding along one intersection line. Conditions at which the elastic energy of quadruplets is zero are specified; they would allow for the existence of permissible quadruplets. The problem has been solved for the species m3¯m-mxmy2z, m3¯m-2xymx¯ymz, m3¯m-3m, and m3¯m-4mm. It is shown that, in general, no mechanically compatible (stress-free) permissible quadruplets exist. The results make it possible to specify those conditions for spontaneous strain components which must be complied to allow for energetically acceptable quadruplets. These conditions are fulfilled in the orthorhombic phase of KNbO3. The theoretical approach offered in this paper can be used for specific discussions of the existence of multidomain states in thin films where some components of spontaneous strain need not play an essential role.
Dynamic range of nanotube- and nanowire-based electromechanical systems
Authors: Postma H. W. Ch. , Kozinsky I. , Husain A. , Roukes M. L.
Published: May 2005

Nanomechanical resonators with high aspect ratio, such as nanotubes and nanowires are of interest due to their expected high sensitivity. However, a strongly nonlinear response combined with a high thermomechanical noise level limits the useful linear dynamic range of this type of device. We derive the equations governing this behavior and find a strong dependence [∝d(d∕L)5] of the dynamic range on aspect ratio.
All-or-none switching of transcriptional activity on single DNA molecules caused by a discrete conformational transition
Authors: Yamada Ayako , Kubo Koji , Nakai Tonau , Yoshikawa Kenichi , Tsumoto Kanta
Published: May 2005

Recently, it has been confirmed that long duplex DNA molecules with a size larger than several tens of kilo-base pairs (kbp), exhibit a discrete conformational transition from an unfolded coil state to a folded compact state upon the addition of various kinds of chemical species that usually induce DNA condensation. In this study, we performed a single-molecule observation on a large DNA, Lambda ZAP II DNA (∼41kbp), in a solution containing RNA polymerase and substrates along with spermine, a tetravalent cation, at different concentrations, by use of fluorescence staining of both DNA and RNA. We found that transcription, or RNA production, is completely inhibited in the compact globule state, but is actively performed in the unfolded coil state. Such an all-or-none effect on transcriptional activity induced by the discrete conformational transition of single DNA molecules is discussed in relation to the mechanism of the regulation of large-scale genetic activity.
Microfluidic application-specific integrated device for monitoring direct cell-cell communication via gap junctions between individual cell pairs
Authors: Lee Philip J. , Hung Paul J. , Shaw Robin , Jan Lily , Lee Luke P.
Published: May 2005

Direct cell-cell communication between adjacent cells is vital for the development and regulation of functional tissues. However, current biological techniques are difficult to scale up for high-throughput screening of cell-cell communication in an array format. In order to provide an effective biophysical tool for the analysis of molecular mechanisms of gap junctions that underlie intercellular communication, we have developed a microfluidic device for selective trapping of cell-pairs and simultaneous optical characterizations. Two different cell populations can be brought into membrane contact using an array of trapping channels with a 2μm by 2μm cross section. Device operation was verified by observation of dye transfer between mouse fibroblasts (NIH3T3) placed in membrane contact. Integration with lab-on-a-chip technologies offers promising applications for cell-based analytical tools such as drug screening, clinical diagnostics, and soft-state biophysical devices for the study of gap junction protein channels in cellular communications. Understanding electrical transport mechanisms via gap junctions in soft membranes will impact quantitative biomedical sciences as well as clinical applications.
GaN-based light-emitting diodes with indium tin oxide texturing window layers using natural lithography
Authors: Horng R. H. , Yang C. C. , Wu J. Y. , Huang S. H. , Lee C. E. , Wuu D. S.
Published: May 2005

There is a significant gap between the internal and external efficiencies of conventional GaN light-emitting diodes (LEDs). The reason for this shortfall is the narrow escape cone for light in high refractive index semiconductors. In this letter, the p-side-up GaN∕sapphire LEDs with surface textured indium tin oxide (ITO) widow layers were investigated using natural lithography with polystyrene spheres as the etching mask. Under optimum etching conditions, the surface roughness of the ITO film can reach 140 nm while the polystyrene sphere on the textured ITO surface is maintained at about 250–300 nm in diameter. The output power of the ITO∕GaN LED with and without surface texturing is 10.9, and 8.5 mW at 20 mA, respectively. The LEDs fabricated using the surface-textured ITO produced an output power that exceeded that of the planar-surface LED by about 28% at 20 mA.
Domain resonance in two-dimensional periodically poled ferroelectric resonator
Authors: Ostrovskii I. V. , Nadtochiy A. B.
Published: May 2005

A two-dimensional periodically poled ferroelectric resonator is reported. The theoretical calculations, computer simulations by the finite element method and experimental data from the lithium tantalite samples reveal a domain acoustoelectric resonance. A polarization inversion in a y-rotated cut of a ferroelectric chip is done. A distribution of an electric potential over crystal surface may be an effective experimental tool for characterization of the periodically poled ferroelectrics.
Integrated chirp compensation in a monolithic passively mode-locked semiconductor diode laser
Authors: Flynn Michael B. , O’Faolain Liam , Krauss Thomas F.
Published: May 2005

We present traveling wave numerical simulations of passively mode-locked diode lasers that incorporate chirp compensation monolithically using a Fabry–Pérot interferometer, which provides a negative group delay. Numerical results show pulse compression of up to 65%. Time-frequency domain study of the pulses reveal a significant reduction in chirp across the pulse. Limitations of this simple linear chirp compensation scheme are examined.
Epitaxially grown La-modified BiFeO3 magnetoferroelectric thin films
Authors: Lee Dongeun , Kim Min G. , Ryu Sangwoo , Jang Hyun M. , Lee Sang G.
Published: May 2005

Effects of the La modification on the structure and magnetoferroelectric properties of BiFeO3 (BFO)-based films were examined. On SrTiO3 (001) planes, all the BFO-based films (for x between 0 and 0.15 in Bi1−xLaxFeO3 with the film thickness of 300 nm) were grown epitaxially along [001] direction of tetragonal symmetry. However, the La modification gradually changes the film structure from a monoclinically tilted state to a nontilted tetragonal-like state. Both extended x-ray absorption fine structure and x-ray absorption near edge structure spectra revealed the presence of a strong in-plane compressive stress. Room-temperature magnetization-field curves indicated that the saturation magnetization of these BFO-based epitaxial films increased with the degree of La modification. La-modified BFO film capacitors fabricated on SrRuO3-buffered SrTiO3 (001) substrates showed fatigue-free ferroelectric switching characteristics up to 4×1010 read∕write cycles at a frequency of 1 MHz.
Cd
2
+
∕
N
H
3
treatment-induced formation of a CdSe surface layer on CuGaSe2 thin-film solar cell absorbers
Authors: Bär M. , Lehmann S. , Rusu M. , Grimm A. , Kötschau I. , Lauermann I. , Pistor P. , Sokoll S. , Schedel-Niedrig Th. , Lux-Steiner M. Ch. , Fischer Ch.-H. , Weinhardt L. , Heske C. , Jung Ch.
Published: May 2005

Cu Ga Se 2 (CGSe)-based high-gap thin-film solar cells have to date not reached their potential level of electrical performance. In order to elucidate possible shortcomings of the electronic interface structure, we have studied the initial stage of the CdS∕CGSe interface formation by use of a simple Cd2+∕NH3 treatment. As in the case of low-gap chalcopyrites, we find a Cd-containing surface layer, in the present case comprised of approximately one monolayer of CdSe. The results indicate that the CdS∕CGSe interface is not abrupt, but contains intermediate layers. Furthermore, they shed light on possible surface modification schemes to enhance the overall performance of high-gap CGSe chalcopyrite solar cells.
Shifting Identities in a Shifting World: Food, Place, Community, and the Politics of Scale in an Inuit Settlement
Authors: Gombay Nicole
Published: May 2005

Using the case of an Inuit settlement in Northern Québec I explore the interactions between place, identity, scale, and the construction of community. This case study provides a discussion of what a relational construction of the identity of place means in practice. Focusing on country foods—foods that people catch from the land, water, and sky—I describe how the getting of these foods affects Inuit notions of place and constructions of identity and community. Sharing country foods is required in order to ensure future success in hunting and fishing. Such sharing and the social capital it generates were prerequisites for survival in the days when Inuit were living on the land in communities that were constantly changing as people traveled from one location to another in search of food. The move to settlements has brought about changes in Inuit notions of sharing food and ideas about identity. By using a particular event in one Inuit community, I explore the ways in which Inuit have developed a relational sense of identity as a result of the changing places and scales in which they live as occupants of fixed settlements who retain the mores of life on the land. As they call upon different identities, Inuit are invisibly shifting between places. I argue that there is a distinction between a settlement and a community, and that as people adjust to life in settlements they learn to manage their shifting places and shifting identities strategically so that they are able to benefit maximally from the conventions appropriate to both life on the land and life within settlements.
The Possibility of Nonsectarian Futures: Emerging Disruptive Identities of Place in the Belfast of Ciaran Carson's The Star Factory
Authors: Stainer Jonathan
Published: May 2005

In this paper I aim to excavate and interpret a series of ‘disruptive’ narratives of place in the novel The Star Factory by Ciaran Carson, a series of prose essays which construct an intimate, remembered, and defining vision of the city of Belfast (1997, Granta, London). I argue throughout that conflict in Northern Ireland is underwritten and informed by the imaginative geographies of rival, antagonistic, and sterile forms of sectarian nationalism, and that it is therefore necessary to seek alternative means of conceptualising social space and ‘the city’ which do not rely on narrow cultural categories and arbiters of difference. The text articulates an imaginative reinvention of the city of Belfast which goes beyond the traditional (and problematic) narratives of sectarianism, suggesting that place identity and the urban geographical experience are characterised by fluidity, hybridity, and changing perspectives.
Perceptual Grouping in Pigeons
Authors: Nagasaka Yasuo , Hori Koji , Osada Yoshihisa
Published: May 2005

Animal studies reveal that many species perceive partially occluded objects in the same way as do humans. Pigeons have been a notable exception. We re-investigated this anomaly of pigeon perception using a different approach from previous studies. With our method, we show that pigeons perceive occluded objects in the same manner as do other species. In addition, we report that pigeons can recognize perceptually transparent surfaces when the effect is induced by the same perceptual mechanisms as occlusion. These results give behavioral evidence that the perception of both occlusion and transparency is a common visual function shared by pigeons and humans, despite the structural differences between their visual systems.
The effect of biosolids on cereals in central New South Wales, Australia. 1. Crop growth and yield
Authors: Cooper J. L.
Published: May 2005

Two forms of biosolids, with and without lime, were applied to acid soils at 2 sites in central New South Wales. Wheat and triticale were then grown on these sites to determine the effect of biosolids on crop growth and yield. The forms of biosolids used were dewatered sewage sludge cake, and N-Viro Soil which is a lime amended sewage sludge. Dewatered sewage sludge cake was applied at rates of 0, 6, 12 and 24 dry Mg/ha, and N-Viro soil at 0, 1.5, 3.0 and 4.5 dry Mg/ha. Biosolids produced grain yield increases of over 50% at both sites, with the largest yield increases at the highest rate of dewatered sewage sludge. Continued cropping at 1 of the sites showed that significant yield increases were still obtained 3 years after the initial application. The addition of lime and N-Viro Soil raised soil pH, and produced small but long lasting yield increases. However, the main benefit of biosolids seems to have come from the nutrients they supplied rather than changes in soil pH.
Effect of continuous and time-control grazing on grassland components in south-eastern Australia
Authors: Dowling P. M. , Kemp D. R. , Ball P. D. , Langford C. M. , Michalk D. L. , Millar G. D. , Simpson P. C. , Thompson R. P.
Published: May 2005

Declining grassland productivity is a major concern in southern temperate Australia. Continuous grazing is thought to be a primary contributor to this decline, which is associated with the loss of perennial grasses. Landholders are evaluating grazing management strategies that might curb the loss of perennials and increase long-term productivity. This study reports on a comparison between continuous grazing and time-control grazing with sheep and cattle using a paired-paddock design at 5 locations in south-eastern Australia (lat. 30–42°S) over 6 years (1994–99). Pasture herbage mass, grassland species composition and basal cover of perennial grasses were assessed at 6-monthly intervals. Species abundance data were analysed by ANOVA, ordination (multi-dimensional scaling) and splining procedures to assess comparative trends between the 2 management treatments at each site. Species were categorised into major functional groups for analysis. Over all 5 sites there were few consistent differences between management treatments (continuous grazing v. time-control grazing). Basal cover was greater on the time-control grazing management compared with continuous grazing for most of the experimental period at 3 sites, but the initial values were also greater, resulting in a non-significant management × time interaction. Based on this study, we conclude that there was no apparent medium-term benefit of a multi-paddock rotational (time-control grazing) grazing system over continuous grazing for encouraging and maintaining a favourable botanical composition. The benefits for land managers from employing systems such as time-control grazing may accrue through other mechanisms. The study also highlights some of the difficulties with conducting on-farm paired-paddock research.
Comparative studies on salt tolerance of seedlings for one cultivar of puccinellia (Puccinellia ciliata) and two cultivars of tall wheatgrass (Thinopyrum ponticum)
Authors: Zhang B. , Jacobs B. C. , O'Donnell M. , Guo J.
Published: May 2005

Salt tolerances of 3 cultivars, Menemen puccinellia (Puccinellia ciliata Bor), Tyrrell and Dundas [tall wheatgrass, Thinopyrum ponticum (Podp.) Z. W. Liu and R. R. C. Wang], were compared with respect to their seed germination, adaptive responses to salt and waterlogging, seedling emergence, plant growth, shoot osmolality and mineral contents in a series of salt-stress experiments. An inverse normal distribution provided good fits for the time to seed germination. Under NaCl stress, 50% of the control (distilled water) seed germination rates of Menemen, Tyrrell and Dundas were achieved in 178.8, 300.9 and 296.8 mmol/L NaCl, respectively. Fifty percent of the control seedling emergence rates of these 3 cultivars were in 92.7, 107.2 and 113.5 mmol/L NaCl, respectively. The seed germination rates of these 3 cultivars under both salt and waterlogging stress were far lower than those germinated only under salt stress at the same salt level. Seed pretreatment by soaking seed in NaCl solutions greatly increased the seed germination rate under salt stress for Menemen and under both salt stress and waterlogging for Dundas. Tyrrell and Dundas were very similar in their tolerance to salt stress, and were significantly (P<0.05) more salt tolerant than Menemen in terms of seed germination and seedling emergence rate. Both shoot height and dry matter of these 3 cultivars were not statistically different among all salt stress levels during the seedling elongation period, indicating that the established plants of these 3 cultivars were very salt tolerant. The salt tolerance mechanisms of these 3 cultivars are possibly related to their abilities to maintain high osmolality in shoots by regulating high sodium and potassium contents, and reducing calcium deficiency under salt stress.
The potential for developing fodder plants for the salt-affected areas of southern and eastern Australia: an overview
Authors: Rogers M. E. , Craig A. D. , Munns R. E. , Colmer T. D. , Nichols P. G. H. , Malcolm C. V. , Barrett-Lennard E. G. , Brown A. J. , Semple W. S. , Evans P. M. , Cowley K. , Hughes S. J. , Snowball R. , Bennett S. J. , Sweeney G. C. , Dear B. S. , Ewing M. A.
Published: May 2005

This paper reviews the major issues that impact upon the development of improved fodder species for saline environments across temperate Australia. It describes past and present research that has been, or is being, undertaken towards improvements in salt tolerance in forage species within Australia in relation to the principal regions where salinity occurs. It includes a discussion on the mechanisms of salt tolerance in plants. An extensive list of known or potential salt-tolerant fodder species is provided and the key opportunities for advancement within each of the 4 major forage groups: grasses, legumes, herbs and shrubs are discussed. Constraints to developing new salt and waterlogging tolerant fodder species are identified. A number of recommendations are made for research that should ensure that Australian producers have access to a new array of productive fodder species suited to saline environments.
Impacts of retained wheat stubble on canola in southern New South Wales
Authors: Bruce S. E. , Kirkegaard J. A. , Pratley J. E. , Howe G. N.
Published: May 2005

Field experiments were conducted in southern New South Wales to determine the effect of surface-retained wheat stubble on the emergence, growth and yield of canola. The 5 experiments included treatments to investigate the impact of stubble load, stubble cultivar and level of decomposition as well as the impact of different environments on the crop response. Overall, 5 t/ha of surface-retained wheat stubble reduced the rate of emergence, plant establishment (mean reduction 33%), vegetative biomass (–56%) and yield (–23%), although the impact varied with site and season. Laboratory experiments assessing the phytoxicity of stubble revealed the possible role of allelopathy in the growth response at 1 site; however, there was no correlation between laboratory phytotoxicity of different stubble cultivars and their impact on canola growth at any other site. Wheat stubble comprising thinner stems (lower straw linear density) had a greater impact on emergence at 2 of the sites, indicating a possible role of reduced light penetration in the growth response. Colder temperatures on the surface of the stubble also reduced emergence and growth, and caused seedling death at the coldest sites. The experiments confirm the widely observed phenomenon of poor canola growth in surface-retained wheat stubble, and suggest several possible mechanisms for the effect, although further studies are required to determine their relative importance in different environments.
Association of pronuclear Z score with rates of aneuploidy in in vitro-fertilised embryos
Authors: Edirisinghe W. R. , Jemmott R. , Smith C. , Allan J.
Published: May 2005

The present study aimed to correlate the Z-scoring system to outcomes in in vitro fertilisation (IVF) cycles performed in conjunction with preimplantation genetic diagnosis. In 178 cycles, a total of 468 pronuclear embryos was scored prospectively using the Z score before culture and biopsy on Day 3 to detect chromosomes 13, 16, 18, 21, 22, X and Y. The results showed significant differences between Z1 and Z4 scoring embryos, with Z1 giving an increased biopsy rate (83.3% v. 51.1%), embryo quality (≥fair: 83.3% v. 57.8%) and embryo growth rate (≥six cells: 87.0% v. 44.4%). The incidence of chromosomally normal embryos decreased from Z1 to Z4 (Z1: 40%; Z2: 29.7%; Z3: 22.7%; Z4: 13.6%; P < 0.04). Thus, the Z scoring, mainly Z1 and Z4, correlated significantly with the expected embryo outcomes and preimplantation genetic diagnosis findings. Further improvement of pronuclear scoring with the use of a two-stage assessment is proposed.
Effect of inclusion of serum and granulocyte - macrophage colony stimulating factor on secretion of interferon-τ during the in vitro culture of ovine embryos
Authors: Rooke John , Ewen Morag , McEvoy Tom , Entrican Gary , Ashworth Cheryl
Published: May 2005

In each of three experiments, in vitro-matured and -fertilised zygotes were cultured to Day 7 post insemination in synthetic oviductal fluid (SOF). In Experiment 1, zygotes were cultured in groups in either SOF plus albumin (SOFA) or serum (SOFS) and then blastocysts were cultured individually for a further 24 h without a change of media. In Experiment 2, zygotes were cultured in groups using a 2 × 2 factorial design in SOFA or SOFS, with or without recombinant ovine granulocyte–macrophage colony stimulating factor (GM-CSF; 5 ng mL−1). Blastocysts were then cultured individually using a split-plot design in SOFA or SOFS with or without GM-CSF. In Experiment 3, zygotes were cultured in SOFA in which GM-CSF was absent (A) or present (P) during Days 1–3, Days 3–5 or Days 5–7 of IVC in six combinations as follows: AAA, AAP, APP, PPP, PPA and PAA. Serum or GM-CSF increased secretion of interferon (IFN)-τ in Experiments 1 and 2 both between Days 5 and 7 of group culture and during individual culture. Secretion of IFN-τ during individual culture was determined by the medium in which embryos were group cultured and the effects of GM-CSF and serum were not additive. In Experiment 3, the presence of GM-CSF between Days 1 and 3 of culture was responsible for stimulation of secretion of IFN-τ between Days 5 and 7; IFN-τ secretion was detected as early as Day 3 post insemination.
Sensitive detection of human papillomavirus in cervical, head/neck, and schistosomiasis-associated bladder malignancies
Authors: Yang H. , Yang K. , Khafagi A. , Tang Y. , Carey T. E. , Opipari A. W. , Lieberman R. , Oeth P. A. , Lancaster W. , Klinger H. P. , Kaseb A. O. , Metwally A. , Khaled H. , Kurnit D. M.
Published: May 2005

We assayed for the presence of human papilloma virus (HPV) DNA in serum and/or peripheral blood fraction (PBF) of individuals with cervical, head/neck, or bladder cancer due to schistosomiasis. Using mass spectroscopy coupled with competitive PCR, HPV DNA was detected at the individual molecule level by using “MassARRAY” assays. The resultant sensitivity was superior to real-time fluorescent PCR-based assays, while specificity was maintained. Our principal findings were: (
i
) Virtually all tested cervical cancers and schistosomiasis-associated bladder cancers, and a plurality of head/neck cancers, are associated with HPV DNA in the tumor. (
ii
) All 27 bladder cancers due to schistosomiasis were associated with the presence of HPV-16 DNA, which can be detected in tumor and serum but not in PBF. In contrast, no serum HPV-16 DNA signal was detected in seven individuals with schistosomiasis-associated bladder cancers after surgical removal of the tumor. (
iii
) Among the head/neck cancers we studied, anterior tumors were more often associated with HPV DNA in tumor, serum, and/or PBF than posterior tumors. (
iv
) In cervical cancer, where all tumors contain HPV DNA, viral DNA could be detected often in serum and/or PBF. Further, HPV-16 DNA was detected in serum and/or PBF of most patients with untreated high-grade cervical dysplasia but disappeared if the dysplasia was eliminated. The sensitive, specific, and quantitative MassARRAY technique should make it feasible to monitor cancer occurrence and treatment and recurrence of malignancies and dysplasias associated with HPV DNA.
Targeted expression of the inositol 1,4,5-triphosphate receptor (IP
3
R) ligand-binding domain releases Ca
2+
via endogenous IP
3
R channels
Authors: Várnai Péter , Balla András , Hunyady László , Balla Tamas
Published: May 2005

Virtually all functions of a cell are influenced by cytoplasmic [Ca
2+
] increases. Inositol 1,4,5-trisphosphate receptor (IP
3
R) channels, located in the endoplasmic reticulum (ER), release Ca
2+
in response to binding of the second messenger, IP
3
.IP
3
Rs thus are part of the information chain interpreting external signals and transforming them into cytoplasmic Ca
2+
transients. IP
3
Rs function as tetramers, each unit comprising an N-terminal ligand-binding domain (LBD) and a C-terminal channel domain linked by a long regulatory region. It is not yet understood how the binding of IP
3
to the LBD regulates the gating properties of the channel. Here, we use the expression of IP
3
binding protein domains tethered to the surface of the endoplasmic reticulum (ER) to show that the all-helical domain of the IP
3
R LBD is capable of depleting the ER Ca
2+
pools by opening the endogenous IP
3
Rs, even without IP
3
binding. This effect requires the domain to be within 50 Å of the ER membrane and is impaired by the presence of the N-terminal inhibitory segment on the LBD. These findings raise the possibility that the helical domain of the LBD functions as an effector module possibly interacting with the channel domain, thereby being part of the gating mechanisms by which the IP
3
-induced conformational change within the LBD regulates Ca
2+
release.
The worldwide air transportation network: Anomalous centrality, community structure, and cities' global roles
Authors: Guimerà R. , Mossa S. , Turtschi A. , Amaral L. A. N.
Published: May 2005

We analyze the global structure of the worldwide air transportation network, a critical infrastructure with an enormous impact on local, national, and international economies. We find that the worldwide air transportation network is a scale-free small-world network. In contrast to the prediction of scale-free network models, however, we find that the most connected cities are not necessarily the most central, resulting in anomalous values of the centrality. We demonstrate that these anomalies arise because of the multicommunity structure of the network. We identify the communities in the air transportation network and show that the community structure cannot be explained solely based on geographical constraints and that geopolitical considerations have to be taken into account. We identify each city's global role based on its pattern of intercommunity and intracommunity connections, which enables us to obtain scale-specific representations of the network.
Optical routing and sensing with nanowire assemblies
Authors: Sirbuly Donald J. , Law Matt , Pauzauskie Peter , Yan Haoquan , Maslov Alex V. , Knutsen Kelly , Ning Cun-Zheng , Saykally Richard J. , Yang Peidong
Published: May 2005

The manipulation of photons in structures smaller than the wavelength of light is central to the development of nanoscale integrated photonic systems for computing, communications, and sensing. We assemble small groups of freestanding, chemically synthesized nanoribbons and nanowires into model structures that illustrate how light is exchanged between subwavelength cavities made of three different semiconductors. The coupling strength of the optical linkages formed when nanowires are brought into contact depends both on their volume of interaction and angle of intersection. With simple coupling schemes, lasing nanowires can launch coherent pulses of light through ribbon waveguides that are up to a millimeter in length. Also, interwire coupling losses are low enough to allow light to propagate across several right-angle bends in a grid of crossed ribbons. The fraction of the guided wave traveling outside the wire/ribbon cavities is used to link nanowires through space and to separate colors within multiribbon networks. In addition, we find that nanoribbons function efficiently as waveguides in liquid media and provide a unique means for probing molecules in solution or in proximity to the waveguide surface. Our results lay the spadework for photonic devices based on assemblies of active and passive nanowire elements and presage the use of nanowire waveguides in microfluidics and biology.
No association between microsomal triglyceride transfer protein (
MTP
) haplotype and longevity in humans
Authors: Nebel Almut , Croucher Peter J. P. , Stiegeler Rieke , Nikolaus Susanna , Krawczak Michael , Schreiber Stefan
Published: May 2005

Human longevity is a multifactorial condition with a significant genetic contribution. A recent association study in two independent samples of long-lived U.S. Caucasians [long-lived individuals (LLI)] identified a SNP haplotype of the microsomal triglyceride transfer protein (
MTP
, 4q25) that was underrepresented among LLI when compared with younger controls. This suggested that variation in the
MTP
gene might modify human longevity. Because of its function in lipid metabolism, the
MTP
gene product could plausibly play a pivotal role in the physiology of aging. However, the association observed in the U.S. samples could not be replicated by the same authors in a larger French LLI sample. We have therefore investigated the
MTP
“risk” haplotype in our own collection of 1,589 German nonagenarians, centenarians, and appropriately matched controls. No statistically significant differences were observed between LLI and controls at the allele, genotype, or haplotype level. This indicates that a noteworthy influence of the respective
MTP
haplotype on human longevity in the German population is unlikely. Furthermore, in comparison with all other U.S. and European samples analyzed, the
MTP
“risk” haplotype was found to be overrepresented only in the U.S. controls. This implies that the putative association is more likely to reflect recent changes in the genetic structure of the U.S. Caucasian population as a whole, rather than genetic effects upon survival to old age. In our view, the original study therefore highlights potential problems that arise when the case-control design is used as a means to map longevity genes in humans.
Theoretical model of prion propagation: A misfolded protein induces misfolding
Authors: Małolepsza Edyta , Boniecki Michał , Kolinski Andrzej , Piela Lucjan
Published: May 2005

There is a hypothesis that dangerous diseases such as bovine spongiform encephalopathy, Creutzfeldt-Jakob, Alzheimer's, fatal familial insomnia, and several others are induced by propagation of wrong or misfolded conformations of some vital proteins. If for some reason the misfolded conformations were acquired by many such protein molecules it might lead to a “conformational” disease of the organism. Here, a theoretical model of the molecular mechanism of such a conformational disease is proposed, in which a metastable (or misfolded) form of a protein induces a similar misfolding of another protein molecule (conformational autocatalysis). First, a number of amino acid sequences composed of 32 aa have been designed that fold rapidly into a well defined native-like α-helical conformation. From a large number of such sequences a subset of 14 had a specific feature of their energy landscape, a well defined local energy minimum (higher than the global minimum for the α-helical fold) corresponding to β-type structure. Only one of these 14 sequences exhibited a strong autocatalytic tendency to form a β-sheet dimer capable of further propagation of protofibril-like structure. Simulations were done by using a reduced, although of high resolution, protein model and the replica exchange Monte Carlo sampling procedure.
Rapid identification and strain-typing of respiratory pathogens for epidemic surveillance
Authors: Ecker David J. , Sampath Rangarajan , Blyn Lawrence B. , Eshoo Mark W. , Ivy Cristina , Ecker Joseph A. , Libby Brian , Samant Vivek , Sannes-Lowery Kristin A. , Melton Rachael E. , Russell Kevin , Freed Nikki , Barrozo Chris , Wu Jianguo , Rudnick Karl , Desai Anjali , Moradi Emily , Knize Duane J. , Robbins David W. , Hannis James C. , Harrell Patina M. , Massire Christian , Hall Thomas A. , Jiang Yun , Ranken Raymond , Drader Jared J. , White Neill , McNeil John A. , Crooke Stanley T. , Hofstadler Steven A.
Published: May 2005

Epidemic respiratory infections are responsible for extensive morbidity and mortality within both military and civilian populations. We describe a high-throughput method to simultaneously identify and genotype species of bacteria from complex mixtures in respiratory samples. The process uses electrospray ionization mass spectrometry and base composition analysis of PCR amplification products from highly conserved genomic regions to identify and determine the relative quantity of pathogenic bacteria present in the sample. High-resolution genotyping of specific species is achieved by using additional primers targeted to highly variable regions of specific bacterial genomes. This method was used to examine samples taken from military recruits during respiratory disease outbreaks and for follow up surveillance at several military training facilities. Analysis of respiratory samples revealed high concentrations of pathogenic respiratory species, including
Haemophilus influenzae
,
Neisseria meningitidis
, and
Streptococcus pyogenes
. When
S. pyogenes
was identified in samples from the epidemic site, the identical genotype was found in almost all recruits. This analysis method will provide information fundamental to understanding the polymicrobial nature of explosive epidemics of respiratory disease.
Loblolly pine abietadienol/abietadienal oxidase
PtAO
(CYP720B1) is a multifunctional, multisubstrate cytochrome P450 monooxygenase
Authors: Ro Dae-Kyun , Arimura Gen-Ichiro , Lau Stephen Y. W. , Piers Edward , Bohlmann Jörg
Published: May 2005

Cytochrome P450 monooxygenases (P450s) are important enzymes for generating some of the enormous structural diversity of plant terpenoid secondary metabolites. In conifers, P450s are involved in the formation of a suite of diterpene resin acids (DRAs). Despite their important role in constitutive and induced oleoresin defense, a P450 gene of DRA formation has not yet been identified. By using phylogenetic cluster analysis of P450-like ESTs from loblolly pine (
Pinus taeda
), functional cDNA screening in yeast (
Saccharomyces cerevisiae
), and
in vitro
enzyme characterization, we cloned and identified a multifunctional and multisubstrate cytochrome P450 enzyme, CYP720B1 [abietadienol/abietadienal oxidase (
PtAO
)]. PtAO catalyzes an array of consecutive oxidation steps with several different diterpenol and diterpenal intermediates in loblolly pine DRA biosynthesis. Recombinant PtAO oxidized the respective carbon 18 of abietadienol, abietadienal, levopimaradienol, isopimara-7,15-dienol, isopimara-7,15-dienal, dehydroabietadienol, and dehydroabietadienal with apparent Michaelis–Menten (
K
m
) values of 0.5–5.3 μM. PtAO expressed in yeast also catalyzed
in vivo
oxidation of abietadiene to abietic acid, but with activity much lower than with abietadienol or abietadienal. Consistent with a role of DRAs in conifer defense,
PtAO
transcript levels increased upon simulated insect attack using methyl jasmonate treatment of loblolly pine. The multisubstrate, multifunctional P450 diterpene oxidase PtAO, in concert with expression of a family of single-product and multiproduct diterpene synthases, allows for formation of a diverse suite of DRA defense metabolites in long-lived conifers.
Increased glutathione
S
-transferase activity rescues dopaminergic neuron loss in a
Drosophila
model of Parkinson's disease
Authors: Whitworth Alexander J. , Theodore Dorothy A. , Greene Jessica C. , Beneš Helen , Wes Paul D. , Pallanck Leo J.
Published: May 2005

Loss-of-function mutations of the
parkin
gene are a major cause of early-onset parkinsonism. To explore the mechanism by which loss of
parkin
function results in neurodegeneration, we are using a genetic approach in
Drosophila
. Here, we show that
Drosophila parkin
mutants display degeneration of a subset of dopaminergic (DA) neurons in the brain. The neurodegenerative phenotype of
parkin
mutants is enhanced by loss-of-function mutations of the
glutathione S-transferase S1
(
GstS1
) gene, which were identified in an unbiased genetic screen for genes that modify
parkin
phenotypes. Furthermore, overexpression of
GstS1
in DA neurons suppresses neurodegeneration in
parkin
mutants. Given the previous evidence for altered glutathione metabolism and oxidative stress in sporadic Parkinson's disease (PD), these data suggest that the mechanism of DA neuron loss in
Drosophila parkin
mutants is similar to the mechanisms underlying sporadic PD. Moreover, these findings identify a potential therapeutic approach in treating PD.
Epigenetic programming in the preimplantation rat embryo is disrupted by chronic paternal cyclophosphamide exposure
Authors: Barton Tara S. , Robaire Bernard , Hales Barbara F.
Published: May 2005

Preconceptional paternal exposure to cyclophosphamide, a widely used anticancer agent, leads to increases in embryo loss, malformations, and behavioral deficits in offspring; these abnormalities are transmissible to subsequent generations [Auroux, M., Dulioust, E., Selva, J. & Rince, P. (1990)Mutat. Res.229, 189–200]. Little information exists on the mechanisms underlying this male-mediated developmental toxicity. We assessed the impact of paternal cyclophosphamide exposure on the dynamic regulation of histone H4 acetylation at lysine 5 and DNA methylation in preimplantation rat embryos. Zygotes sired by drug-treated males displayed advanced developmental progression, increased pronuclear areas, and disruption of the epigenetic programming of both parental genomes. Early postfertilization zygotic pronuclei were hyperacetylated; by mid-zygotic development, male pronuclei were dramatically hypomethylated, whereas female pronuclei were hypermethylated. Micronuclei were substantially elevated, and histone H4 acetylation at lysine 5 localization to the nuclear periphery was disrupted in two-cell embryos fertilized by cyclophosphamide-exposed spermatozoa. This finding demonstrates that paternal exposure to this drug induces aberrant epigenetic programming in early embryos. We hypothesize that disturbances in epigenetic programming contribute to heritable instabilities later in development, emphasizing the importance of epigenetic risk assessment after chemotherapy.
Emergence of unique primate T-lymphotropic viruses among central African bushmeat hunters
Authors: Wolfe Nathan D. , Heneine Walid , Carr Jean K. , Garcia Albert D. , Shanmugam Vedapuri , Tamoufe Ubald , Torimiro Judith N. , Prosser A. Tassy , LeBreton Matthew , Mpoudi-Ngole Eitel , McCutchan Francine E. , Birx Deborah L. , Folks Thomas M. , Burke Donald S. , Switzer William M.
Published: May 2005

The human T-lymphotropic viruses (HTLVs) types 1 and 2 originated independently and are related to distinct lineages of simian T-lymphotropic viruses (STLV-1 and STLV-2, respectively). These facts, along with the finding that HTLV-1 diversity appears to have resulted from multiple cross-species transmissions of STLV-1, suggest that contact between humans and infected nonhuman primates (NHPs) may result in HTLV emergence. We investigated the diversity of HTLV among central Africans reporting contact with NHP blood and body fluids through hunting, butchering, and keeping primate pets. We show that this population is infected with a wide variety of HTLVs, including two previously unknown retroviruses: HTLV-4 is a member of a phylogenetic lineage that is distinct from all known HTLVs and STLVs; HTLV-3 falls within the phylogenetic diversity of STLV-3, a group not previously seen in humans. We also document human infection with multiple STLV-1-like viruses. These results demonstrate greater HTLV diversity than previously recognized and suggest that NHP exposure contributes to HTLV emergence. Our discovery of unique and divergent HTLVs has implications for HTLV diagnosis, blood screening, and potential disease development in infected persons. The findings also indicate that cross-species transmission is not the rate-limiting step in pandemic retrovirus emergence and suggest that it may be possible to predict and prevent disease emergence by surveillance of populations exposed to animal reservoirs and interventions to decrease risk factors, such as primate hunting.
Stress release drives symmetry breaking for actin-based movement
Authors: van der Gucht Jasper , Paluch Ewa , Plastino Julie , Sykes Cécile
Published: May 2005

By using a simple assay composed of purified proteins, we studied the spontaneous polarization of actin networks polymerizing on spherical beads, which subsequently undergo movement. We show evidence that this symmetry breaking is based on the release of elastic energy, analogous to the fracture of polymer gels. The dynamics of this process and the thickness at which it occurs depend on the growth rate and mechanical properties of the actin gel. We explain our experimental results with a model based on elasticity theory and fracture mechanics.
Anthrax lethal factor inhibition
Authors: Shoop W. L. , Xiong Y. , Wiltsie J. , Woods A. , Guo J. , Pivnichny J. V. , Felcetto T. , Michael B. F. , Bansal A. , Cummings R. T. , Cunningham B. R. , Friedlander A. M. , Douglas C. M. , Patel S. B. , Wisniewski D. , Scapin G. , Salowe S. P. , Zaller D. M. , Chapman K. T. , Scolnick E. M. , Schmatz D. M. , Bartizal K. , MacCoss M. , Hermes J. D.
Published: May 2005

The primary virulence factor of
Bacillus anthracis
is a secreted zinc-dependent metalloprotease toxin known as lethal factor (LF) that is lethal to the host through disruption of signaling pathways, cell destruction, and circulatory shock. Inhibition of this proteolytic-based LF toxemia could be expected to provide therapeutic value in combination with an antibiotic during and immediately after an active anthrax infection. Herein is shown the crystal structure of an intimate complex between a hydroxamate, (2R)-2-[(4-fluoro-3-methylphenyl)sulfonylamino]-
N
-hydroxy-2-(tetrahydro-2H-pyran-4-yl)acetamide, and LF at the LF-active site. Most importantly, this molecular interaction between the hydroxamate and the LF active site resulted in (
i
) inhibited LF protease activity in an enzyme assay and protected macrophages against recombinant LF and protective antigen in a cell-based assay, (
ii
) 100% protection in a lethal mouse toxemia model against recombinant LF and protective antigen, (
iii
) ≈50% survival advantage to mice given a lethal challenge of
B. anthracis
Sterne vegetative cells and to rabbits given a lethal challenge of
B. anthracis
Ames spores and doubled the mean time to death in those that died in both species, and (
iv
) 100% protection against
B. anthracis
spore challenge when used in combination therapy with ciprofloxacin in a rabbit “point of no return” model for which ciprofloxacin alone provided 50% protection. These results indicate that a small molecule, hydroxamate LF inhibitor, as revealed herein, can ameliorate the toxemia characteristic of an active
B. anthracis
infection and could be a vital adjunct to our ability to combat anthrax.
Involvement of clathrin and AP-2 in the trafficking of MHC class II molecules to antigen-processing compartments
Authors: McCormick Peter J. , Martina José A. , Bonifacino Juan S.
Published: May 2005

Major histocompatibility complex class II (MHC-II) molecules are composed of two polymorphic chains, α and β, which assemble with an invariant chain, Ii, in the endoplasmic reticulum. The assembled MHC-II complexes are transported to the Golgi complex and then to late endosomes/lysosomes, where Ii is degraded and αβ dimers bind peptides derived from exogenous antigens. Targeting of MHC-II molecules to these compartments is mediated by two dileucine-based signals in the cytoplasmic domain of Ii. These signals bindin vitroto two adaptor protein (AP) complexes, AP-1 and AP-2, which are components of clathrin coats involved in vesicle formation and cargo sorting. The physiological roles of these proteins in MHC-II molecule trafficking, however, remain to be addressed. Here, we report the use of RNA interference to examine the involvement of clathrin and four AP complexes (AP-1, AP-2, AP-3, and AP-4) in MHC-II molecule traffickingin vivo. We found that depletion of clathrin or AP-2 caused >10-fold increases in Ii expression on the cell surface and a concomitant decrease in Ii localization to endosomal/lysosomal vesicles. In addition, depletion of clathrin or AP-2 delayed the degradation of Ii and reduced the surface expression of peptide-loaded αβ dimers. In contrast, depletion of AP-1, AP-3, or AP-4 had little or no effect. These findings demonstrate that clathrin and AP-2 participate in MHC-II molecule traffickingin vivo. Because AP-2 is only associated with the plasma membrane, these results also indicate that a significant pool of MHC-II molecules traffic to the endosomal–lysosomal system by means of the cell surface.