bluuebunny/crossref_metadata_2025 huggingface dataset:
Iron and the translation of the amyloid precursor protein (APP) and ferritin mRNAs: riboregulation against neural oxidative damage in Alzheimer's disease
Authors: Rogers Jack T. , Bush Ashley I. , Cho Hyan-Hee , Smith Deborah H. , Thomson Andrew M. , Friedlich Avi L. , Lahiri Debomoy K. , Leedman Peter J. , Huang Xudong , Cahill Catherine M.
Published: December 2008

The essential metals iron, zinc and copper deposit near the Aβ (amyloid β-peptide) plaques in the brain cortex of AD (Alzheimer's disease) patients. Plaque-associated iron and zinc are in neurotoxic excess at 1 mM concentrations. APP (amyloid precursor protein) is a single transmembrane metalloprotein cleaved to generate the 40–42-amino-acid Aβs, which exhibit metal-catalysed neurotoxicity. In health, ubiquitous APP is cleaved in a non-amyloidogenic pathway within its Aβ domain to release the neuroprotective APP ectodomain, APP(s). To adapt and counteract metal-catalysed oxidative stress, as during reperfusion from stroke, iron and cytokines induce the translation of both APP and ferritin (an iron storage protein) by similar mechanisms. We reported that APP was regulated at the translational level by active IL (interleukin)-1 (IL-1-responsive acute box) and IRE (iron-responsive element) RNA stem–loops in the 5′ untranslated region of APP mRNA. The APP IRE is homologous with the canonical IRE RNA stem–loop that binds the iron regulatory proteins (IRP1 and IRP2) to control intracellular iron homoeostasis by modulating ferritin mRNA translation and transferrin receptor mRNA stability. The APP IRE interacts with IRP1 (cytoplasmic cis-aconitase), whereas the canonical H-ferritin IRE RNA stem–loop binds to IRP2 in neural cell lines, and in human brain cortex tissue and in human blood lysates. The same constellation of RNA-binding proteins [IRP1/IRP2/poly(C) binding protein] control ferritin and APP translation with implications for the biology of metals in AD.
Copper and the structural biology of the prion protein
Authors: Viles John H. , Klewpatinond Mark , Nadal Rebecca C.
Published: December 2008

PrP (prion-related protein) is a cell-surface Cu2+-binding glycoprotein which, when misfolded, is responsible for a number of transmissible spongiform encephalopathies. The co-ordination geometry, stoichiometry and affinity of Cu2+ for PrP are the subject of much debate. In the present paper, we review the recent progress we have made in these areas. As many as six Cu2+ ions bind to PrP with submicromolar affinity. Initially, two Cu2+ ions bind to full-length PrP in the amyloidogenic region, between the octarepeats and the structured domain, at His95 and His110. Only subsequent Cu2+ ions bind to single histidine residues within the octarepeat region. Competitive chelators have been used to determine the affinity of the first molar equivalent of Cu2+ bound to full-length PrP; this approach places the affinity in the nanomolar range. The affinity and number of Cu2+-binding sites support the suggestion that PrP could act as an antioxidant by binding potentially harmful Cu2+ ions and sacrificially quenching of free radicals generated as a result of copper redox cycling. Finally, the effect of Cu2+ on the prion structure and misassembly into oligomers and fibres is discussed.
Amyloidogenic metal-binding proteins: new investigative pathways
Authors: Davies Paul , Fontaine Sarah N. , Moualla Dima , Wang Xiaoyan , Wright Josephine A. , Brown David R.
Published: December 2008

Neurodegenerative diseases remain perplexing and problematic for modern research. Those associated with amyloidogenic proteins have often been lumped together simply because those proteins aggregate. However, research has identified a more logical reason to group some of these diseases together. The associated proteins not only aggregate, but also bind copper. The APP (amyloid precursor protein) binds copper in an N-terminal region. Binding of copper has been suggested to influence generation of β-amyloid from the protein. PrP (prion protein) binds copper, and this appears to be necessary for its normal function and might also reduce its probability of conversion into an infectious prion. α-Synuclein, a protein associated with Parkinson's disease, also binds copper, but, in this case, it potentially increases the rate at which the protein aggregates. The similarities between these proteins, in terms of metal binding, has allowed us to investigate them using similar approaches. In the present review, we discuss some of these approaches.
Investigating the pathology of Emery–Dreifuss muscular dystrophy
Authors: Brown Susan C. , Piercy Richard J. , Muntoni Francesco , Sewry Caroline A.
Published: December 2008

EDMD (Emery–Dreifuss muscular dystrophy) is caused by mutations in either the gene encoding for lamin A/C (LMNA) located at 1q21.2–q21.3 or emerin (EMD) located at Xq28. Autosomal dominant EDMD caused by LMNA mutations is more common than the X-linked form and often more severe, with an earlier onset. At the histological and histochemical levels, both X-linked and autosomal dominant EDMD appear similar. However, individuals with the same genetic disorder often show remarkable differences in clinical severity, a finding generally attributed to the genetic background. The clinical and pathological findings in EDMD patients found to have mutations in more than one gene are also discussed. There is now much interest in the phenotype of several animal models for EDMD which should lead to an increased insight into the pathogenesis of this disorder, particularly that relating to the heart phenotype.
Patterns of evolutionary conservation in the nesprin genes highlight probable functionally important protein domains and isoforms
Authors: Simpson Jennifer G. , Roberts Roland G.
Published: December 2008

The nesprins [also known as SYNEs (synaptic nuclear envelope proteins)] are a family of type II transmembrane proteins implicated in the tethering of membrane-bound organelles and in the genetic aetiology of cerebellar ataxia and Emery–Dreifuss muscular dystrophy. They are characterized by a common structure of an SR (spectrin repeat) rod domain and a C-terminal transmembrane KLS (klarsicht)/KASH [klarsicht/ANC-1 (anchorage 1)/SYNE homology] domain which interacts with SUN [Sad1p/UNC (uncoordinated)-84] proteins in the nuclear envelope; most nesprins also have N-terminal actin-binding CH (calponin homology) domains. The genes encoding the three vertebrate nesprins (five in bony fish) and the small transmembrane actin-binding protein calmin are related to each other by ancient duplications and rearrangements. In the present paper, we collate sequence data for nesprins and calmins across the vertebrate clade and use these to study evolutionary constraints acting on their genes. We show that the rod domains of the larger nesprins are composed almost entirely of unbroken SR-like structures (74 in nesprin-1 and 56 in nesprin-2) and that these range from poorly conserved purely structural elements to highly conserved regions with a presumed protein–protein interaction function. The analysis suggests several interesting regions for future study. We also assess the evolutionary and EST (expressed sequence tag) expression support for nesprin isoforms, both known and novel; our findings suggest that substantial reassessment is required.
KASH-domain proteins and the cytoskeletal landscapes of the nuclear envelope
Authors: Schneider Maria , Noegel Angelika A. , Karakesisoglou Iakowos
Published: December 2008

Over the last few years, several novel proteins have been identified that facilitate the physical integration of the nucleus with the cytoplasmic compartment. The majority belong to the evolutionarily conserved KASH [klarsicht/ANC-1 (anchorage 1)/SYNE (synaptic nuclear envelope protein) homology]-domain family, which function primarily as exclusive outer nuclear membrane scaffolds that associate with the cytoskeleton, the centrosome and the motor protein apparatus. In the present paper, we propose a novel model, which may explain why these proteins also determine nuclear architecture. Moreover, we discuss further nuclear membrane-tethering devices, which indicate collectively the presence of specific molecular mechanisms that organize the cytoplasmic–nuclear membrane interface in mammalian cells.
Towards a Drosophila model of Hutchinson–Gilford progeria syndrome
Authors: Beard Gemma S. , Bridger Joanna M. , Kill Ian R. , Tree David R.P.
Published: December 2008

The laminopathy Hutchinson–Gilford progeria syndrome (HGPS) is caused by the mutant lamin A protein progerin and leads to premature aging of affected children. Despite numerous cell biological and biochemical insights into the basis for the cellular abnormalities seen in HGPS, the mechanism linking progerin to the organismal phenotype is not fully understood. To begin to address the mechanism behind HGPS using Drosophila melanogaster, we have ectopically expressed progerin and lamin A. We found that ectopic progerin and lamin A phenocopy several effects of laminopathies in developing and adult Drosophila, but that progerin causes a stronger phenotype than wild-type lamin A.
Competition between LIM-binding domains
Authors: Matthews Jacqueline M. , Bhati Mugdha , Craig Vanessa J. , Deane Janet E. , Jeffries Cy , Lee Christopher , Nancarrow Amy L. , Ryan Daniel P. , Sunde Margaret
Published: December 2008

LMO (LIM-only) and LIM-HD (LIM-homeodomain) proteins form a family of proteins that is required for myriad developmental processes and which can contribute to diseases such as T-cell leukaemia and breast cancer. The four LMO and 12 LIM-HD proteins in mammals are expressed in a combinatorial manner in many cell types, forming a transcriptional ‘LIM code’. The proteins all contain a pair of closely spaced LIM domains near their N-termini that mediate protein–protein interactions, including binding to the ∼30-residue LID (LIM interaction domain) of the essential co-factor protein Ldb1 (LIM domain-binding protein 1). In an attempt to understand the molecular mechanisms behind the LIM code, we have determined the molecular basis of binding of LMO and LIM-HD proteins for Ldb1LID through a series of structural, mutagenic and biophysical studies. These studies provide an explanation for why Ldb1 binds the LIM domains of the LMO/LIM-HD family, but not LIM domains from other proteins. The LMO/LIM-HD family exhibit a range of affinities for Ldb1, which influences the formation of specific functional complexes within cells. We have also identified an additional LIM interaction domain in one of the LIM-HD proteins, Isl1. Despite low sequence similarity to Ldb1LID, this domain binds another LIM-HD protein, Lhx3, in an identical manner to Ldb1LID. Through our and other studies, it is emerging that the multiple layers of competitive binding involving LMO and LIM-HD proteins and their partner proteins contribute significantly to cell fate specification and development.
Topological properties of protein interaction networks from a structural perspective
Authors: Gursoy Attila , Keskin Ozlem , Nussinov Ruth
Published: December 2008

Protein–protein interactions are usually shown as interaction networks (graphs), where the proteins are represented as nodes and the connections between the interacting proteins are shown as edges. The graph abstraction of protein interactions is crucial for understanding the global behaviour of the network. In this mini review, we summarize basic graph topological properties, such as node degree and betweenness, and their relation to essentiality and modularity of protein interactions. The classification of hub proteins into date and party hubs with distinct properties has significant implications for relating topological properties to the behaviour of the network. We emphasize that the integration of protein interface structure into interaction graph models provides a better explanation of hub proteins, and strengthens the relationship between the role of the hubs in the cell and their topological properties.
Colicins exploit native disorder to gain cell entry: a hitchhiker's guide to translocation
Authors: Bonsor Daniel A. , Meenan Nicola A. , Kleanthous Colin
Published: December 2008

The translocation of protein toxins into a cell relies on a myriad of protein–protein interactions. One such group of toxins are enzymatic E colicins, protein antibiotics produced by Escherichia coli in times of stress. These proteins subvert ordinary nutrient uptake mechanisms to enter the cell and unleash nuclease activity. We, and others, have previously shown that uptake of ColE9 (colicin E9) is dependent on engagement of the OM (outer membrane) receptors BtuB and OmpF as well as recruitment of the periplasmic protein TolB, forming a large supramolecular complex. Intriguingly, colicins bind TolB using a natively disordered region to mimic the interaction of TolB with Pal (peptidoglycan-associated lipoprotein). This is thought to trigger OM instability and prime the system for translocation. Here, we review key interactions in the assembly of this ‘colicin translocon’ and discuss the key role disorder plays in achieving uptake.
FunHunt: model selection based on energy landscape characteristics
Authors: London Nir , Schueler-Furman Ora
Published: December 2008

Protein folding and binding is commonly depicted as a search for the minimum energy conformation in a vast energy landscape. Indeed, modelling of protein complex structures by RosettaDock often results in a set of low-energy conformations near the native structure. Ensembles of low-energy conformations can appear, however, in other regions of the energy landscape, especially when backbone movements occur upon binding. What then characterizes the energy landscape near the correct orientation? We have applied a machine learning algorithm to distinguish ensembles of low-energy conformations around the native conformation from other low-energy ensembles. FunHunt, the resulting classifier, identified the native orientation for 50/52 protein complexes in a test set, and for all of 12 recent CAPRI targets. FunHunt is also able to choose the near-native orientation among models created by algorithms other than RosettaDock, demonstrating its general applicability for model selection. The features used by FunHunt teach us about the nature of native interfaces. Remarkably, the energy decrease of trajectories toward near-native orientations is significantly larger than for other orientations. This provides a possible explanation for the stability of association in the native orientation. The FunHunt approach, discriminating models based on ensembles of structures that map the nearby energy landscape, can be adapted and extended to additional tasks, such as ab initio model selection, protein interface design and specificity predictions.
Modulation of the Rcs-mediated signal transfer by conformational flexibility
Authors: Rogov Vladimir V. , Schmöe Kerstin , Löhr Fank , Rogova Natalia Yu. , Bernhard Frank , Dötsch Volker
Published: December 2008

The Rcs (regulator of capsule synthesis) signalling complex comprises the membrane-associated hybrid sensor kinases RcsC and RcsD, the transcriptional regulator RcsB and the two co-inducers RcsA and RcsF. Acting as a global regulatory network, the Rcs phosphorelay controls multiple cellular pathways including capsule synthesis, cell division, motility, biofilm formation and virulence mechanisms. Signal-dependent communication of the individual Rcs domains showing histidine kinase, phosphoreceiver, phosphoryl transfer and DNA-binding activities is characteristic and essential for the modulation of signal transfer. We have analysed the structures of core elements of the Rcs network including the RcsC-PR (phosphoreceiver domain of RcsC) and the RcsD-HPt (histidine phosphotransfer domain of RcsD), and we have started to characterize the dynamics and recognition mechanisms of the proteins. RcsC-PR represents a typical CheY-like α/β/α sandwich fold and it shows a large conformational flexibility near the active-site residue Asp875. NMR analysis revealed that RcsC-PR is able to adopt preferred conformations upon Mg2+ co-ordination, BeF3− activation, phosphate binding and RcsD-HPt recognition. In contrast, the α-helical structure of RcsD-HPt is conformationally stable and contains a recognition area in close vicinity to the active-site His842 residue. Our studies indicate the importance of protein dynamics and conformational exchange for the differential response to the variety of signals perceived by complex regulatory networks.
Lessons learned from murine models of mannose-binding lectin deficiency
Authors: Takahashi Kazue
Published: December 2008

MBL (mannose-binding lectin) is a pattern recognition molecule and a component of innate immunity, the first line of the host defence system against foreign bodies and pathogens. MBL deficiency is common in humans and has been associated with immunodeficiency. We have generated mouse models of MBL deficiency in order to explore the molecular mechanisms of MBL function in disease and health. In addition to confirming findings from human clinical research, these model studies have uncovered unexpected roles of MBL and evidence of its interaction with other molecules of the innate immune system.
Sponsorship and it Vendor Management of Projects
Authors: Liu Li , Yetton Philip
Published: December 2008

Project sponsorship is assumed to be critical to the success of information systems development and implementation. However, there is limited research on the effect of vendor-based sponsorship on the management of information technology (IT) projects. This paper contributes to that emerging body of evidence. Drawing on literature on psychological contract, management control and project sponsorship, the authors propose that vendor-based sponsors influence project performance in two main ways. One is to protect project quality by renegotiating contract with the client; and the other is to resource the project. Based on a survey of senior managers in IT services vendor organisations, it reports that project sponsorship improves the quality, but not the cost or timeliness, of vendor delivery of IT projects. The findings suggest that IT services vendors can improve their project delivery capability by appointing project sponsors.
Piezoresponse force microscopy on doubly clamped KNbO3 nanowires
Authors: Wang J. , Stampfer C. , Roman C. , Ma W. H. , Setter N. , Hierold C.
Published: December 2008

We present piezoresponse force microscopy measurements on individual integrated potassium niobate (KNbO3) nanowires. The devices consist of KNbO3 nanowires on SiO2 substrates being mechanically clamped and electrically biased by lithographically defined metal electrodes. This configuration allows to apply electrical fields parallel to the nanowire axis. Measured piezoelectric displacements reveal a multidomain structure of the nanowire. We observed displacements in the range of 3–13pm on different domains under Vac of 2V, that have typical section length of ≈200nm, along a doubly clamped nanowire with ≈100nm diameter. A maximum nominal piezoelectric coefficient of 7.9pm∕V has been extracted.
A molecular simulation study of methylated and hydroxyl sugar-based self-assembled monolayers: Surface hydration and resistance to protein adsorption
Authors: Hower Jason C. , He Yi , Jiang Shaoyi
Published: December 2008

In this work molecular simulations are performed to investigate protein interactions with hydroxylated and methylated mannitol and sorbitol terminated self-assembled monolayer (SAM) surfaces in the presence of explicit water molecules. The role of surface hydrogen bond donor versus acceptor groups is evaluated by comparing the hydration layer structure and resulting forces generated by the two classes of sugar SAM surfaces. Both hydroxyl and methyl-terminated sugar SAM surfaces interact with hydrating water molecules. Regardless of hydrogen bond donor or acceptor groups, both classes of sugar SAM surface groups interact strongly with hydrating water molecules to induce significant repulsive forces and resistance to protein adsorption. Our results indicate that the repulsive force generated on the probe protein is related to the ability of the surface to orient the hydration layer water. The repulsive force is also proportional to the number of hydrating water molecules interacting with the protein. The repulsive force and subsequent resistance to protein adsorption are dependent on the surface hydration, not the origin of that hydration.
On the c-Si surface passivation mechanism by the negative-charge-dielectric Al2O3
Authors: Hoex B. , Gielis J. J. H. , van de Sanden M. C. M. , Kessels W. M. M.
Published: December 2008

Al 2 O 3 is a versatile high-κ dielectric that has excellent surface passivation properties on crystalline Si (c-Si), which are of vital importance for devices such as light emitting diodes and high-efficiency solar cells. We demonstrate both experimentally and by simulations that the surface passivation can be related to a satisfactory low interface defect density in combination with a strong field-effect passivation induced by a negative fixed charge density Qf of up to 1013 cm−2 present in the Al2O3 film at the interface with the underlying Si substrate. The negative polarity of Qf in Al2O3 is especially beneficial for the passivation of p-type c-Si as the bulk minority carriers are shielded from the c-Si surface. As the level of field-effect passivation is shown to scale with Qf2, the high Qf in Al2O3 tolerates a higher interface defect density on c-Si compared to alternative surface passivation schemes.
Intraband absorption in solar cells with an intermediate band
Authors: Levy Michael Y. , Honsberg Christiana
Published: December 2008

This article presents a thermodynamic treatment of an intermediate band solar cell that includes photoinduced electronic transitions between two distinct states of the intermediate band. The treatment also allows for two black-body sources, interband photoinduced electronic transitions, overlapping absorption coefficients, multiple electron-hole pair generation, and nonradiative processes. A schematic of the device’s thermodynamic configuration shows that the solar cell is composed of three particle engines operating in tandem. The authors present detailed-balance results where it is assumed that when there is the physical possibility of both photoinduced intra- and interband electronic transitions at intermediate levels that the latter predominates. Results indicate that as the intermediate band’s width increases, the efficiencies saturate to those of two-stack tandem solar cells while the band structures approach that of a material that should operate as a black body. The authors conclude that the assumption that interband transitions predominate over intraband transitions, which is equivalent to ignoring or excluding intraband transitions, may yield results inconsistent with physical reality. The larger the difference between the intermediate band width and the smallest band gap in the system, the more pronounced will be the inconsistency.
Room-temperature nanolaser from CdSe nanotubes embedded in anodic aluminum oxide nanocavity arrays
Authors: Lin Tsung-Ju , Chen Hsin-Liang , Chen Yang-Fang , Cheng Soofin
Published: December 2008

Room-temperature visible lasing in CdSe semiconductor nanotube arrays embedded in anodic aluminum oxide template has been demonstrated. The cylindrical nanocavities of anodic aluminum oxide template form laser resonators, and the laser oscillation was achieved through whispering gallery mode gain from the interior semiconductor nanotubes. The linearly polarized stimulated emission, the one dimensionality, and the chemical accessibility to nanotubes render them significant potential for serving as various applications in optoelectronic devices.
Quantification of the ion and momentum fluxes toward the substrate during reactive magnetron sputtering
Authors: Mahieu S. , Van Aeken K. , Depla D.
Published: December 2008

The ion and momentum fluxes toward the growing film during reactive magnetron sputtering of a Ti target in a mixture of Ar and N2 are determined. For the ion flux and ion energy distribution a retarding field energy analyzer has been employed. The results were confronted with planar and cylindrical probe measurements, two more common used techniques. For the momentum flux, energy resolved mass spectrometry and simulations with the binary collision Monte Carlo code SIMTRA were performed to determine the contribution to this flux by the impact of ions and sputtered and reflected particles. Based on the quantification of both fluxes, it can be concluded that there is a relation between the hardness and elastic modulus of the TiN films and the momentum flux.
Thermal conductivity of Si/SiGe superlattice films
Authors: Liu Chun-Kai , Yu Chih-Kuang , Chien Heng-Chieh , Kuo Sheng-Liang , Hsu Chung-Yen , Dai Ming-Ji , Luo Guang-Li , Huang Shih-Chiang , Huang Mei-Jiau
Published: December 2008

We have evaluated the thermal conductivity of Si/SiGe superlattice films by theoretical analysis and experiment. In experiments, the ultrahigh vacuum chemical vapor deposition is employed to form the Si/Si0.71Ge0.29 and Si/Si0.8Ge0.2 superlattice films. The cross-plane thermal conductivities of these superlattice films are measured based on the 3ω method. In the theoretical analysis, the phonon transport in Si/Si1−xGex superlattice film is explored by solving the phonon Boltzmann transport equation. The dependence of the thermal conductivity of the Si/Si1−xGex superlattice films on the superlattice period, the ratio of layer thicknesses, and the interface roughness is of interest. The calculations show that when the layer thickness is on the order of one percentage of the mean free path or even thinner, the phonons encounter few intrinsic scatterings and consequently concentrate in the directions having high transmissivities. Nonlinear temperature distributions are observed near the interfaces, arising from the size confinement effect and resulting in a slight increase in the film thermal resistances. The interface resistance due to the interface scattering/roughness, which is nearly independent of the film thickness, nonetheless dominates the effective thermal conductivity, especially when the superlattice period is small. Finally the experimental measurements agree with the theoretical predictions if the specular fraction associated with the interface is properly taken.
Determination of large third-order optical nonlinearities in tetra-tert-butylphthalocyaninatogallium iodide film
Authors: Shi Guang , Wang Yuxiao , Liu Dajun , Zhang Xueru , Yang Junyi , Yang Kun , Song Yinglin
Published: December 2008

Using the Z-scan technique with 532 nm 4 ns laser pulses at various energy levels and repetition rates, we investigated the optical nonlinearities of tetra-tert-butylphthalocyaninatogallium iodide (t-Bu)4PcGaI. As a result, we found that the soluble peripherally tert-butyl-substituted phthalocyanine bound with the core of gallium iodide exhibited a giant two-photon absorption coefficient and Kerr refractive index. This suggests the potential applications of this material in numerous fields of nonlinear optics. However, when tackling the large nonlinearly induced loss and phase distortion analytically, we failed to fit the corresponding experimental results with the existent series sum formulas, which retain only the first few terms in the expansion. We performed the fitting by retrieving the high-order terms and justified this approach by dealing with the light-matter interaction and wave propagation.
Low-temperature sterilization of wrapped materials using flexible sheet-type dielectric barrier discharge
Authors: Eto Hiroyuki , Ono Yoshihito , Ogino Akihisa , Nagatsu Masaaki
Published: December 2008

A flexible sheet-type dielectric barrier discharge (DBD) was studied for the low-temperature sterilization of medical instruments wrapped with Tyvek packaging. Sterilization experiments using Geobacillus stearothermophilus spores with a population of 106 were carried out with various mixtures of nitrogen and oxygen. We confirmed the inactivation of spores after 4.5 min of DBD irradiation at a temperature of 28.4 °C and relative humidity of 64.4%. The main sterilizing factors of this method are the ozone and UV emissions generated by DBD in dry air and synergistic OH radicals generated by DBD in moist air.
High optimization process for increasing the attenuation properties of acoustic metamaterials by means of the creation of defects
Authors: Romero-García V. , Sánchez-Pérez J. V. , García-Raffi L. M. , Herrero J. M. , García-Nieto S. , Blasco X.
Published: December 2008

An improvement in the attenuation capabilities of acoustic metamaterials by means of the creation of defects is considered here as a multiobjective optimization problem. From this point of view, it is possible to define the optimum strategy in the creation of defects to achieve an important increase in acoustic attenuation in a predetermined range of frequencies. A powerful multiobjective optimization algorithm called evMOGA has been used to solve this problem. The study has been restricted to the case of a two-dimensional sonic crystal formed by rigid cylinders in air, the defects being vacancies in the initial structure.
Ultrahigh-brightness 850 nm GaAs/AlGaAs photonic crystal laser diodes
Authors: Posilovic K. , Kettler T. , Shchukin V. A. , Ledentsov N. N. , Pohl U. W. , Bimberg D. , Fricke J. , Ginolas A. , Erbert G. , Tränkle G. , Jönsson J. , Weyers M.
Published: December 2008

One-dimensional photonic crystal lasers emitting in the 850 nm range show high internal quantum efficiencies of 93% and very narrow vertical beam divergence of 7.1° (full width at half maximum). 50 μm broad area lasers with unpassivated facets exhibit a high total output power of nearly 20 W in pulsed mode with a divergence of 9.5°×11.3° leading to a record brightness of 3×108 W cm−2 sr−1, being presently the best value ever reported for a single broad area laser diode. 100 μm broad devices with unpassivated facets show continuous wave operation with an output power of 1.9 W.
Twisted liquid crystal pi cell stabilized by polymer-sustained alignment
Authors: Chen Tien-Jung , Cheng Yuan-Hsin , Wu Sheng-Ming
Published: December 2008

A uniform π-twist liquid crystal (LC) alignment was stabilized in a pi cell by photopolymerization of a minute amount of monomers without using any chiral material. Controlling UV exposure time can vary the LC pretilt angle to achieve a stabilized π-twist state. This type of π-twisted LC cell made using the polymer-sustained alignment has a pretilt angle estimated to be ∼20°. This cell can quickly transform into a bend state at a low driving voltage and shows excellent brightness and optical contrast, as compared with a conventional pi cell and a chiral-doped cell.
X-ray light valve emerges as a low-cost, digital radiographic imager
Authors: Wilson Mark
Published: December 2008

The instrument combines the physics of amorphous semiconductors, liquid crystals, and the common document scanner.
Environmental consequences of nuclear war
Authors: Toon Owen B. , Robock Alan , Turco Richard P.
Published: December 2008

A regional war involving 100 Hiroshima-sized weapons would pose a worldwide threat due to ozone destruction and climate change. A superpower confrontation with a few thousand weapons would be catastrophic.
Traffic and tillage effects on wheat production on the Loess Plateau of China: 2. Soil physical properties
Authors: Bai Yuhua , Chen Fu , Li Hongwen , Chen Hao , He Jin , Wang Qingjie , Tullberg J. N. , Gong Yuanshi
Published: December 2008

Controlled traffic zero and minimum tillage management with residue cover has been proposed as a solution to erosion and other soil degradation challenges to the sustainability of dryland farming on the Loess Plateau of China. This was assessed between 1998 and 2007 in a field experiment involving a conventional tillage treatment, and 2 controlled traffic treatments, no tillage and shallow tillage, with full straw cover in both cases. This paper reports the soil physical properties after 9 years of dryland wheat production under these treatments, and the substantial improvements seen in soils under controlled traffic. Compared with conventional tillage, controlled traffic significantly reduced soil bulk density in the 0–0.15 m soil layer, and increased total porosity in the 0–0.60 m soil layer, where macroporosity (>60 µm) and mesoporosity (0.2–60 µm) increased at the expense of microporosity (<0.2 µm). Readily available water content and saturated hydraulic conductivity were greater in controlled traffic treatments. Controlled traffic farming appears to be an improvement on current farming systems on the Loess Plateau, and valuable for the sustainable development agriculture in this region.
K - Ca - Mg binary cation exchange in saline soils from the north of Chile
Authors: Gacitúa Manuel , Antilén Mónica , Briceño Margarita
Published: December 2008

The selectivities of the K–Ca and K–Mg cation exchange reactions were studied in batch experiments carried out with 7 Chilean saline sandy soils with low organic matter (OM) content, and rich in quartz and halite, by using the experimental Gaines and Thomas procedure and the semi-empirical Rothmund–Kornfeld approach.
The soils present high reactivity to the exchange process in terms of CEC and a preference order from the surface for the cation of K > Ca > Mg. In addition, the existence of different types of exchange sites was determined; some were specific for determined cations and others presented free competition. The proposed exchange reaction for both equilibria was thermodynamically possible and the studied cations presented a decreasing mobility order K > Ca > Mg, which follows the increasing order of hydrated ionic radii.
As for the Rothmund–Kornfeld semi-empirical approach, it can be employed on soils classified as Aridisol due to good fit with the experimental data. On the other hand, the Gaines and Thomas approach is only experimentally applicable since poses some restrictions concerning to salinity and carbonate contents in the studied soils.
Spring wheat performance and water use efficiency on permanent raised beds in arid northwest China
Authors: He Jin , Li Hongwen , McHugh A. D. , Ma Zhongmin , Cao Xinhui , Wang Qingjie , Zhang Xuemin , Zhang Xirui
Published: December 2008

Permanent raised beds have been proposed as a more productive and water-efficient alternative to the conventional system of flat, flood-irrigated bays for planting narrow-spaced crops in arid north-west China. Data from a field experiment (2005–2007) conducted in the Hexi Corridor at Zhangye, Gansu Province, China, were used to compared the effects of traditional tillage (TT), zero tillage (ZT), and permanent raised beds (PRB) on crop growth, yield, and water use in a spring wheat monoculture. The results show that PRB significantly (P < 0.05) increased soil water content to 0.30 m depth by 7.2–10.7% and soil temperature to 0.05 m depth by 0.2–0.9°C during the wheat-growing period relative to TT and ZT treatments. Bulk density in 0–0.10 m soil layer under PRB was also 5.8% less than for flat planting treatments. Mean wheat yields over 3 years on PRB plots were slightly greater and furrow irrigation in permanent beds was particularly effective in increasing irrigation water use efficiency (~18%), compared with TT and ZT treatments. This increase in water use efficiency is of considerable importance for these arid areas where irrigation water resources are scarce.
Small-scale, high-intensity rainfall simulation under-estimates natural runoff P concentrations from pastures on hill-slopes
Authors: Dougherty W. J. , Nash D. M. , Cox J. W. , Chittleborough D. J. , Fleming N. K.
Published: December 2008

Rainfall simulation is a widely used technique for studying the processes, and quantifying the mobilisation, of phosphorus (P) from soil/pasture systems into surface runoff. There are conflicting reports in the literature of the effects of rainfall simulation on runoff P concentrations and forms of P compared to those under natural rainfall runoff conditions. Furthermore, there is a dearth of information on how rainfall simulation studies relate to hill-slope and landscape scale processes and measures. In this study we compare P mobilisation by examining P forms and concentrations in runoff from small-scale, high-intensity (SH, 1.5 m2, 80 mm/h) rainfall simulation and large-scale, low-intensity (LL, 1250 m2, 8 mm/h) simulations that have previously been shown to approximate natural runoff on hill-slopes. We also examined the effect of soil P status on this comparison. The SH methodology resulted in lower (average 56%) runoff P concentrations than those measured under the LL methodology. The interaction method × soil P status was highly significant (P < 0.001). There was no significant effect of method (SH v. LL) and soil P status on P forms (%).The hydrological characteristics were very different between the 2 methods, runoff rates being c. 42 and 3 mm/h for the SH and LL methods, respectively. We hypothesise that the lower runoff P concentrations from the SH method are the result of a combination of (i) the P mobilisation being a rate-limited process, and (ii) the relatively high runoff rates and short runoff path-lengths of the SH method allowing for relatively incomplete attainment of equilibrium between P in the soil/pasture system and runoff. We conclude that small-scale, high-intensity rainfall simulation provides a useful tool for studying treatment effects and processes of mobilisation in pastures, but concentration and load data should not be inferred for natural conditions at larger scales without a clear understanding of the effects of the rainfall simulation methodology on the results for the system being studied.
Traffic and tillage effects on runoff and soil loss on the Loess Plateau of northern China
Authors: Wang Xiaoyan , Gao Huanwen , Tullberg J. N. , Li Hongwen , Kuhn Nikolaus , McHugh A. D. , Li Yuxia
Published: December 2008

This paper reports the outcome of 5 years of field plot runoff monitoring, 2 years of water erosion measurement, and a rainfall simulation experiment on moderately sloping farmland on the loess plateau of north-west China. The objective was to test different conservation tillage systems compared with the control treatment, conventional mouldboard plough practice (CK). Tillage, residue cover, and compaction effects were assessed in terms of runoff and soil erosion.
Results from the runoff plots showed that conservation tillage, with more residue cover, less compaction, and less soil disturbance, could substantially reduce runoff and soil erosion compared with the control. No tillage with residue cover and no compaction produced the least runoff and soil erosion. Compared with the control, it reduced runoff and soil erosion by about 40% and 80%, respectively. At the start of the experiment, residue cover appeared to be the most important factor affecting soil and water conservation, particularly when antecedent soil moisture was limited. With the accumulation of tractor wheeling effects over the course of the experiment, soil compaction appeared to become a more important factor affecting runoff.
Rainfall simulation was then used to assess the effect of non-inverting surface tillage and different levels of residue cover and wheel compaction on infiltration and runoff. This confirmed that wheel compaction effects could be greater than those of tillage and residue cover, at least under the 82.5 mm/h rainfall rate produced by the simulator. The wheeling effect was particularly large when the treatment was applied to wet soil, and severe even after wheeling by small tractors.
ATP release through connexin hemichannels and gap junction transfer of second messengers propagate Ca
2+
signals across the inner ear
Authors: Anselmi Fabio , Hernandez Victor H. , Crispino Giulia , Seydel Anke , Ortolano Saida , Roper Stephen D. , Kessaris Nicoletta , Richardson William , Rickheit Gesa , Filippov Mikhail A. , Monyer Hannah , Mammano Fabio
Published: December 2008

Extracellular ATP controls various signaling systems including propagation of intercellular Ca
2+
signals (ICS). Connexin hemichannels, P2x7 receptors (P2x7Rs), pannexin channels, anion channels, vesicles, and transporters are putative conduits for ATP release, but their involvement in ICS remains controversial. We investigated ICS in cochlear organotypic cultures, in which ATP acts as an IP
3
-generating agonist and evokes Ca
2+
responses that have been linked to noise-induced hearing loss and development of hair cell-afferent synapses. Focal delivery of ATP or photostimulation with caged IP
3
elicited Ca
2+
responses that spread radially to several orders of unstimulated cells. Furthermore, we recorded robust Ca
2+
signals from an ATP biosensor apposed to supporting cells outside the photostimulated area in WT cultures. ICS propagated normally in cultures lacking either P2x7R or pannexin-1 (Px1), as well as in WT cultures exposed to blockers of anion channels. By contrast, Ca
2+
responses failed to propagate in cultures with defective expression of connexin 26 (Cx26) or Cx30. A companion paper demonstrates that, if expression of either Cx26 or Cx30 is blocked, expression of the other is markedly down-regulated in the outer sulcus. Lanthanum, a connexin hemichannel blocker that does not affect gap junction (GJ) channels when applied extracellularly, limited the propagation of Ca
2+
responses to cells adjacent to the photostimulated area. Our results demonstrate that these connexins play a dual crucial role in inner ear Ca
2+
signaling: as hemichannels, they promote ATP release, sustaining long-range ICS propagation; as GJ channels, they allow diffusion of Ca
2+
-mobilizing second messengers across coupled cells.
Coordinated control of connexin 26 and connexin 30 at the regulatory and functional level in the inner ear
Authors: Ortolano Saida , Di Pasquale Giovanni , Crispino Giulia , Anselmi Fabio , Mammano Fabio , Chiorini John A.
Published: December 2008

Connexin 26 (Cx26) and connexin 30 (Cx30) are encoded by two genes (
GJB2
and
GJB6
, respectively) that are found within 50 kb in the same complex deafness locus, DFNB1. Immunocytochemistry and quantitative PCR analysis of Cx30 KO mouse cultures revealed that Cx26 is downregulated at the protein level and at the mRNA level in nonsensory cells located between outer hair cells and the stria vascularis. To explore connexin coregulation, we manipulated gene expression using the bovine adeno-associated virus. Overexpression of Cx30 in the Cx30 KO mouse by transduction with bovine adeno-associated virus restored Cx26 expression, permitted the formation of functional gap junction channels, and rescued propagating Ca
2+
signals. Ablation of Cx26 by transduction of Cx26

loxP/loxP

cultures with a Cre recombinase vector caused concurrent downregulation of Cx30 and impaired intercellular communication. The coordinated regulation of Cx26 and Cx30 expression appears to occur as a result of signaling through PLC and the NF-κB pathway, because activation of IP
3
-mediated Ca
2+
responses by stimulation of P2Y receptors for 20 min with 20 nM ATP increased the levels of Cx26 transcripts in Cx30 KO cultures. This effect was inhibited by expressing a stable form of the IκB repressor protein that prevents activation/translocation of NF-κB. Thus, our data reveal a Ca
2+
-dependent control in the expression of inner ear connexins implicated in hereditary deafness as well as insight into the hitherto unexplained observation that some deafness-associated DFNB1 alleles are characterized by hereditable reduction of both
GJB2
and
GJB6
expression.
Kinesin's cover-neck bundle folds forward to generate force
Authors: Khalil Ahmad S. , Appleyard David C. , Labno Anna K. , Georges Adrien , Karplus Martin , Belcher Angela M. , Hwang Wonmuk , Lang Matthew J.
Published: December 2008

Each step of the kinesin motor involves a force-generating molecular rearrangement. Although significant progress has been made in elucidating the broad features of the kinesin mechanochemical cycle, molecular details of the force generation mechanism remain a mystery. Recent molecular dynamics simulations have suggested a mechanism in which the forward drive is produced when the N-terminal
cover strand
forms a β-sheet with the neck linker to yield the
cover-neck bundle
. We tested this proposal by comparing optical trapping motility measurements of cover strand mutants with the wild-type. Motility data, as well as kinetic analyses, revealed impairment of the force-generating capacity accompanied by a greater load dependence in the mechanochemical cycle. In particular, a mutant with the cover strand deleted functioned only marginally, despite the fact that the cover strand, the N-terminal “dangling end,” unlike the neck linker and nucleotide-binding pocket, is not involved with any previously considered energy transduction pathway. Furthermore, a constant assisting load, likely in lieu of a power stroke, was shown to rescue forward motility in the cover strand deletion mutant. Our results support a stepping mechanism driven by dynamic cover-neck bundle formation. They also suggest a strategy to generate motors with altered mechanical characteristics by targeting the force-generating element.
Growth of uterine leiomyomata among premenopausal black and white women
Authors: Peddada Shyamal D. , Laughlin Shannon K. , Miner Kelly , Guyon Jean-Philippe , Haneke Karen , Vahdat Heather L. , Semelka Richard C. , Kowalik Ania , Armao Diane , Davis Barbara , Baird Donna Day
Published: December 2008

Uterine leiomyomata (fibroids) are the leading cause of hysterectomy in the United States. Black women have a greater fibroid burden than whites, yet no study has systematically evaluated the growth of fibroids in blacks and whites. We prospectively tracked growth for 262 fibroids (size range: 1–13 cm in diameter) from 72 premenopausal participants (38 blacks and 34 whites). Fibroid volume was measured by computerized analysis of up to four MRI scans over 12 months. We used mixed effects models to identify factors that are associated with growth, and results were converted to percent change per 6 months for clinical relevance. The median growth rate was 9% (range: −89% to +138%). Seven percent of fibroids regressed (>20% shrinkage). Tumors from the same woman grew at different rates (within-woman component of variation was twice the component among women; both were significant,
P
< 0.001). Black and white women less than 35 years of age had similar fibroid growth rates. However, growth rates declined with age for whites but not for blacks (
P
= 0.05). The odds of a tumor growing more than 20% in 6 months also decreased with age for whites but not for blacks (
P
< 0.01). Growth rates were not influenced by tumor size, location, body mass index, or parity. We conclude that (
i
) spontaneous regression of fibroids occurs; (
ii
) fibroids from the same woman grow at different rates, despite a uniform hormonal milieu; (
iii
) fibroid size does not predict growth rate; and (
iv
) age-related differences in fibroid growth between blacks and whites may contribute to the higher symptom burden for black women.