bluuebunny/crossref_metadata_2025 huggingface dataset:
A thermodynamic free energy function for potassium niobate
Authors: Liang Linyun , Li Y. L. , Chen Long-Qing , Hu S. Y. , Lu Guang-Hong
Published: February 2009

A thermodynamic free energy function in the form of an eighth-order polynomial has been developed for bulk potassium niobate (KNbO3), based on the Landau–Ginsburg–Devonshire phenomenological theory. The obtained free energy function successfully models the ferroelectric single domain (intrinsic) properties of KNbO3, including the three sequential phase transition temperatures as well as polarizations, dielectric constants, and lattice constants along the whole ferroelectric temperature range. It is applicable to explaining and predicting the extrinsic contributions such as hydrostatic pressure on the bulks properties and substrate constraints on the thin films properties.
Measurement of the energy distribution of an intense electron beam in an external magnetic field
Authors: Myers M. C. , Swanekamp S. B. , Friedman M. , Hegeler F.
Published: February 2009

An energy analyzer device has been developed which utilizes a series of stacked foils and Rogowski current monitors to the measure time resolved current of an intense electron beam. The energy distribution of the electron beam is unfolded from measured current ratios using computer simulations. This device is particularly useful where electron beams are guided by external magnetic fields which may make other electron energy measurement techniques difficult. This technique was used to determine the energy distribution of a 550 keV, 95 kA electron beam as it propagates in the gas mixture of a high power KrF laser. The resulting energy distributions at various depths in the gas are in agreement with three-dimensional particle-in-cell simulations providing confidence in the measurement technique.
Influence of annealing on spin-dependent tunneling characteristics of fully epitaxial Co2MnGe/MgO/Co50Fe50 magnetic tunnel junctions
Authors: Taira Tomoyuki , Ishikawa Takayuki , Itabashi Naoki , Matsuda Ken-ichi , Uemura Tetsuya , Yamamoto Masafumi
Published: February 2009

We found that the tunnel magnetoresistance ratio of fully epitaxial Co2MnGe/MgO/Co50Fe50 magnetic tunnel junctions (MTJs) increased discontinuously and significantly from 92% at room temperature (RT) (244% at 4.2 K) for Ta of 475 °C to 160% at RT (376% at 4.2 K) for Ta of 500 °C, where Ta is the temperature at which the MTJ trilayer was in situ annealed right after deposition of the upper electrode. We also found that the dI/dV versus V characteristics for the parallel and antiparallel magnetization configurations changed discontinuously and markedly with increasing Ta from 475 °C or less to 500 °C or higher. These significant changes are discussed in terms of a possible change in the spin-dependent interfacial density of states.
Jahn–Teller-like origin of the tetragonal distortion in disordered Fe–Pd magnetic shape memory alloys
Authors: Opahle Ingo , Koepernik Klaus , Nitzsche Ulrike , Richter Manuel
Published: February 2009

The electronic structure and magnetic properties of disordered FexPd100−x alloys (50<x<85) are investigated in the framework of density functional theory using the full potential local orbital method. Disorder is treated in the coherent potential approximation. Our calculations explain the experimental magnetization data. The origin of the tetragonal distortion in the Fe–Pd magnetic shape memory alloys is found to be a Jahn–Teller-like effect, which allows the system to reduce its band energy in a narrow composition range. Prospects for an optimization of the alloys’ properties by adding third elements are discussed.
A magnetically active terahertz plasmonic artificial material
Authors: Baron C. A. , Elezzabi A. Y.
Published: February 2009

We present an actively tunable plasmonic artificial material consisting of random mixtures of subwavelength metallic and dielectric particles. Active control of terahertz particle plasmons is achieved via anisotropic magnetoresistance in ferromagnetic microparticles. The phenomenon is exploited to alter the group velocity of terahertz pulses by an amount adjustable via an external magnetic field. In a proof of principle experimental demonstration, we show how the artificial material can dynamically alter the propagation direction of terahertz pulses. Active terahertz plasmonic devices remain relatively unexplored, and the means of control enabled by this work may be applicable in photonic based information technologies.
High-performance dye-sensitized solar cell with a multiple dye system
Authors: Ogura Reiko Yoneya , Nakane Shigeru , Morooka Masahiro , Orihashi Masaki , Suzuki Yusuke , Noda Kazuhiro
Published: February 2009

A dye-sensitized solar cell (DSC) using two dyes achieved high external quantum efficiency as sensitizers. We confirmed that terpyridine complex (black dye, Solaronix) and an indoline dye (D131, Mitsubishi Paper Mill) were adsorbed by the TiO2 electrode without either dye interfering with the electron transfer of the other dye to the electrode. The high performance of the new arrangement is made possible by the dissociation function of these two particular dyes. The multiple dye system achieved a power conversion efficiency of 11.0%. Moreover, the fabrication of the multiple dye system only mixed the two reagents in one pot.
Color-variable highly efficient organic electrophosphorescent diodes manipulating molecular exciton and excimer emissions
Authors: Cocchi Massimo , Kalinowski Jan , Fattori Valeria , Williams J. A. Gareth , Murphy Lisa
Published: February 2009

A simple way of tuning the emission color and electroluminescence efficiency from vacuum-deposited emitters of phosphorescent organic light emitting diodes (LEDs) is demonstrated. For each color a single-emissive layer consisting of a blend of two materials, one of Pt(N∧C∧N) complex series [where (N∧C∧N)=di(2-pyridinyl)benzene-based tridentate ligands] as either the low-concentration bluish green (molecular) phosphorescence emitter or high-concentration red (excimer) phosphorescence emitter, and (4,4′,4″-tris(N-carbazolyl-triphenylamine) as the host was employed. By adjusting the relative amount of blue and red emissive species, the color of the light emission was tuned from bluish green through green and white up to red. Very high external quantum efficiency (up to 18.3±0.5%) and current efficiency (up to 44.8±0.5 cd/A) at ∼500 cd/m2 four-layer devices were achieved with white and greenish light emitting layers, respectively. It is found that the introduction of electron-withdrawing fluorine atoms at the central ring and electron-donating groups at the lateral rings of the Pt complex leads to a blueshift in the molecular and excimer emissions, respectively. This allows to refine colors and optimize the efficiency of the LEDs by selecting suitable substituents.
Modulation of superconductivity by spin canting in a hybrid antiferromagnet/superconductor oxide
Authors: Mani Awadhesh , Kumary T. Geetha , Hsu Daniel , Lin J. G. , Chern Chyh-Hong
Published: February 2009

The proximity effect of a C-type antiferromagnet with the spin canting at low temperature is investigated in the hybrid Nd0.35Sr0.65MnO3/YBa2Cu3O7 oxide system through magnetic and transport measurements. It is found that the onset of a spin-canted state destroys partially the superconducting order parameter. Interestingly, due to the instability of this spin-canted state, zero resistivity recovers at the offset of spin canting. Our result demonstrates clearly the high sensitivity of superconducting order parameter to a modulation of internal field.
Mn-doped amorphous Si:H films with anomalous Hall effect up to 150 K
Authors: Yao Jia-Hsien , Li Shin-Chih , Lan Ming-Der , Chin Tsung-Shune
Published: February 2009

Structural, magnetic, and electrical properties were investigated of Mn-doped amorphous silicon films prepared by magnetron sputtering with and without hydrogen. Ferromagnetism at room temperature was observed and no clusters or second phases were detected from x-ray diffraction and high-resolution transmission electron microscopy analyses. Hydrogenation enhances saturation magnetization, carrier concentration, and Curie temperature by about 500%, 300%–500%, and 100 K, respectively. The M-T curve of hydrogenated sample fits very well by combination of Curie–Weiss law and three-dimensional spin-wave. Anomalous Hall effect was reproducibly obtained at 150 K. These suggest that the origin of ferromagnetism may arise from the carrier mediated mechanism.
Is sediment mud content a significant predictor of macrobenthos abundance in low-mud-content tidal flats?
Authors: Sakamaki T. , Nishimura O.
Published: February 2009

Sediment mud content is a significant predictor of macrobenthos abundance in marine soft-bottom habitats. However, the mechanisms behind the non-linearity generally shown in mud–macrobenthos relationships have not been examined. The present study analysed spatial distributions of sediment properties and macrobenthos in a tidal flat system of the north-east coast of Japan and tested the hypothesis: the non-linearity of mud–macrobenthos relationship corresponds to changes in bed elevation variability and sediment cohesiveness. For two macrobenthos species studied, Nuttallia olivacea (Bivalvia) and Hediste spp. (Polychaeta), the relationships between mud content (<75 μm) and their density showed discontinuities at ~0.1% and ~20% mud contents. In stations with <0.1% mud content, the densities of both species were related positively to mud content and negatively to bed elevation variability, suggesting that mud content reflected negative effects of bed elevation variability on macrobenthos abundance. The stations where distinct changes were observed in macrobenthos densities below or above ~20% mud content were within an area where a shift between non-cohesive and cohesive sediments was found. Hence, the results of the present study support the hypothesis and also suggest that sediment mud content can be a sensitive predictor of macrobenthos abundance even within a relatively low and narrow range of mud content.
Assuring that 1080 toxicosis in the red fox (Vulpes vulpes) is humane. II. Analgesic drugs produce better welfare outcomes
Authors: Marks Clive A. , Gigliotti Frank , Busana Frank
Published: February 2009

Fluoroacetic acid (1080) is a widely used vertebrate pesticide in Australia and New Zealand. In Australia it is used in meat baits as the primary method of control for the introduced red fox (Vulpes vulpes). Subsequent to the onset of initial signs, collapse and convulsions are associated with central nervous system disruptions where the animal is unresponsive to external stimuli, making an assessment of humaneness difficult. Prior to collapse and unconsciousness it would appear that there is potential for suffering to occur although its extent and nature during the entire toxicosis remains unclear. We investigated various formulations of 1080 with either analgesic or anxiolytic drugs in order to manage possible suffering experienced during 1080 poisoning of red foxes. Oral doses of 0.5 mg kg−1 1080 alone produced no visible signs for a mean of 205.3 min (±28 min, P < 0.05), but were lethal after signs that lasted a mean of 103 min (±16 min, P < 0.05). Combinations of 0.5 mg kg−1 1080 with either 10 mg kg−1 carprofen (CA), 0.4 mg kg−1 copper indomethacin (CI) or 10 mg kg−1 buspirone (BS) were assessed in pen trials and compared with a group that received 0.5 mg kg−1 1080 only and one that received the drug dose only. CI reduced the time between the onset of signs and death (P < 0.01) and CA reduced the overall intensity of activity from dosage to death (P < 0.05). A significant reduction in the incidence of retching during the onset of signs was observed in foxes that were coadministered CA (P < 0.05) or CI (P < 0.01) with 1080 compared with 1080 alone. The combination of BS and 1080 halved the mean activity from first signs to death, but was not statistically significant. In a separate trial, drug and 1080 combinations were delivered to penned foxes using an M-44 ejector. Neither 70 mg CA nor 2.8 mg CI appeared to affect the lethality of 1080 doses, although 70 mg BS produced a result that was equivocal and warrants further investigation. Coadministration of 70 mg diazepam was associated with the survival of six of nine foxes and suggests that there may be the potential for diazepam to act in the treatment of accidentally poisoned domestic dogs and this is discussed briefly. Given evidence for both central and peripheral analgesia, its potential to reduce the duration of signs and incidence of retching, CI shows immediate potential to be used with 1080 fox baits and to assist in delivering better welfare outcomes in fox control.
The relationship between hunting methods and sex, age and body weight in a non-trophy animal, the red fox
Authors: Tryjanowski Piotr , Sparks Tim H. , Kamieniarz Robert , Panek Marek
Published: February 2009

Recently, hunting has represented a major source of mortality in game animals, including red fox, Vulpes vulpes, populations. Data from hunting studies have been used to explain evolutionary changes (body size, dental structure) in fox populations; however, knowledge of potential sources of bias in these kinds of data is lacking. Moreover, nature and game managers as well as conservationists have recently been seeking methods to limit European fox populations, which are increasing. In the present study in Polish farmland, we show that three different hunting methods (individual – lying in wait, with dogs at dens, with beating undergrowth to flush out foxes) resulted in differences in the age, sex ratio and body size of shot foxes. Taking account of seasonal differences in hunting methods used, shooting assisted by beating gave a higher proportion of male foxes, whereas individual hunting resulted in smaller foxes in shot samples. Hunting with dogs resulted in heavier female foxes, with the results being skewed towards females. Thus, this method may help limit the breeding capacity of a population and is recommended to assist in the control of red fox populations, at least in farmland areas.
Use of artificial tree hollows by Australian birds and bats
Authors: Goldingay Ross L. , Stevens Jane R.
Published: February 2009

Artificial tree hollows (nest or roost boxes) may be of considerable importance to the conservation and management of Australian hollow-using birds and microbats. This is suggested by recognition that the rate of collapse of hollow-bearing trees may exceed replacement in some landscapes. We review the published literature to synthesise current information on the use of artificial hollows by Australian birds and bats, and to provide guidance to future research and management. The use of artificial hollows has been documented in some detail for 15 native bird and eight microbat species. A range of hollow designs has been employed but there is a limited understanding of favoured designs. General designs (e.g. front-entry plywood boxes) have been used extensively by some species and should continue to be used until more effective designs are identified. Species tend to use artificial hollows that have entrance sizes just sufficient for their body size, and this should guide hollow design. Competitive interactions with a range of non-target species (native and non-native) may have a pronounced influence on artificial hollow use and must be considered in any management program involving artificial hollows. We highlight some design elements that may reduce interference by non-target species. Temperature inside artificial hollows may have a particular influence on their use by bats due to the role of microclimate in bat thermoregulation. Trials are needed to investigate this factor and to inform general approaches to positioning of artificial hollows. Several distinct management uses exist for artificial hollows, including assisting threatened species recovery, e.g. Kangaroo Island glossy black-cockatoo (Calyptorhynchus lathami halmaturinus) and orange-bellied parrot (Neophema chrysogaster). Artificial hollows offer an interim solution to hollow shortage but their full potential will only be realised when preferences for different designs are better understood. This will require a commitment to monitoring and should be conducted in an adaptive management context. Increased knowledge of the use of artificial hollows by Australian birds and bats should be of global relevance to the management of hollow-using species because it provides an independent test of ideas and strengthens any generalisations.
Versatile selection technology for intracellular protein–protein interactions mediated by a unique bacterial hitchhiker transport mechanism
Authors: Waraho Dujduan , DeLisa Matthew P.
Published: February 2009

We have developed a reliable genetic selection strategy for isolating interacting proteins based on the “hitchhiker” mechanism of the
Escherichia coli
twin-arginine translocation (Tat) pathway. This method, designated FLI-TRAP (functional ligand-binding identification by Tat-based recognition of associating proteins), is based on the unique ability of the Tat system to efficiently cotranslocate noncovalent complexes of 2 folded polypeptides. In the FLI-TRAP assay, the protein to be screened for interactions is engineered with an N-terminal Tat signal peptide, whereas the known or putative partner protein is fused to mature TEM-1 β-lactamase (Bla). Using a series of c-Jun and c-Fos leucine zipper (JunLZ and FosLZ) variants of known affinities, we observed that only those chimeras that expressed well and interacted strongly in the cytoplasm were able to colocalize Bla into the periplasm and confer β-lactam antibiotic resistance to cells. Likewise, the assay was able to efficiently detect interactions between intracellular single-chain Fv (scFv) antibodies and their cognate antigens. The utility of FLI-TRAP was then demonstrated through random library selections of amino acid substitutions that restored (
i
) heterodimerization to a noninteracting FosLZ variant, and (
ii
) antigen binding to a low-affinity scFv antibody. Because Tat substrates must be correctly folded before transport, FLI-TRAP favors the identification of soluble, nonaggregating, protease-resistant protein pairs and, thus, provides a powerful tool for routine selection of interacting partners (e.g., antibody-antigen), without the need for purification or immobilization of the binding target.
Fos and Jun potentiate individual release sites and mobilize the reserve synaptic-vesicle pool at the
Drosophila
larval motor synapse
Authors: Kim Susy M. , Kumar Vimlesh , Lin Yong-Qi , Karunanithi Shanker , Ramaswami Mani
Published: February 2009

In all nervous systems, short-term enhancement of transmitter release is achieved by increasing the weights of unitary synapses; in contrast, long-term enhancement, which requires nuclear gene expression, is generally thought to be mediated by the addition of new synaptic vesicle release sites. In
Drosophila
motor neurons, induction of AP-1, a heterodimer of Fos and Jun, induces cAMP- and CREB-dependent forms of presynaptic enhancement. Light and electron microscopic studies indicate that this synaptic enhancement is caused by increasing the weight of unitary synapses and not through the insertion of additional release sites. Electrophysiological and optical measurements of vesicle dynamics demonstrate that enhanced neurotransmitter release is accompanied by an increase in the actively cycling synaptic vesicle pool at the expense of the reserve pool. Finally, the observation that AP-1 mediated enhancement eliminates tetanus-induced forms of presynaptic potentiation suggests: (
i
) that reserve-pool mobilization is required for tetanus-induced short-term synaptic plasticity; and (
ii
) that long-term synaptic plasticity may, in some instances, be accomplished by stable recruitment of mechanisms that normally underlie short-term synaptic change.
Spatially confined folding of chromatin in the interphase nucleus
Authors: Mateos-Langerak Julio , Bohn Manfred , de Leeuw Wim , Giromus Osdilly , Manders Erik M. M. , Verschure Pernette J. , Indemans Mireille H. G. , Gierman Hinco J. , Heermann Dieter W. , van Driel Roel , Goetze Sandra
Published: February 2009

Genome function in higher eukaryotes involves major changes in the spatial organization of the chromatin fiber. Nevertheless, our understanding of chromatin folding is remarkably limited. Polymer models have been used to describe chromatin folding. However, none of the proposed models gives a satisfactory explanation of experimental data. In particularly, they ignore that each chromosome occupies a confined space, i.e., the chromosome territory. Here, we present a polymer model that is able to describe key properties of chromatin over length scales ranging from 0.5 to 75 Mb. This random loop (RL) model assumes a self-avoiding random walk folding of the polymer backbone and defines a probability
P
for 2 monomers to interact, creating loops of a broad size range. Model predictions are compared with systematic measurements of chromatin folding of the q-arms of chromosomes 1 and 11. The RL model can explain our observed data and suggests that on the tens-of-megabases length scale
P
is small, i.e., 10–30 loops per 100 Mb. This is sufficient to enforce folding inside the confined space of a chromosome territory. On the 0.5- to 3-Mb length scale chromatin compaction differs in different subchromosomal domains. This aspect of chromatin structure is incorporated in the RL model by introducing heterogeneity along the fiber contour length due to different local looping probabilities. The RL model creates a quantitative and predictive framework for the identification of nuclear components that are responsible for chromatin–chromatin interactions and determine the 3-dimensional organization of the chromatin fiber.
Tissue destruction caused by cytotoxic T lymphocytes induces deletional tolerance
Authors: Parish Ian A. , Waithman Jason , Davey Gayle M. , Belz Gabrielle T. , Mintern Justine D. , Kurts Christian , Sutherland Robyn M. , Carbone Francis R. , Heath William R.
Published: February 2009

Autoimmune diseases tend to be chronic and progressive, but how these responses are sustained is not clear. One cell type that might contribute to autoimmunity is the cytotoxic T lymphocyte (CTL), which, as a consequence of causing tissue destruction and production of cytokines, could provide a sustained supply of antigen and inflammatory signals for dendritic cells to maintain immune stimulation. Here we examined whether such CTL-mediated tissue damage alone could provide antigen in the right context to recruit immune effectors and sustain autoimmunity. We show that while CTL-mediated tissue damage caused the release of self-antigens that stimulated the proliferation of naive autoreactive CD8
+
T cells, such responses failed to precipitate disease and, instead, led to deletional tolerance. These findings indicate that despite the capacity of CTLs to produce inflammatory cytokines and to cause tissue damage, their responses are not sustaining, but instead favor induction of self-tolerance.
Sequence context-specific profiles for homology searching
Authors: Biegert A. , Söding J.
Published: February 2009

Sequence alignment and database searching are essential tools in biology because a protein's function can often be inferred from homologous proteins. Standard sequence comparison methods use substitution matrices to find the alignment with the best sum of similarity scores between aligned residues. These similarity scores do not take the local sequence context into account. Here, we present an approach that derives context-specific amino acid similarities from short windows centered on each query sequence residue. Our results demonstrate that the sequence context contains much more information about the expected mutations than just the residue itself. By employing our context-specific similarities (CS-BLAST) in combination with NCBI BLAST, we increase the sensitivity more than 2-fold on a difficult benchmark set, without loss of speed. Alignment quality is likewise improved significantly. Furthermore, we demonstrate considerable improvements when applying this paradigm to sequence profiles: Two iterations of CSI-BLAST, our context-specific version of PSI-BLAST, are more sensitive than 5 iterations of PSI-BLAST. The paradigm for biological sequence comparison presented here is very general. It can replace substitution matrices in sequence- and profile-based alignment and search methods for both protein and nucleotide sequences.
Invasive Japanese beetles facilitate aggregation and injury by a native scarab pest of ripening fruits
Authors: Hammons Derrick L. , Kurtural S. Kaan , Newman Melissa C. , Potter Daniel A.
Published: February 2009

Invasive species' facilitation, or benefiting, of native species is rarely considered in biological invasion literature but could have serious economic consequences should a non-native herbivore facilitate injury by a native pest of high-value crops. Japanese beetle (JB),Popillia japonica, a polyphagous scarab, facilitates feeding by the obligate fruit-feeding native green June beetle (GJB),Cotinis nitida, by biting into intact grape berries that GJB, which has blunt spatulate mandibles, is otherwise unable to exploit. Here, we show JB further facilitates GJB by contaminating fruits with yeasts, and by creating infection courts for yeasts associated with GJB, that elicit volatiles exploited as aggregation kairomones by GJB. Traps baited with combinations of grapes and beetles were used to show that fruits injured by JB alone, or in combination with GJB, become highly attractive to both sexes of GJB. Such grapes emit high amounts of fermentation compounds compared with intact grapes. Beetle feeding on grape mash induced the same volatiles as addition of winemaker's yeast, and similar attraction of GJB in the field. Eight yeast species were isolated and identified from JB collected from grapevine foliage. Establishment and spread of JB throughout fruit-growing regions of the United States is likely to elevate the pest status of GJB and other pests of ripening fruits in vineyards and orchards.
Pathogenic adaptation of intracellular bacteria by rewiring a
cis
-regulatory input function
Authors: Osborne Suzanne E. , Walthers Don , Tomljenovic Ana M. , Mulder David T. , Silphaduang Uma , Duong Nancy , Lowden Michael J. , Wickham Mark E. , Waller Ross F. , Kenney Linda J. , Coombes Brian K.
Published: February 2009

The acquisition of DNA by horizontal gene transfer enables bacteria to adapt to previously unexploited ecological niches. Although horizontal gene transfer and mutation of protein-coding sequences are well-recognized forms of pathogen evolution, the evolutionary significance of
cis
-regulatory mutations in creating phenotypic diversity through altered transcriptional outputs is not known. We show the significance of regulatory mutation for pathogen evolution by mapping and then rewiring a
cis
-regulatory module controlling a gene required for murine typhoid. Acquisition of a binding site for the
Salmonella
pathogenicity island-2 regulator, SsrB, enabled the
srfN
gene, ancestral to the
Salmonella
genus, to play a role in pathoadaptation of
S. typhimurium
to a host animal. We identified the evolved
cis
-regulatory module and quantified the fitness gain that this regulatory output accrues for the bacterium using competitive infections of host animals. Our findings highlight a mechanism of pathogen evolution involving regulatory mutation that is selected because of the fitness advantage the new regulatory output provides the incipient clones.
Seasonal changes of macrobenthos distribution and diversity in Zhoushan sea area
Authors: Shou Lu , Huang Yijun , Zeng Jiangning , Gao Aigen , Liao Yibo , Chen Quanzhen
Published: February 2009

To understand the distribution and seasonal changes of macrobenthos in Zhoushan sea area, two cruise surveys were carried out in the summer and winter. A total of 219 species were recorded in the sampling sediment during the two seasons. Two-way ANOVA results showed that the differences were not significant among sections in all the community parameters (species number, biomass and density) and species diversity (Shannon-Weiner index and Pielou's evenness index), but significant between seasons in species number, density and Shannon-Weiner index. This might be influenced by two factors as follows: (1) water currents' differences between seasons; (2) considerable differences in temperature between seasons.
Lost in translation – using bilingual differences to increase emotional mastery following bullying
Authors: Tehrani Noreen , Vaughan Sarah
Published: February 2009

Aims & Objectives: This paper critically examines the nature and benefits of a therapeutic alliance created between a fluent, bilingual woman who had suffered a period of extreme bullying and her monolingual therapist. Method: The paper uses a case study approach to consider the underpinning psycho‐neurology and describes the theoretical frameworks used to inform the therapeutic process and facilitate recovery. Results: The therapeutic approach proved successful in dealing with the physical, emotional and psychological impact of the bullying and has enabled the subject to return to work successfully. Conclusions: The emotional distancing provided by language switching can be invaluable in enabling a traumatised person to make sense of their experience.
Working therapeutically with mothers who experience the trauma of homelessness: An opportunity for growth
Authors: Tischler Victoria , Edwards Vicki , Vostanis Panos
Published: February 2009

Homelessness is recognised to be a traumatic event in itself and is often preceded by the experience of violence. More recent research has indicated that homelessness can function to enact growth and resilience in women with dependent children. This review paper draws together findings from a series of studies involving women with dependent children who experience homelessness. It identifies key psychosocial and health priorities in this population and how findings related to resilience and growth can be harnessed in therapeutic work. Pragmatic service developments and examples of good practice in therapeutic and multi‐agency interventions from the domestic violence and homelessness literature are described and recommendations are made for developing services and working therapeutically with marginalised and transient populations. Therapists need to work in a flexible and integrated way with other key services, so that the crisis and long term needs of this population are met.
Dynamic gamma knife radiosurgery
Authors: Luan Shuang , Swanson Nathan , Chen Zhe , Ma Lijun
Published: February 2009

Gamma knife has been the treatment of choice for various brain tumors and functional disorders. Current gamma knife radiosurgery is planned in a ‘ball-packing’ approach and delivered in a ‘step-and-shoot’ manner, i.e. it aims to ‘pack’ the different sized spherical high-dose volumes (called ‘shots’) into a tumor volume. We have developed a dynamic scheme for gamma knife radiosurgery based on the concept of ‘dose-painting’ to take advantage of the new robotic patient positioning system on the latest Gamma Knife C™ and Perfexion™ units. In our scheme, the spherical high dose volume created by the gamma knife unit will be viewed as a 3D spherical ‘paintbrush’, and treatment planning reduces to finding the best route of this ‘paintbrush’ to ‘paint’ a 3D tumor volume. Under our dose-painting concept, gamma knife radiosurgery becomes dynamic, where the patient moves continuously under the robotic positioning system. We have implemented a fully automatic dynamic gamma knife radiosurgery treatment planning system, where the inverse planning problem is solved as a traveling salesman problem combined with constrained least-square optimizations. We have also carried out experimental studies of dynamic gamma knife radiosurgery and showed the following. (1) Dynamic gamma knife radiosurgery is ideally suited for fully automatic inverse planning, where high quality radiosurgery plans can be obtained in minutes of computation. (2) Dynamic radiosurgery plans are more conformal than step-and-shoot plans and can maintain a steep dose gradient (around 13% per mm) between the target tumor volume and the surrounding critical structures. (3) It is possible to prescribe multiple isodose lines with dynamic gamma knife radiosurgery, so that the treatment can cover the periphery of the target volume while escalating the dose for high tumor burden regions. (4) With dynamic gamma knife radiosurgery, one can obtain a family of plans representing a tradeoff between the delivery time and the dose distributions, thus giving the clinician one more dimension of flexibility of choosing a plan based on the clinical situations.
MOM: maximum oligonucleotide mapping
Authors: Eaves Hugh L. , Gao Yuan
Published: February 2009

Summary: Current short read mapping programs are based on the reasonable premise that most sequencing errors occur near the 3′ end of the read. These programs map reads with either a small number of mismatches in the entire read, or a small number of mismatches in the segment remaining after trimming bases from the 3′ end or a single base from the 5′ end. Though multiple sequencing errors most likely occur near the 3′ end of the reads, they can still occur at the 5′ end of the reads. Trimming from the 3′ end will not be able to map these reads. We have developed a program, Maximum Oligonucleotide Mapping (MOM), based on the concept of query matching that is designed to capture a maximal length match within the short read satisfying the user defined error parameters. This query matching approach thus accommodates multiple sequencing errors at both ends. We demonstrate that this technique achieves greater sensitivity and a higher percentage of uniquely mapped reads when compared to existing programs such as SOAP, MAQ and SHRiMP.

Software and Test Data Availability:  http://mom.csbc.vcu.edu

Contact:  ygao@vcu.edu  hleaves@vcu.edu
Supervised feature selection in mass spectrometry-based proteomic profiling by blockwise boosting
Authors: Gertheiss Jan , Tutz Gerhard
Published: February 2009

Summary: When feature selection in mass spectrometry is based on single m/z values, problems arise from the fact that variability is not only in vertical but also in horizontal direction, i.e. also slightly differing m/z values may correspond to the same feature. Hence, we propose to use the full spectra as input to a classifier, but to select small groups – or blocks – of adjacent m/z values, instead of single m/z values only. For that purpose we modify the LogitBoost to obtain a version of the so-called blockwise boosting procedure for classification. It is shown that blockwise boosting has high potential in predictive proteomics.

Availability: R-code is freely available at http://www.statistik.lmu.de/~gertheiss/research.html.

Contact:  jan.gertheiss@stat.uni-muenchen.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
An integrative scoring system for ranking SNPs by their potential deleterious effects
Authors: Lee Phil Hyoun , Shatkay Hagit
Published: February 2009

Motivation: Identifying single nucleotide polymorphisms (SNPs) that underlie common and complex human diseases, such as cancer, is of major interest in current molecular epidemiology. Nevertheless, the tremendous number of SNPs on the human genome requires computational methods for prioritizing SNPs according to their potentially deleterious effects to human health, and as such, for expediting genotyping and analysis. As of yet, little has been done to quantitatively assess the possible deleterious effects of SNPs for effective association studies.

Results: We propose a new integrative scoring system for prioritizing SNPs based on their possible deleterious effects within a probabilistic framework. We applied our system to 580 disease-susceptibility genes obtained from the OMIM (Online Mendelian Inheritance in Man) database, which is one of the most widely used databases of human genes and genetic disorders. The scoring results clearly show that the distribution of the functional significance (FS) scores for already known disease-related SNPs is significantly different from that of neutral SNPs. In addition, we summarize distinct features of potentially deleterious SNPs based on their FS score, such as functional genomic regions where they occur or bio-molecular functions that they mainly affect. We also demonstrate, through a comparative study, that our system improves upon other function-assessment systems for SNPs, by assigning significantly higher FS scores to already known disease-related SNPs than to neutral SNPs.

Availability:  http://compbio.cs.queensu.ca/F-SNP and http://compbio.cs.queensu.ca/RankingSNPs/default.html.

Contact:  lee@cs.queensu.ca
INTEGRALL: a database and search engine for integrons, integrases and gene cassettes
Authors: Moura Alexandra , Soares Mário , Pereira Carolina , Leitão Nuno , Henriques Isabel , Correia António
Published: February 2009

Summary: INTEGRALL is a freely available, text-based search system developed with the aim of collecting and organizing information on integrons in a single database. The current release (1.2) contains more than 4800 integron sequences and provides a public genetic repository for sequence data and nomenclature, offering scientists an easy and interactive access to integron's DNA sequences, their molecular arrangements as well as their genetic contexts.

Availability:  http://integrall.bio.ua.pt

Contact:  amoura@ua.pt
A Chinese Herbal Decoction, Dang Gui Bu Xue Tang, Prepared from Radix Astragali and Radix Angelicae sinensis, Ameliorates Insulin Resistance Induced by A High‐Fructose Diet in Rats
Authors: Liu I-Min , Tzeng Thing-Fong , Liou Shorong-Shii
Published: February 2009

Dang Gui Bu Xue Tang (DBT), a Chinese medicinal decoction contains Radix Angelicae sinensis (Danggui) and Radix Astragali (Huangqi) at a ratio of 1 : 5, is used commonly for treating women′s ailments. This study was conducted to explore the effects of this preparation on insulin resistance in rats fed with 6‐week diet containing 60% fructose. Similar to the action of rosiglitazone (4 mg kg-1 per day by an oral administration), repeated oral administration of DBT (2.5 g kg-1 per day) for 14 days was found to significantly alleviate the hyperglycemia but made no influence on plasma lipid profiles nor weight gain in fructose chow‐fed rats. Also, the higher degree of insulin resistance as measured by homeostasis model assessment of basal insulin resistance in fructose chow‐fed rats was significantly decreased by repeated DBT treatment. DBT displays the characteristic of rosiglitazone by increasing the whole‐body insulin sensitivity in fructose chow‐fed rats after 2‐week treatment, as evidenced by the marked elevation of composite whole‐body insulin sensitivity index during the oral glucose tolerance test. DBT improves insulin sensitivity through increased post‐receptor insulin signaling mediated by enhancements in insulin receptor substrate‐1‐associated phosphatidylinositol 3‐kinase step and glucose transporter subtype 4 translocation in soleus muscles of animals exhibiting insulin resistance. DBT is therefore proposed as potentially useful adjuvant therapy for patients with insulin resistance and/or the patients who wish to increase insulin sensitivity.
Comparison of data-processing algorithms for the lidar detection of mackerel in the Norwegian Sea
Authors: Churnside James H. , Tenningen Eirik , Wilson James J.
Published: February 2009

Churnside, J. H., Tenningen, E., and Wilson, J. J. 2009. Comparison of data-processing algorithms for the lidar detection of mackerel in the Norwegian Sea. – ICES Journal of Marine Science, 66: 1023–1028. A broad-scale lidar survey was conducted in the Norwegian Sea in summer 2002. Since then, various data-processing techniques have been developed, including manual identification of fish schools, multiscale median filtering, and curve fitting of the lidar profiles. In the automated techniques, applying a threshold to the data, as carrried out already to eliminate plankton scattering, has been demonstrated previously to improve the correlation between lidar and acoustic data. We applied these techniques to the lidar data of the 2002 survey and compared the results with those of a mackerel (Scomber scombrus) survey done by FV “Endre Dyrøy” and FV “Trønderbas” during the same period. Despite a high level of variability in both lidar and trawl data, the broad-scale distribution of fish inferred from the lidar agreed with that of mackerel caught by the FV “Endre Dyrøy”. This agreement was obtained using both manual and automated processing of the lidar data. This work is the first comparison of concurrent lidar and trawl surveys, and it demonstrates the utility of airborne lidar for mackerel studies.
Erythropoietin Protects against Local Anesthetic Myotoxicity during Continuous Regional Analgesia
Authors: Nouette-Gaulain Karine , Bellance Nadège , Prévost Baptiste , Passerieux Emilie , Pertuiset Claire , Galbes Olivier , Smolkova Katarina , Masson Françoise , Miraux Sylvain , Delage Jean-Paul , Letellier Thierry , Rossignol Rodrigue , Capdevila Xavier , Sztark François
Published: February 2009

Background

Local anesthetics offer the benefits of extended analgesia with greater patient satisfaction and faster rehabilitation compared with intravenous morphine. These benefits, however, can be offset by adverse iatrogenic muscle pain caused by bupivacaine. Here, the authors describe the mechanisms of local anesthetic-induced myotoxicity and a partial protective effect of recombinant human erythropoietin (rhEPO).

Methods

The authors developed a rat analgesia model with femoral nerve catheter and a cell culture model of human skeletal muscle myoblasts to study local anesthetic effects. Rats were randomly assigned to four different groups: daily intraperitoneal injection with 5,000 U/kg rhEPO or saline coupled to a perineural catheter injection with 1 ml/kg bupivacaine, 0.25%, or saline. In psoas rat muscle, oxygen consumption rates were measured using a Clark-type electrode in saponin-skinned fibers. Mitochondrial adenosine triphosphate synthesis rates were determined by bioluminescence. Enzymatic activity of mitochondrial respiratory chain complexes was measured on tissue homogenates using spectrophotometric procedures, and mitochondrial morphology was analyzed by transmission electron microscopy. In addition, the interaction between bupivacaine and rhEPO was investigated on human skeletal muscle myoblasts by fluorescence microscopy using mitotracker green and using the lipophilic cation JC-1.

Results

Bupivacaine caused impairment of mitochondrial structure and bioenergetics in rats. Human myoblasts treated with bupivacaine showed a dose-dependent decrease in mitochondrial membrane potential associated with unusual morphologies. Impairment of mitochondrial bioenergetics was prevented partially by the use of rhEPO coadministered with bupivacaine.

Conclusions

The authors demonstrated a dose- and time-dependent protective effect of rhEPO against bupivacaine-induced myotoxicity in regional analgesia.
Desflurane-induced Postconditioning Is Mediated by β-Adrenergic Signaling
Authors: Lange Markus , Redel Andreas , Lotz Christopher , Smul Thorsten M. , Blomeyer Christoph , Frank Anja , Stumpner Jan , Roewer Norbert , Kehl Franz
Published: February 2009

Background

Anesthetic preconditioning is mediated by beta-adrenergic signaling. This study was designed to elucidate the role of beta-adrenergic signaling in desflurane-induced postconditioning.

Methods

Pentobarbital-anesthetized New Zealand White rabbits were subjected to 30 min of coronary artery occlusion followed by 3 h of reperfusion and were randomly assigned to receive vehicle (control), 1.0 minimum alveolar concentration of desflurane, esmolol (30 mg x kg(-1) x h(-1)) for the initial 30 min of reperfusion or throughout reperfusion, the beta2-adrenergic receptor blocker ICI 118,551 (0.2 mg/kg), the protein kinase A inhibitor H-89 (250 microg/kg), or the calcium/calmodulin-dependent protein kinase II inhibitor KN-93 (300 microg/kg) in the presence or absence of desflurane. Protein expression of protein kinase B, calcium/calmodulin-dependent protein kinase II, and phospholamban was measured by Western immunoblotting. Myocardial infarct size was assessed by triphenyltetrazolium staining.

Results

Infarct size was 57 +/- 5% in control. Desflurane postconditioning reduced infarct size to 36 +/- 5%. Esmolol given during the initial 30 min of reperfusion had no effect on infarct size (54 +/- 4%) but blocked desflurane-induced postconditioning (58 +/- 5%), whereas esmolol administered throughout reperfusion reduced infarct size in the absence or presence of desflurane to 42 +/- 6% and 41 +/- 7%, respectively. ICI 118,551 and KN-93 did not affect infarct size (62 +/- 4% and 62 +/- 6%, respectively) but abolished desflurane-induced postconditioning (57 +/- 5% and 64 +/- 3%, respectively). H-89 decreased infarct size in the absence (36 +/- 5%) or presence (33 +/- 5%) of desflurane.

Conclusions

Desflurane-induced postconditioning is mediated by beta-adrenergic signaling. However, beta-adrenergic signaling displays a differential role in cardioprotection during reperfusion.
Subcellular Localization and Functional Analysis of the Arabidopsis GTPase RabE
Authors: Speth Elena Bray , Imboden Lori , Hauck Paula , He Sheng Yang
Published: February 2009

Membrane trafficking plays a fundamental role in eukaryotic cell biology. Of the numerous known or predicted protein components of the plant cell trafficking system, only a relatively small subset have been characterized with respect to their biological roles in plant growth, development, and response to stresses. In this study, we investigated the subcellular localization and function of an Arabidopsis (Arabidopsis thaliana) small GTPase belonging to the RabE family. RabE proteins are phylogenetically related to well-characterized regulators of polarized vesicle transport from the Golgi apparatus to the plasma membrane in animal and yeast cells. The RabE family of GTPases has also been proposed to be a putative host target of AvrPto, an effector protein produced by the plant pathogen Pseudomonas syringae, based on yeast two-hybrid analysis. We generated transgenic Arabidopsis plants that constitutively expressed one of the five RabE proteins (RabE1d) fused to green fluorescent protein (GFP). GFP-RabE1d and endogenous RabE proteins were found to be associated with the Golgi apparatus and the plasma membrane in Arabidopsis leaf cells. RabE down-regulation, due to cosuppression in transgenic plants, resulted in drastically altered leaf morphology and reduced plant size, providing experimental evidence for an important role of RabE GTPases in regulating plant growth. RabE down-regulation did not affect plant susceptibility to pathogenic P. syringae bacteria; conversely, expression of the constitutively active RabE1d-Q74L enhanced plant defenses, conferring resistance to P. syringae infection.