bluuebunny/crossref_metadata_2025 huggingface dataset:
Generalized Scatter Plots
Authors: Keim Daniel A. , Hao Ming C. , Dayal Umeshwar , Janetzko Halldor , Bak Peter
Published: December 2009

Scatter Plots are one of the most powerful and most widely used techniques for visual data exploration. A well-known problem is that scatter plots often have a high degree of overlap, which may occlude a significant portion of the data values shown. In this paper, we propose the generalized scatter plot technique, which allows an overlap-free representation of large data sets to fit entirely into the display. The basic idea is to allow the analyst to optimize the degree of overlap and distortion to generate the best-possible view. To allow an effective usage, we provide the capability to zoom smoothly between the traditional and our generalized scatter plots. We identify an optimization function that takes overlap and distortion of the visualization into acccount. We evaluate the generalized scatter plots according to this optimization function, and show that there usually exists an optimal compromise between overlap and distortion. Our generalized scatter plots have been applied successfully to a number of real-world IT services applications, such as server performance monitoring, telephone service usage analysis and financial data, demonstrating the benefits of the generalized scatter plots over traditional ones.
Influence of the temporal shape of femtosecond pulses on silicon micromachining
Authors: Gunaratne Tissa C. , Zhu Xin , Lozovoy Vadim V. , Dantus Marcos
Published: December 2009

The influence of femtosecond laser pulse shaping on silicon wafer micromachining is explored. Surface second harmonic generation provides in situ pulse characterization of the laser pulses, and plasma and atomic emissions were identified as valuable indicators of the micromachining process. The ablation threshold was found to decrease as the bandwidth of the pulses increases, as well as for shorter pulses. Dependence of atomic and plasma emissions on temporal shape of the pulses confirmed that emission preceded ablation and has a threshold as well. The morphology of micromachined holes was observed to be dependent upon pulse duration.
The effective diffusion coefficient of a small molecule in a two-phase gel medium
Authors: Kingsburry Christine , Slater Gary W.
Published: December 2009

Using simple theoretical arguments and exact numerical lattice calculations, Hickey et al. [J. Chem. Phys. 124, 204903 (2006)] derived and tested an expression for the effective diffusion coefficient of a probe molecule in a two-phase medium consisting of a hydrogel with large gel-free inclusions. Although providing accurate predictions, this expression neglects important characteristics that such two-phase systems can present. In this article, we extend the previously derived expression in order to include local interactions between the gel and the analyte, interfacial effects between the main phase and the inclusions, and finally a possible incomplete separation between the two phases. We test our new, generalized expressions using exact numerical calculations. These generalized equations should be a useful tool for the development of novel multiphase systems for specific applications, such as drug-delivery platforms.
Microstructure and tribological properties of Ti-contained amorphous carbon film deposited by DC magnetron sputtering
Authors: Li R. L. , Tu J. P. , Hong C. F. , Liu D. G. , Zhou D. H. , Sun H. L.
Published: December 2009

Pure amorphous carbon (a-C) film and that with a small amount of Ti were deposited on high speed steel (W18Cr4V) substrates by means of dc closed field unbalanced magnetron sputtering. The chemical composition and microstructure of the a-C films were performed using x-ray photoelectron spectroscopy, x-ray diffraction, Raman spectra, and transmission electron microscopy. The mechanical and tribological properties were evaluated using a nanoindentor, Rockwell and scratch tests, and a conventional ball-on-disk tribometer, respectively. The pure a-C film showed the high hardness (53 GPa), elastic modulus (289 GPa), but the poor adhesive strength. When adding a small amount of Ti to the a-C film, both the adhesive strength and the tribological properties were improved. The Ti contained a-C film had the low wear rate (1.9×10−17 m3 N−1 m−1) and friction coefficient in humid air.
Analysis of the energetic parameters of a theta pinch
Authors: Cavalcanti G. H. , Farias E. E.
Published: December 2009

This work is devoted to study experimentally the performance of a theta pinch when the number of capacitors and turns of magnetic coil and the diameter of the glass tube are changed. To model the theta pinch a simple RLC circuit is used and the measurement of energy transmission from the bank of capacitors to the plasma is made using few experimental resources. In this work it was analyzed more than 2500 curves with a nonlinear procedure. Our results show that it is possible to design an optimized theta pinch making the appropriated choice of energetic parameters and therefore to reduce the stress of the system.
Observation of pulsed x-ray trains produced by laser-electron Compton scatterings
Authors: Sakaue Kazuyuki , Washio Masakazu , Araki Sakae , Fukuda Masafumi , Higashi Yasuo , Honda Yosuke , Omori Tsunehiko , Taniguchi Takashi , Terunuma Nobuhiro , Urakawa Junji , Sasao Noboru
Published: December 2009

X-ray generation based on laser-electron Compton scattering is one attractive method to achieve a compact laboratory-sized high-brightness x-ray source. We have designed, built, and tested such a source; it combines a 50 MeV multibunch electron linac with a mode-locked 1064 nm laser stored and amplified in a Fabry–Pérot optical cavity. We directly observed trains of pulsed x rays using a microchannel plate detector; the resultant yield was found to be 1.2×105 Hz in good agreement with prediction. We believe that the result has demonstrated good feasibility of linac-based compact x-ray sources via laser-electron Compton scatterings.
Experimental study of the bouncing trajectory of a particle along a rotating wall
Authors: Le Quiniou A. , Rioual F. , Héritier P. , Lapusta Y.
Published: December 2009

We intend to present a new experimental setup that allows the study of the trajectory of a solid spherical particle bouncing at a high velocity along a rotating plate. Using different surface treatments for the plate, we can explore the phase space for the mechanical parameters of the problem (normal restitution coefficient en and dynamic friction coefficient μ). An accurate statistical analysis of the trajectory (radial and angular velocities) has been conducted based on an image analysis procedure. Experiments show a regime of successive bounces, followed by a regime of permanent contact of the particle along the vane and a transition from a rolling with a sliding regime to a rolling without sliding regime triggered by the friction particle/wall. A simple model using two mechanical parameters (normal coefficient of restitution en and friction coefficient μ), as proposed recently [A. Le Quiniou and F. Rioual, “Flow of a particle along a rotating wall,” Europhys. Lett. 82, 34001 (2008)], is sufficient to reproduce quantitatively all the features of the trajectory. The friction coefficient has to be determined independently using a mechanical protocol of impact of a single particle on a fixed wall—following Foerster et al. [“Measurements of the collision properties of small spheres,” Phys. Fluids 6, 1108 (1994)]—in particular, an outcome of this study is that the initial spin of the particle appears to have no effect on the features of the impact as long as the relative velocities at the contact are considered.
Chemical composition anomalies of nanotubes stretched from Au-Si(Ge) liquid alloy by an intense electric field
Authors: Joyes P. , Van de Walle J. , Tarento R.-J.
Published: December 2009

Nanotubes are stretched by intense electric fields (few volts per angstrom) supplied by an eutectic Au0.73Ge0.27 or Au0.82Si0.18 alloy liquid metal ion source. Chemical composition anomalies are observed in the stretched nanotubes. In the Au-Ge system, nanotubes are the smaller two-shell pure gold nanowires. In the Au-Si system, nanotubes have same geometric structures as previously but now silicon atoms can substitute gold atoms. Nanotubes are mainly formed by SiAu3 alloy zones separated by smaller pure gold parts. Our results are consistent with local modifications of the chemical composition of the alloy liquid in the nanotube vicinity submitted to intense electric field gradients.
Ferroelectricity triggered in the quantum paraelectric AgTaO3 by Li-substitution
Authors: Soon Hwee Ping , Taniguchi Hiroki , Itoh Mitsuru
Published: December 2009

Ferroelectricity has been induced in the quantum paraelectric AgTaO3 (AT) by Li+ substitution, as evidence by both the dielectric anomaly and the hysteretic loop of electrical displacement versus applied electric field. The transition temperature (Tc) of Li-doped AT was found to increase with increasing level of Li+ substitution. Also, by substituting 12 mol % of Li+ into AT, which is close to the solubility limit, a ferroelectric material with a residual polarization ∼15 μC/cm2 and Tc at 258 K was then triggered.
Postfrontal nanoparticles at Cape Grim: impact on cloud nuclei concentrations
Authors: Gras John L.
Published: December 2009

Environmental context. Accurate prediction of climate change requires good knowledge of all the contributing processes; those processes controlling clouds and cloud properties are of particular importance. In this study the growth of bursts of nanometre-sized particles observed following cold fronts over the Southern Ocean was modelled to assess their importance as a source of cloud droplet nuclei. This showed that these post-frontal events were responsible for ~8% of the cloud nucleus population in winter but much less in summer.
Abstract. Aerosol removal and growth rates were determined for the Cape Grim marine boundary layer (MBL) using local observations. Background particle growth rates, estimated using replacement of condensable sulfur species lost to particle removal are 0.04 nm h–1 (winter) and 0.17 nm h–1 (summer) and for post-frontal nucleation-events growth rates determined using evolution of the concentration ratio of particles with diameter >3 nm and 11 nm are ~0.3–0.4 nm h–1, consistent with reported high-latitude events. A box model using region-specific loss and growth rates predicts free-troposphere/MBL N3 ratios of 1.3–2.1 and 2.4–2.5 for background and event growth rates, compared with observations in the range of 0.7–1.5. Post-frontal nucleation events were found to contribute from <1 to ~8% of the CCN population depending on season and growth rate. However, these events help maintain the MBL Aitken population, contributing up to ~30%.
Methane formation in aerobic environments
Authors: Keppler Frank , Boros Mihály , Frankenberg Christian , Lelieveld Jos , McLeod Andrew , Pirttilä Anna Maria , Röckmann Thomas , Schnitzler Jörg-Peter
Published: December 2009

Environmental context. Methane is an important greenhouse gas and its atmospheric concentration has drastically increased since pre-industrial times. Until recently biological methane formation has been associated exclusively with anoxic environments and microbial activity. In this article we discuss several alternative formation pathways of methane in aerobic environments and suggest that non-microbial methane formation may be ubiquitous in terrestrial and marine ecosystems. Abstract. Methane (CH4), the second principal anthropogenic greenhouse gas after CO2, is the most abundant reduced organic compound in the atmosphere and plays a central role in atmospheric chemistry. Therefore a comprehensive understanding of its sources and sinks and the parameters that control emissions is prerequisite to simulate past, present and future atmospheric conditions. Until recently biological CH4 formation has been associated exclusively with anoxic environments and methanogenic activity. However, there is growing and convincing evidence of alternative pathways in the aerobic biosphere including terrestrial plants, soils, marine algae and animals. Identifying and describing these sources is essential to complete our understanding of the biogeochemical cycles that control CH4 in the atmospheric environment and its influence as a greenhouse gas.
Chiral porphyrazine near-IR optical imaging agent exhibiting preferential tumor accumulation
Authors: Trivedi Evan R. , Harney Allison S. , Olive Mary B. , Podgorski Izabela , Moin Kamiar , Sloane Bonnie F. , Barrett Anthony G.M. , Meade Thomas J. , Hoffman Brian M.
Published: December 2009

A chiral porphyrazine (pz), H2[pz(trans-A2B2)] (247), has been prepared that exhibits preferential in vivo accumulation in the cells of tumors. Pz 247 exhibits near-infrared (NIR) emission withλ > 700 nm in the required wavelength range for maximum tissue penetration. When MDA-MB-231 breast tumor cells are treated with 247, the agent shows strong intracellular fluorescence with an emission maximum, 704 nm, which indicates that it localizes within a hydrophobic microenvironment. Pz 247 is shown to associate with the lipophilic core of LDL and undergo cellular entry primarily through receptor-mediated endocytosis accumulating in lysosomes. Preliminary in vivo studies show that 247 exhibits preferential accumulation and retention in the cells of MDA-MB-231 tumors subcutaneously implanted in mice, thereby enabling NIR optical imaging with excellent contrast between tumor and surrounding tissue. The intensity of fluorescence from 247 within the tumor increases over time up to 48 h after injection presumably due to the sequestration of circulating 247/LDL complex by the tumor tissue. As the need for cholesterol, and thus LDL, is elevated in highly proliferative tumor cells over nontumorigenic cells, 247 has potential application for all such tumors.
Successful Implementation of the World Health Organization Hand Hygiene Improvement Strategy in a Referral Hospital in Mali, Africa
Authors: Allegranzi Benedetta , Sax Hugo , Bengaly Loséni , Riebet Hervé , Minta Daouda K. , Chraiti Marie-Noelle , Sokona Fatoumata Maiga , Gayet-Ageron Angele , Bonnabry Pascal , Pittet Didier ,   behalf of the World Health Organization “Point G” Project Management Committee
Published: December 2009

Objective.

To assess the feasibility and effectiveness of the World Health Organization hand hygiene improvement strategy in a low-income African country.

Design.

A before-and-after study from December 2006 through June 2008, with a 6-month baseline evaluation period and a follow-up period of 8 months from the beginning of the intervention.

Setting.

University Hospital, Bamako, Mali.

Participants.

TWO hundred twenty-four healthcare workers.

Methods.

The intervention consisted of introducing a locally produced, alcohol-based handrub; monitoring hand hygiene compliance; providing performance feedback; educating staff; posting reminders in the workplace; and promoting an institutional safety climate according to the World Health Organization multimodal hand hygiene improvement strategy. Hand hygiene infrastructure, compliance, healthcare workers' knowledge and perceptions, and handrub consumption were evaluated at baseline and at follow-up.

Results.

Severe deficiencies in the infrastructure for hand hygiene were identified before the intervention. Local handrub production and quality control proved to be feasible, affordable, and satisfactory. At follow-up, handrubbing was the quasi-exclusive hand hygiene technique (93.3%). Compliance increased from 8.0% at baseline to 21.8% at follow-up (P< .001). Improvement was observed across all professional categories and medical specialities and was independently associated with the intervention (odds ratio, 2.50; 95% confidence interval, 1.8-3.5). Knowledge enhanced significantly (P< .05), and perception surveys showed a high appreciation of each strategy component by staff.

Conclusions.

Multimodal hand hygiene promotion is feasible and effective in a low-income country. Access to handrub was critical for its success. These findings motivated the government of Mali to expand the intervention nationwide. This experience represents a significant advancement for patient safety in developing countries.
Power to detect selective allelic amplification in genome-wide scans of tumor data
Authors: Dewal Ninad , Freedman Matthew L. , LaFramboise Thomas , Pe'er Itsik
Published: December 2009

Motivation: Somatic amplification of particular genomic regions and selection of cellular lineages with such amplifications drives tumor development. However, pinpointing genes under such selection has been difficult due to the large span of these regions. Our recently-developed method, the amplification distortion test (ADT), identifies specific nucleotide alleles and haplotypes that confer better survival for tumor cells when somatically amplified. In this work, we focus on evaluating ADT's power to detect such causal variants across a variety of tumor dataset scenarios.

Results: Towards this end, we generated multiple parameter-based, synthetic datasets—derived from real data—that contain somatic copy number aberrations (CNAs) of various lengths and frequencies over germline single nucleotide polymorphisms (SNPs) genome-wide. Gold-standard causal sub-regions were assigned within these CNAs, followed by an assessment of ADT's ability to detect these sub-regions. Results indicate that ADT possesses high sensitivity and specificity in large sample sizes across most parameter cases, including those that more closely reflect existing SNP and CNA cancer data.

Availability: ADT is implemented in the Java software HADiT and can be downloaded through the SVN repository (via Develop→ Code→SVN Browse) at: http://sourceforge.net/projects/hadit/.

Contact:  ninad.dewal@dbmi.columbia.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Red Mold Rice Mitigates Oral Carcinogenesis in 7,12‐Dimethyl‐1,2‐Benz[a]anthracene‐Induced Oral Carcinogenesis in Hamster
Authors: Tsai Ruei-Lan , Ho Bing-Ying , Pan Tzu-Ming
Published: December 2009

The prevalence of oral tumor has exponentially increased in recent years; however, the effective therapies or prevention strategies are not sufficient. Red mold rice is a traditional Chinese food, and several reports have demonstrated that red mold rice had an anti‐tumor effect. However, the possible anti‐tumor mechanisms of the red mold rice are unclear. In this study, we examined the anti‐tumor effect of red mold rice on 7,12‐dimethyl‐1,2‐benz[a]anthracene (DMBA)‐induced oral tumor in hamster. The ethanol extract of red mold rice (RMRE) treatment significantly decreases the levels of DMBA‐induced reactive oxygen species, nitro oxide and prostaglandin E2 than those of the lovastatin‐treated group (P  <  .001). Moreover, RMRE decreases the formation of oral tumor induced by DMBA. Monacolin K, monascin, ankaflavin or other red mold rice metabolites had been reported to decrease inflammation and oxidative stress and exerted anti‐tumor effects. Therefore, we evaluated the anti‐inflammation and anti‐oxidative stress effects of monacolin K, monascin, ankaflavin and citrinin in lipopolysaccharide‐treated RAW264.7 cells. We found that RMRE reduced the LPS‐induced nitrite levels in RAW264.7 cells better than monacolin K, monascin, ankaflavin or citrinin (P  <  .05).
Temporal patterns of spatial genetic structure and effective population size in European plaice (Pleuronectes platessa) along the west coast of Scotland and in the Irish Sea
Authors: Watts Phillip C. , Kay Suzanne M. , Wolfenden Drew , Fox Clive J. , Geffen Audrey J. , Kemp Stephen J. , Nash Richard D. M.
Published: December 2009

Watts, P. C., Kay, S. M., Wolfenden, D., Fox, C. J., Geffen, A. J., Kemp, S. J., and Nash, R. D. M. 2010. Temporal patterns of spatial genetic structure and effective population size in European plaice (Pleuronectes platessa) along the west coast of Scotland and in the Irish Sea. – ICES Journal of Marine Science, 67: 607–616. The European plaice (Pleuronectes platessa) is a relatively mobile flatfish species, and previous studies have reported broad-scale genetic homogeneity among samples distributed throughout much of its northern European range, with no evidence for isolation-by-distance (IBD) population structure. Using microsatellite loci, the pattern of spatial genetic structure and effective population size is characterized for >800 plaice collected from locations off the west coast of Great Britain over a 3-year period (2001–2003). The plaice populations are characterized by weak spatial genetic structure, consistent with tagging data, and relatively low effective population sizes. In contrast to previous work, a pattern of isolation by distance is present among pairs of plaice from within each sampling period. However, IBD spatial structure was not observed for comparisons of plaice from different sampling years or using the entire dataset, indicating a patchy temporal genetic structure. Therefore, pooling the data from several years can mask subtle patterns of population structure and potentially confound estimation of other important demographic parameters, such as effective population size.
Development of long-term larval indices for Atlantic herring (Clupea harengus) on the northeast US continental shelf
Authors: Richardson David E. , Hare Jonathan A. , Overholtz William J. , Johnson Donna L.
Published: December 2009

Richardson, D. E., Hare, J. A., Overholtz, W. J., and Johnson, D. L. 2010. Development of long-term larval indices for Atlantic herring (Clupea harengus) on the northeast US continental shelf. – ICES Journal of Marine Science, 67: 617–627. The incorporation of data from ichthyoplankton programmes into the stock assessment process has lagged far behind the use of data from comparable adult-monitoring programmes. This can in part be attributed to a mismatch between established analytical approaches to larval-index development and the inconsistencies in sampling for many long-term ichthyoplankton datasets. Along the northeast US continental shelf, ichthyoplankton surveys have been carried out by the Northeast Fisheries Science Center (NMFS/NOAA) multiple times annually since 1971, but the spatial and seasonal allocation of sampling has varied substantially. Here, we present a non-linear least-squares approach to larval-index development. We use the age structure and abundance of larvae on each survey to derive the larval index, along with parameters describing the survival of larvae and the seasonal cycle of hatching. Application to Atlantic herring (Clupea harengus) revealed a large drop in the index around 1976, an increase in the index through the late 1980s, and another large drop in 2004. This index was correlated with the stock assessment estimate of Atlantic herring spawning-stock biomass from 1971 to 2003, but differed substantially during 2004. Our results demonstrate that our approach to larval-index development is flexible to the inconsistencies in sampling effort.
Climatic warming increases voltinism in European butterflies and moths
Authors: Altermatt Florian
Published: December 2009

Climate change is altering geographical ranges, population dynamics and phenologies of many organisms. For ectotherms, increased ambient temperatures frequently have direct consequences for metabolic rates, activity patterns and developmental rates. Consequently, in many insect species both an earlier beginning and prolongation of seasonal duration occurred in parallel with recent global warming. However, from an ecological and evolutionary perspective, the number of generations (voltinism) and investment into each generation may be even more important than seasonality, since an additional generation per unit time may accelerate population growth or adaptation. Using a dataset extending back to the mid-nineteenth century, I report changes in the voltinism of butterfly and moth species of Central Europe. A significant proportion of 263 multi-voltine species showed augmented frequency of second and subsequent generations relative to the first generation in a warm period since 1980, and 44 species even increased the number of generations after 1980. Expected ecological consequences are diverse. Since multi-voltinism has been linked to insect outbreaks they include an increase in the abundance of herbivorous pests of agriculture and forestry. However, disruption of the developmental synchrony associated with multi-voltinism and host plant phenology may also reduce fitness, potentially having unexpected consequences for species of conservation concern. The ability of species to adapt evolutionarily to a changing environment may be facilitated by increased voltinism.
Infection of the Circulifer haematoceps cell line Ciha-1 by Spiroplasma citri: the non-insect-transmissible strain 44 is impaired in invasion
Authors: Duret Sybille , Batailler Brigitte , Danet Jean-Luc , Béven Laure , Renaudin Joël , Arricau-Bouvery Nathalie
Published: December 2009

Successful transmission of Spiroplasma citri by its leafhopper vector requires a specific interaction between the spiroplasma surface and the insect cells. With the aim of studying these interactions at the cellular and molecular levels, a cell line, named Ciha-1, was established using embryonic tissues from the eggs of the S. citri natural vector Circulifer haematoceps. This is the first report, to our knowledge, of a cell line for this leafhopper species and of its successful infection by the insect-transmissible strain S. citri GII3. Adherence of the spiroplasmas to the cultured Ciha-1 cells was studied by c.f.u. counts and by electron microscopy. Entry of the spiroplasmas into the insect cells was analysed quantitatively by gentamicin protection assays and qualitatively by double immunofluorescence microscopy. Spiroplasmas were detected within the cell cytoplasm as early as 1 h after inoculation and survived at least 2 days inside the cells. Comparing the insect-transmissible GII3 and non-insect-transmissible 44 strains revealed that adherence to and entry into Ciha-1 cells of S. citri 44 were significantly less efficient than those of S. citri GII3.
Pan-genome analysis provides much higher strain typing resolution than multi-locus sequence typing
Authors: Hall Barry G. , Ehrlich Garth D. , Hu Fen Z.
Published: December 2009

The most widely used DNA-based method for bacterial strain typing, multi-locus sequence typing (MLST), lacks sufficient resolution to distinguish among many bacterial strains within a species. Here, we show that strain typing based on the presence or absence of distributed genes is able to resolve all completely sequenced genomes of six bacterial species. This was accomplished by the development of a clustering method, neighbour grouping, which is completely consistent with the lower-resolution MLST method, but provides far greater resolving power. Because the presence/absence of distributed genes can be determined by low-cost microarray analyses, it offers a practical, high-resolution alternative to MLST that could provide valuable diagnostic and prognostic information for pathogenic bacterial species.
Expression of, and in vivo stressosome formation by, single members of the RsbR protein family in Bacillus subtilis
Authors: Reeves Adam , Martinez Luis , Haldenwang William
Published: December 2009

The Bacillus subtilis stressosome is a 1.8 MDa complex that is the focal point for activating the bacterium's general response to physical stress. In vitro studies demonstrated that the stressosome's core element can be formed from one or more of a family of paralogous proteins (RsbRA, -RB, -RC and -RD) onto which the system's activator protein (RsbT) and its principal inhibitor (RsbS) are bound. The RsbR components of the stressosome are envisioned to be the initial receptors of stress signalling with the stressosome structure itself serving as a device to integrate multiple stress signals for a coordinated response. In the current work, we examine several of the in vivo characteristics of the RsbR family members, including their expression and ability to form stressosomes to regulate σ
B. Translational fusions of lacZ to each rsbR paralogue revealed that rsbRA, -RB and -RC are expressed at similar levels, which remain relatively constant during growth, ethanol stress and entry into stationary phase. rsbRD, in contrast, is expressed at a level that is only slightly above background during growth, but is induced to 30 % of the rsbRA expression level following ethanol stress. Velocity sedimentation analyses of B. subtilis extracts from strains expressing single rsbR paralogues demonstrated that each incorporates RsbS into fast-sedimenting complexes. However, consistent with rsbRD's lower expression, the RsbRD-dependent RsbS complexes were present at only 20 % of the level of the complexes seen in a wild-type strain. The lower stressosome level in the RsbRD strain is still able to hold RsbT's activity in check, implying that the RsbR/S component of stressosomes is normally in excess for the control of RsbT. Consistent with such a notion, reporter gene and Western blot assays demonstrate that although RsbT is synthesized at the same rate as RsbRA and RsbS, RsbT's ultimate level in growing B. subtilis is only 10 % that of RsbRA. Apparently, RsbT's inherent structure and/or its passage between the stressosome and its activation target compromises its persistence.
Transcriptional regulation of bone and joint remodeling by NFAT
Authors: Sitara Despina , Aliprantis Antonios O.
Published: December 2009

Summary: Osteoporosis and arthritis are highly prevalent diseases and a significant cause of morbidity and mortality worldwide. These diseases result from aberrant tissue remodeling leading to weak, fracture‐prone bones or painful, dysfunctional joints. The nuclear factor of activated T cells (NFAT) transcription factor family controls diverse biologic processes in vertebrates. Here, we review the scientific evidence that links NFAT‐regulated gene transcription to bone and joint pathology. A particular emphasis is placed on the role of NFATs in bone resorption and formation by osteoclasts and osteoblasts, respectively. In addition, emerging data that connect NFATs with cartilage biology, angiogenesis, nociception, and neurogenic inflammation are explored. The goal of this article is to highlight the importance of tissue remodeling in musculoskeletal disease and situate NFAT‐driven cellular responses within this context to inspire future research endeavors.
Combination of RET siRNA and irinotecan inhibited the growth of medullary thyroid carcinoma TT cells and xenografts via apoptosis
Authors: Koga Kimiko , Hattori Yoshiyuki , Komori Mihoko , Narishima Ryota , Yamasaki Masahiro , Hakoshima Motoki , Fukui Tetsuya , Maitani Yoshie
Published: December 2009

Medullary thyroid carcinoma (MTC) is a rare endocrine tumor that frequently metastasizes, and treatment with irinotecan (CPT‐11) is limited because of side effects. Mutations in the Rearranged during transfection (RET) proto‐oncogene are considered the causative event of MTC. The objective of this study was to examine whether small interfering RNA (siRNA) and its combined treatment with CPT‐11 could inhibit MTC cell growth in vitro and in vivo. The transfection of RET siRNA suppressed RET expression, reduced proliferation, and increased caspase‐3/7 activity via the down‐regulation of Bcl‐2 expression. Combined treatments with CPT‐11 or SN‐38 significantly increased caspase 3/7 activity compared with RET siRNA, CPT‐11 or SN‐38 treatment alone. Importantly, intratumoral injection of RET siRNA along with intravenous injection of CPT‐11 significantly inhibited the tumor growth of MTC xenografts via an increased apoptotic effect. These findings that RET siRNA enhanced sensitivity for CPT‐11 will provide a novel strategy for the treatment of MTC with RET mutation.

(Cancer Sci 2010; 101: 941–947)
The trouble with drink: why ideas matter
Authors: Edwards Griffith
Published: December 2009

This paper builds upon the work of previous authors who have explored the evolution of ideas in the alcohol arena. With revisions in the relevant sections of ICD and DSM forthcoming, such matters are of considerable contemporary importance. The focus here will be upon the history of the last 200 years. The main themes to be explored include the flux of ideas on what, over time, has counted as the trouble with drink, ideas on the cause of the problem and the impact of this thinking on public action. Medical authorities of the late Enlightenment period made the revolutionary suggestion that habitual drunkenness constituted a disease, rather than a vice. The thread of that idea can be traced to the present day, but with an alternative perception of drink itself or alcohol‐related problems generally, as cause for concern, also having a lineage. There are several inferences to be drawn from this history: the need for vigilance lest disease formulations become stalking‐horses for moralism and social control, the need to integrate awareness of alcohol dependence as a dimensional individual‐level problem, with a public health understanding of the vastly amorphous and at least equally important universe of alcohol‐related problems; the dangers lurking in scientific reductionism when the problems at issue truly require a multi‐disciplinary analysis; and the need for global consensus rather than cultural imposition of ideas on what counts as the problem with drink.
Immune function in hypopituitarism: time to reconsider?
Authors: Mukherjee Annice , Helbert Matthew , Davis Julian , Shalet Stephen
Published: December 2009

Hypopituitarism is not currently considered as a potential cause of immune disruption in humans. Accumulating data from in vitro and animal models support a role for the pituitary gland in immune regulation. Furthermore, the increased mortality risk noted in patients with adult hypopituitarism remains poorly explained and immune dysfunction could conceivably contribute to this observation. In a recent issue of Clinical & Experimental Immunology, we presented new data relating to immune status in adults with treated, severe hypopituitarism. We observed humoral immune deficiency in a significant proportion, despite stable pituitary replacement, including growth hormone (GH). This was especially evident in those with low pretreatment IGF‐I levels and appeared independent of anticonvulsant use or corticosteroid replacement. These observations require substantiation with future studies. In this short review, we summarize existing data relating to the effects of pituitary hormones on immune function and discuss potential clinical implications surrounding the hypothesis of immune dysregulation in severe hypopituitarism.
How reliably can autoimmune hypophysitis be diagnosed without pituitary biopsy
Authors: Howlett Trevor A. , Levy Miles J. , Robertson Iain J.
Published: December 2009

Autoimmune hypophysitis is a rare chronic inflammatory condition of the pituitary gland which typically presents with hypopituitarism and a pituitary mass. Cases involving anterior pituitary alone (65%) are six times more common in women, typically presenting during pregnancy or postpartum (57%). Anterior and posterior pituitary involvement (25%) are twice as common in women, and neurohypophysis alone (10%) occurs equally in both sexes. It has a prevalence of around 5 per million, an annual incidence of 1 in 7 to 9 million and in our experience represents the known or suspected cause of 0·5% of cases of hypopituitarism, <1% of pituitary masses and 2% of nonfunctioning macro lesions presenting to an endocrine clinic. However, ‘missed’ cases of autoimmune hypophysitis may be the aetiology of some other unexplained cases of hypopituitarism. Clinically, headache and visual disturbance are common. Anterior hypopituitarism shows a characteristic but atypical pattern of deficiency of ACTH followed by TSH, gonadotrophins and prolactin deficiency or hyperprolactinaemia. Eighteen percent of cases have evidence of another autoimmune condition. On magnetic resonance imaging (MRI), autoimmune hypophysitis is typically symmetrical and homogeneous with thickened but undisplaced stalk in contrast to typical findings with pituitary tumours. Ultimately, the histological diagnosis of autoimmune hypophysitis can only be confirmed by surgery but a presumptive diagnosis can often be made on the basis of a combination of context and clinical features, and pituitary biopsy is not always clinically necessary for effective clinical management of the patient.
Evaluation of documented nursing care plans by the use of nursing‐sensitive outcome indicators
Authors: Jansson Inger , Pilhammar‐Andersson Ewa , Forsberg Anna
Published: December 2009

Rationale and aim  There is a lack of evidence that nursing care plans affect patient outcomes. The aim of the present study was to evaluate whether documented nursing care plans affect patient outcomes by the use of nursing‐sensitive outcome indicators.

Method  A retrospective, cross‐sectional design with patients surveyed at time of discharge from two hospital units for patients with stroke and after 2–3 weeks at home. The control unit (A) did not employ care plans. The intervention unit (B) used care plans on a daily basis. Outcome was measured by ‘the National Stroke Register’ and the two questionnaires: ‘Quality of patients' perspective’ and ‘Euroquol five dimensions’. Data were collected over a 5‐month period (October 2007–February 2008).

Results  In total, 87 patients were included in the study. Patient characteristics in the two groups at admission and the health‐related quality of life 2 to 3 weeks after discharge were similar. The patients from unit B were more satisfied with individual care (P = 0.03) and participation (P = 0.007). Unit B also had a shorter length of stay (P = 0.004).

Conclusions  The effects of documented care plans are difficult to evaluate from a patient perspective, as many factors can improve the outcome. However, documentation of care plans is a prerequisite for measuring the quality and outcome of the care provided. This small study indicates that documented care plans may affect patient satisfaction regarding individual care, participation and length of hospital stay.
Microstructure and mechanical properties of the NiNbZrTiAl amorphous alloys with 10 and 25 at.% Nb content
Authors: CZEPPE T. , OCHIN P. , SYPIEŃ A. , MAJOR Ł.
Published: December 2009

The results of investigation of two different Ni‐based glasses with compositions Ni58Nb10Zr13Ti12Al7 and Ni58Nb25Zr8Ti6Al3 are presented. The structure of the melt spun ribbons was amorphous. The supercooled liquid range decreased and primary crystallization temperature increased with increasing Nb content while the parameter Tg/Tm slightly increased. The crystallization process proceeded in a different way. The ribbon containing 10 at.% Nb showed typical primary crystallization of the 50 nm grains of the NiTi(Nb) cubic phase; the ribbon containing 25 at.% of Nb revealed high thermal stability of the amorphous phase, which crystallized only in a small amount in the range of primary crystallization, preserving large fraction of the amorphous phase even high above the end of the crystallization. The tensile load–displacement curves were also different. In both cases, the ribbons revealed quite a large range of the plastic elongation. The ribbon containing 10% Nb showed stress relaxation and was maximally elongated up to 0.6. The ribbon with 25 at.% Nb revealed a hardening effect and the slightly smaller maximal elongation following it. The microstructure of the deformed specimens showed deformation bands parallel to the tensile axis, microcracks formation along shear bands and river‐like pattern at the fracture surfaces. In both cases, high resolution electron microscope did not reveal any crystallization after deformation.
Morphology and chemical composition of Ag/Sn/Ag interconnections
Authors: SKRZYNIARZ P. , WOJEWODA‐BUDKA J. , WIERZBICKA‐MIERNIK A. , ZIEBA P.
Published: December 2009

The main goal of the present contribution was to describe morphology and chemical composition of the intermetallic phases, which were formed during diffusion soldering process of the silver using tin. The Ag3Sn intermetallics is the main constituent of the joint after diffusion soldering at 235°C and 265°C. A closer inspection of the Ag/Ag3Sn interface revealed also the small crystallites of the second intermetallic phase, Ag5Sn, which was not previously observed using scanning electron microscope. Both phases are characterized by high melting temperatures: 480°C and 724°C, respectively. Therefore, their presence guarantees high thermal stability of the interconnection, which can be even three times higher than the temperature used for soldering.
The chemical phenol extraction of intermetallic particles from casting AlSi5Cu1Mg alloy
Authors: MRÓWKA‐NOWOTNIK G. , SIENIAWSKI J. , NOWOTNIK A.
Published: December 2009

This paper presents a chemical extraction technique for determination of intermetallic phases formed in the casting AlSi5Cu1Mg aluminium alloy. Commercial aluminium alloys contain a wide range of intermetallic particles that are formed during casting, homogenization and thermomechanical processing. During solidification, particles of intermetallics are dispersed in interdendritic spaces as fine primary phases. Coarse intermetallic compounds that are formed in this aluminium alloy are characterized by unique atomic arrangement (crystallographic structure), morphology, stability, physical and mechanical properties. The volume fraction, chemistry and morphology of the intermetallics significantly affect properties and material behaviour during thermomechanical processing. Therefore, accurate determination of intermetallics is essential to understand and control microstructural evolution in Al alloys. Thus, in this paper it is shown that chemical phenol extraction method can be applied for precise qualitative evaluation. The results of optical light microscopy LOM, scanning electron microscopy SEM and X‐ray diffraction XRD analysis reveal that as‐cast AlSi5Cu1Mg alloy contains a wide range of intermetallic phases such as Al4Fe, γ‐ Al3FeSi, α‐Al8Fe2Si, β‐Al5FeSi, Al12FeMnSi.
Formation and reduction of streak artefacts in electron tomography
Authors: CAO M. , ZHANG H.‐B. , LU Y. , NISHI R. , TAKAOKA A.
Published: December 2009

We have analysed the formation of streak artefacts in the reconstruction based on the filtered back projection algorithm in electron tomography (ET) and accordingly applied an adaptive interpolation technique to artefact reduction. In the adaptive interpolation to recover the missing information, the edge positions in a projection curve were tracked to reduce the interpolation error. A simulation was used to demonstrate the effectiveness of the artefact reduction. Furthermore, image reconstruction of integrated circuit specimens in the ET experiments with the ultra‐high voltage electron microscope show that the strong streak artefacts can be reduced effectively by our artefact reduction technique.
Association of plasma pentosidine concentrations with renal function in kidney graft recipients
Authors: Slowik‐Zylka Dorota , Safranow Krzysztof , Dziedziejko Violetta , Ciechanowski Kazimierz , Chlubek Dariusz
Published: December 2009

Slowik‐Zylka D, Safranow K, Dziedziejko V, Ciechanowski K, Chlubek D. Association of plasma pentosidine concentrations with renal function in kidney graft recipients.  Clin Transplant 2010: 24: 839–847. © 2009 John Wiley & Sons A/S.

Abstract:  Background:  Advanced glycation end‐products accumulate in the plasma of uremic patients. We aimed to assess the changes of free (Pfree) and total (Ptot) plasma pentosidine concentrations in kidney graft recipients, create a model describing their profile and analyze associations with clinical parameters.

Material and methods:  We measured Pfree and Ptot in the plasma of 12 non‐diabetic patients before and after kidney transplantation by HPLC.

Results:  P
tot concentrations were significantly decreasing after transplantation. The changes were well described by the exponential model assuming an asymptotic fall until the steady‐state concentration is attained. Ptot before and after transplantation displayed a strong negative correlation with mean daily diuresis (Rs = −0.64, p < 0.05 before; Rs = −0.94, p < 0.01 after 20 d). The rate of fall of the Ptot was positively correlated with the mean daily volume of urine passed in the second week after operation (Rs = +0.58, p < 0.05).

Conclusions:  The rate of fall of the Ptot after transplantation displays a strong correlation with diuresis, and the Ptot before transplantation is a potential prognostic factor for diuresis after the operation. Further prospective studies are necessary to demonstrate whether an effort to reduce carbonyl stress and pentosidine concentration before transplantation improves renal outcome.
Investigation of neuromuscular abnormalities in neurotrophin‐3‐deficient mice
Authors: Sheard Philip W. , Bewick Guy S. , Woolley Adele G. , Shaw Jacqueline , Fisher Lorryn , Fong Sitt Wai , Duxson Marilyn J.
Published: December 2009

Neurotrophin‐3 (NT‐3) is a trophic factor that is essential for the normal development and maintenance of proprioceptive sensory neurons and is widely implicated as an important modulator of synaptic function and development. We have previously found that animals lacking NT‐3 have a number of structural abnormalities in peripheral nerves and skeletal muscles. Here we investigated whether haploinsufficiency‐induced reduction in NT‐3 resulted in impaired neuromuscular performance and synaptic function. Motor nerve terminal function was tested by monitoring the uptake/release of the fluorescent membrane dye FM1‐43 by the electrophysiological examination of synaptic transmission and electron microscopic determination of synaptic vesicle density at the presynaptic active zone. We investigated skeletal muscle form and function by measuring force in response to both nerve‐mediated and direct muscle stimulation and by quantification of fiber number and area from transverse sections. Synaptic transmission was not markedly different between the two groups, although the uptake and release of FM1‐43 were impaired in mature NT‐3‐deficient mice but not in immature mice. The electron microscopic examination of mature nerve terminals showed no genotype‐dependent variation in the number of synaptic vesicles near the active zone. NT‐3+/− mice had normal soleus muscle fiber numbers but their fibers had smaller cross‐sectional areas and were more densely‐packed than wild‐type littermates. Moreover, the muscles of adult NT‐3‐deficient animals were weaker than those of wild‐type animals to both nerve and direct muscle stimulation. The results indicate that a reduction in NT‐3 availability during development impairs motor nerve terminal maturation and synaptic vesicle recycling and leads to a reduction in muscle fiber diameter.
Lagged cells in the inferior colliculus of the awake ferret
Authors: Shechter Barak , Marvit Peter , Depireux Didier A.
Published: December 2009

Neurons in the primary auditory cortex (AI) encode complex features of the spectral content of sound, such as direction selectivity. Recent findings of temporal symmetry in AI predict a specific organization of the subcortical input into the cortex that contributes to the emergence of direction selectivity. We demonstrate two subpopulations of neurons in the central nucleus of the inferior colliculus, which differ in their steady‐state temporal response profile: lagged and non‐lagged. The lagged cells (23%) are shifted in temporal phase with respect to non‐lagged cells, and are characterized by an ‘inhibition first’ and delayed excitation in their spectro‐temporal receptive fields. Non‐lagged cells (77%) have a canonical ‘excitation first’ response. However, we find no difference in the response onset latency to pure tone stimuli between the two subpopulations. Given the homogeneity of tonal response latency, we predict that these lagged cells receive inhibitory input mediated by cortical feedback projections.