bluuebunny/crossref_metadata_2025 huggingface dataset:
Electron beam heating effects during environmental scanning electron microscopy imaging of water condensation on superhydrophobic surfaces
Authors: Rykaczewski K. , Scott J. H. J. , Fedorov A. G.
Published: March 2011

Superhydrophobic surfaces (SHSs) show promise as promoters of dropwise condensation. Droplets with diameters below ∼10 μm account for the majority of the heat transferred during dropwise condensation but their growth dynamics on SHS have not been systematically studied. Due to the complex topography of the surface environmental scanning electron microscopy is the preferred method for observing the growth dynamics of droplets in this size regime. By studying electron beam heating effects on condensed water droplets we establish a magnification limit below which the heating effects are negligible and use this insight to study the mechanism of individual drop growth.
Influence of self-assembled monolayer dielectrics on the morphology and performance of α,ω-dihexylquaterthiophene in thin film transistors
Authors: Novak Michael , Schmaltz Thomas , Faber Hendrik , Halik Marcus
Published: March 2011

Three different ultrathin hybrid dielectrics based on self-assembled monolayers (SAMs) from phosphonic acid molecules were investigated on aluminum oxide. The impact of the underlying SAMs on the semiconductor morphology and transistor device performance was studied by reducing the film thickness of the subsequently deposited α,ω-dihexylquaterthiophene semiconductor to one monolayer and less. The nature of the SAM relates to the molecular orientation of submonolayer films, which is investigated by photoluminescence microscopy and atomic force microscopy. SAMs with high surface energy tend to induce a face-on growing of the semiconductor, whereas for SAMs with low surface energy an edge-on growth is favorable.
First-principles study on migration mechanism in SrTiO3
Authors: Mizoguchi Teruyasu , Takahashi Nobuaki , Lee Hak-Sung
Published: March 2011

The atomistic behavior of migration in SrTiO3 was investigated by first-principles nudged elastic band calculations. Calculated migration energies for Sr and oxygen are consistent with experimental values. In contrast, the calculated energy for Ti with a simple Ti-vacancy mechanism is far larger than the experimental value. In examining different Ti-migration mechanisms, the Ti-migration energy is found to decrease and become comparable to the Sr-migration energy by introducing a Sr vacancy. This Sr-vacancy-mediated Ti migration, which is consistent with the experimentally proposed mechanism by Gömann et al. [Phys. Chem. Chem. Phys. 6, 3639 (2004)], is confirmed theoretically by the present calculations.
Dielectric charging in capacitive microelectromechanical system switches with silicon nitride
Authors: Koutsoureli M. , Tavassolian N. , Papaioannou G. , Papapolymerou J.
Published: March 2011

The paper attempts to elaborate on the basic problem of dielectric charging in insulating films for microelectromechanical capacitive switches, the dependence of the film electrical properties on material stoichiometry and the uncertainty of whether the implementation of a leaky dielectric would reduce the charging effects. Silicon nitride films with stoichiometries (N/Si) ranging from 0.36 to 0.85 were assessed in metal-insulator-metal capacitors using the thermally stimulated depolarization current method and by obtaining the current-voltage characteristics. Capacitive switches were also fabricated with the same dielectric films. Results from both devices revealed an enhanced charging in the case of silicon-rich films.
Polarization independent visible color filter comprising an aluminum film with surface-plasmon enhanced transmission through a subwavelength array of holes
Authors: Inoue Daisuke , Miura Atsushi , Nomura Tsuyoshi , Fujikawa Hisayoshi , Sato Kazuo , Ikeda Naoki , Tsuya Daiju , Sugimoto Yoshimasa , Koide Yasuo
Published: March 2011

The enhanced transmission through periodic arrays of sub-wavelength holes in optically-thick metallic films has many potential applications, such as in wavelength filters, light extraction from light emission diodes, and subwavelength photolithography. A color filter comprising arrays of subwavelength holes in an aluminum film has been fabricated. In addition to the simplicity of the process, the aluminum film enables the excitation of visible-range surface plasmons due to its high plasma frequency. Periodic nanostructures in the aluminum film open the way for new visible color filters.
Functionalized graphene nanoroads for quantum well device
Authors: Zhou Y. G. , Yang P. , Wang Z. G. , Xiao H. Y. , Zu X. T. , Sun X. , Khaleel M. A. , Gao F.
Published: March 2011

Using density functional theory, a series of calculations of structural and electronic properties of Si-substituted graphene were conducted. Through substituting C atoms by Si atoms on graphene in the present study, we found that the band gap of graphene can be continuously tuned with differently substitutional concentration. To utilize such substitution-induced band gap changes, we proposed a special design to fabricate graphene-based quantum well device.
Accurate freezing and melting equations for the Lennard-Jones system
Authors: Khrapak Sergey A. , Morfill Gregor E.
Published: March 2011

Analyzing three approximate methods to locate liquid–solid coexistence in simple systems, an observation is made that all of them predict the same functional dependence of the temperature on density at freezing and melting of the conventional Lennard-Jones (LJ) system. The emerging equations can be written as \documentclass[12pt]{minimal}\begin{document}$T={\mathcal A}\rho ^4+{\mathcal B}\rho ^2$\end{document}T=Aρ4+Bρ2 in normalized units. We suggest to determine the values of the coefficients \documentclass[12pt]{minimal}\begin{document}${\mathcal A}$\end{document}A at freezing and melting from the high-temperature limit, governed by the inverse 12th power repulsive potential. The coefficients \documentclass[12pt]{minimal}\begin{document}${\mathcal B}$\end{document}B can be determined from the triple point parameters of the LJ fluid. This produces freezing and melting equations which are exact in the high-temperature limit and at the triple point and show remarkably good agreement with numerical simulation data in the intermediate region.
Increase in current density for metal contacts to n-germanium by inserting TiO2 interfacial layer to reduce Schottky barrier height
Authors: Lin J.-Y. Jason , Roy Arunanshu M. , Nainani Aneesh , Sun Yun , Saraswat Krishna C.
Published: March 2011

Metal contacts to n-type Ge have poor performance due to the Fermi level pinning near the Ge valence band at metal/Ge interfaces. The electron barrier height can be reduced by inserting ultrathin dielectrics at the metal-semiconductor interface. However, this technique introduces tunneling resistance from the large conduction band offset (CBO) between the insulator and Ge. In this work, the CBO between TiO2 and Ge is estimated to range from −0.06 to −0.26 eV so tunneling resistance can be reduced. By inserting 7.1 nm TiO2 between Al and n-Ge, current densities increased by about 900× at 0.1 V and 1200× at −0.1 V compared to contacts without TiO2.
Vertical ZnO nanorod/Si contact light-emitting diode
Authors: Lee Sang Wuk , Cho Hak Dong , Panin Gennady , Won Kang Tae
Published: March 2011

Blue-white light emission was obtained from glass/indium tin oxide (ITO)/n-ZnO nanorod array (NRA)/p+-Si vertical contact light emitting diodes (VCLEDs). The nanoscale p-n heterojunction VCLEDs were formed by direct engagement n−-tips of n-ZnO NRA grown vertically on an ITO/glass substrate with p+-Si wafer. Proposed configuration of the VCLED allows creating a high density (∼109 cm−2) of self-assembled ZnO/Si nanodiodes with point junctions of high quality due to structural perfection of the Si wafer and the tips of ZnO nanorods as well as providing a high injection current and light emission from the NRA VCLED required for solid state lighting.
Communication: Direct angle-resolved measurements of collision dynamics with electronically excited molecules: NO(A2Σ+) + Ar
Authors: Kay Jeffrey J. , Paterson Grant , Costen Matthew L. , Strecker Kevin E. , McKendrick Kenneth G. , Chandler David W.
Published: March 2011

We report direct doubly differential (quantum state and angle-resolved) scattering measurements involving short-lived electronically excited molecules using crossed molecular beams. In our experiment, supersonic beams of nitric oxide and argon atoms collide at 90°. In the crossing region, NO molecules are excited to the A2Σ+state by a pulsed nanosecond laser, undergo rotationally inelastic collisions with Ar atoms, and are then detected 400 ns later (approximately twice the radiative lifetime of the A2Σ+state) by 1 + 1′ multiphoton ionization via the E2Σ+ state. The velocity distributions of the scattered molecules are recorded using velocity-mapped ion imaging. The resulting images provide a direct measurement of the state-to-state differential scattering cross sections. These results demonstrate that sufficient scattering events occur during the short lifetimes typical of molecular excited states (∼200 ns, in this case) to allow spectroscopically detected quantum-state-resolved measurements of products of excited-state collisions.
Insights into the evolutionary history of Indo-Pacific bloodfeeding terrestrial leeches (Hirudinida:Arhynchobdellida:Haemadipisdae)
Authors: Borda Elizabeth , Siddall Mark E.
Published: March 2011

Haemadipsidae is a clade of notorious bloodfeeding annelids adapted to tropical and sub-tropical rainforests found throughout the Indo-Pacific. This family traditionally includes duognathous (two-jawed) endemics, each placed in their own genus, from continental and volcanic islands including: Australia, Indonesia, Madagascar, Papua New Guinea, Philippines, Seychelles, and South Pacific islands, while trignathous (three-jawed) Tritetrabdella species and the speciose Haemadipsa are exclusive to the Indian subcontinent ranging into east and south-east Asia. One of the more compelling aspects of haemadipsids is their distribution on post-Gondwanan landmasses. In this study, the phylogenetic relationships, taxonomy and biogeographic patterns of Haemadipsidae were examined. Over 5 kb of sequence data from three genes (nuclear 18S rDNA and 28S rDNA and mitochondrial COI) for 37 haemadipsid exemplars, representing 12 of the 15 recognised genera, were analysed under the criteria of maximum parsimony and Bayesian inference. The results show that widespread duognathous species form a monophyletic group derived from trignathous ancestry and are sister to a new trignathous clade for Haemadipsidae. This phylogenetic hypothesis rejected Gondwanan vicariance as an explanation for the diversification of haemadipsids. Haemadipsidae is accepted as the formal name for these Indo-Pacific leeches. Whereas the subdivisions Haemadipsinae and Domanibdellinae are clarified, there is a need to establish a new subfamily, Tritetrabdellinae, for the newly identified trignathous clade that is sister to Domanibdellinae. This study provides a basis for continued elucidation of the evolutionary relationships and classification of these terrestrial annelids.
Generalized Bragg–Williams model for the size-dependent order–disorder transition of bimetallic nanoparticles
Authors: Li Y J , Qi W H , Huang B Y , Wang M P , Liu J F , Xiong S Y
Published: March 2011

Considering the different effects of exterior atoms (face, edge and corner atoms), the Bragg–Williams model is generalized to account for the size, shape and composition-dependent order–disorder transition of bimetallic nanoparticles (NPs) with B2, L10 and L12 ordered structures. The results show that the order–disorder temperatures T
C,p are different for different shapes even in the identical particle size. The order of order–disorder temperatures of different shapes varies for different sizes. The long-range order parameter decreases with the increase in temperature in all size ranges and decreases smoothly in large sizes, but drops dramatically in small sizes. Moreover, it is also found that the order–disorder temperature of bimetallic NPs rises with increasing particle sizes and decreases with a deviation from the ideal compositions. The present predictions are consistent with the available literature results, indicating its capability in predicting other order–disorder transition phenomena of bimetallic NPs.
Abnormal accumulation of intermetallic compound at cathode in a SnAg3.0Cu0.5 lap joint during electromigration
Authors: Li Mingyu , Chang Hong , Pang Xiaochao , Wang Ling , Fu Yonggao
Published: March 2011

Interfacial reactions in a SnAg3.0Cu0.5/Cu lap joint for naked and encompassed specimens were investigated contrastively under electric current stressing. After applying a constant direct current at 6.5 A for 144 h, an abnormal accumulation of bulk Cu6Sn5 intermetallic compound was found at the cathode for the naked specimen. But normal polarization phenomenon arose for the encompassed specimen at the same current density for 504 h. The abnormal accumulation phenomenon was explained by the mechanism that thermomigration and stress migration induced by temperature gradient dominated the migration process. A three-dimensional joint simulation model was designed to demonstrate how current crowding and temperature gradient can enhance the local atomic flux.
Yet1p–Yet3p interacts with Scs2p–Opi1p to regulate ER localization of the Opi1p repressor
Authors: Wilson Joshua D. , Thompson Sarah L. , Barlowe Charles
Published: March 2011

Lipid sensing mechanisms at the endoplasmic reticulum (ER) coordinate an array of biosynthetic pathways. A major phospholipid regulatory circuit in yeast is controlled by Scs2p, an ER membrane protein that binds the transcriptional repressor protein Opi1p. Cells grown in the absence of inositol sequester Scs2p–Opi1p at the ER and derepress target genes including INO1. We recently reported that Yet1p and Yet3p, the yeast homologues of BAP29 and BAP31, are required for normal growth in the absence of inositol. Here we show that the Yet1p–Yet3p complex acts in derepression of INO1 through physical association with Scs2p–Opi1p. Yet complex binding to Scs2p–Opi1p was enhanced by inositol starvation, although the interaction between Scs2p and Opi1p was not influenced by YET1 or YET3 deletion. Interestingly, live-cell imaging analysis indicated that Opi1p does not efficiently relocalize to the ER during inositol starvation in yet3Δ cells. Together our data demonstrate that a physical association between the Yet complex and Scs2p–Opi1p is required for proper localization of the Opi1p repressor to ER membranes and subsequent INO1 derepression.
Intraperoxisomal redox balance in mammalian cells: oxidative stress and interorganellar cross-talk
Authors: Ivashchenko Oksana , Van Veldhoven Paul P. , Brees Chantal , Ho Ye-Shih , Terlecky Stanley R. , Fransen Marc
Published: March 2011

Reactive oxygen species (ROS) are at once unsought by-products of metabolism and critical regulators of multiple intracellular signaling cascades. In nonphotosynthetic eukaryotic cells, mitochondria are well-investigated major sites of ROS generation and related signal initiation. Peroxisomes are also capable of ROS generation, but their contribution to cellular oxidation–reduction (redox) balance and signaling events are far less well understood. In this study, we use a redox-sensitive variant of enhanced green fluorescent protein (roGFP2-PTS1) to monitor the state of the peroxisomal matrix in mammalian cells. We show that intraperoxisomal redox status is strongly influenced by environmental growth conditions. Furthermore, disturbances in peroxisomal redox balance, although not necessarily correlated with the age of the organelle, may trigger its degradation. We also demonstrate that the mitochondrial redox balance is perturbed in catalase-deficient cells and upon generation of excess ROS inside peroxisomes. Peroxisomes are found to resist oxidative stress generated elsewhere in the cell but are affected when the burden originates within the organelle. These results suggest a potential broader role for the peroxisome in cellular aging and the initiation of age-related degenerative disease.
Comparative visualization of genetic and physical maps with Strudel
Authors: Bayer Micha , Milne Iain , Stephen Gordon , Shaw Paul , Cardle Linda , Wright Frank , Marshall David
Published: March 2011

Summary: Data visualization can play a key role in comparative genomics, for example, underpinning the investigation of conserved synteny patterns. Strudel is a desktop application that allows users to easily compare both genetic and physical maps interactively and efficiently. It can handle large datasets from several genomes simultaneously, and allows all-by-all comparisons between these.

Availability and implementation: Installers for Strudel are available for Windows, Linux, Solaris and Mac OS X at http://bioinf.scri.ac.uk/strudel/.

Contact:  strudel@scri.ac.uk; micha.bayer@scri.ac.uk
GBOOST: a GPU-based tool for detecting gene–gene interactions in genome–wide case control studies
Authors: Yung Ling Sing , Yang Can , Wan Xiang , Yu Weichuan
Published: March 2011

Motivation: Collecting millions of genetic variations is feasible with the advanced genotyping technology. With a huge amount of genetic variations data in hand, developing efficient algorithms to carry out the gene–gene interaction analysis in a timely manner has become one of the key problems in genome-wide association studies (GWAS). Boolean operation-based screening and testing (BOOST), a recent work in GWAS, completes gene–gene interaction analysis in 2.5 days on a desktop computer. Compared with central processing units (CPUs), graphic processing units (GPUs) are highly parallel hardware and provide massive computing resources. We are, therefore, motivated to use GPUs to further speed up the analysis of gene–gene interactions.

Results: We implement the BOOST method based on a GPU framework and name it GBOOST. GBOOST achieves a 40-fold speedup compared with BOOST. It completes the analysis of Wellcome Trust Case Control Consortium Type 2 Diabetes (WTCCC T2D) genome data within 1.34 h on a desktop computer equipped with Nvidia GeForce GTX 285 display card.

Availability: GBOOST code is available at http://bioinformatics.ust.hk/BOOST.html#GBOOST.

Contact:  timyung@ust.hk; eeyu@ust.hk

Supplementary information:  Supplementary data are avaliable at Bioinformatics online.
A probabilistic model of nuclear import of proteins
Authors: Mehdi Ahmed M. , Sehgal Muhammad Shoaib B. , Kobe Bostjan , Bailey Timothy L. , Bodén Mikael
Published: March 2011

Motivation: Nucleo-cytoplasmic trafficking of proteins is a core regulatory process that sustains the integrity of the nuclear space of eukaryotic cells via an interplay between numerous factors. Despite progress on experimentally characterizing a number of nuclear localization signals, their presence alone remains an unreliable indicator of actual translocation.

Results: This article introduces a probabilistic model that explicitly recognizes a variety of nuclear localization signals, and integrates relevant amino acid sequence and interaction data for any candidate nuclear protein. In particular, we develop and incorporate scoring functions based on distinct classes of classical nuclear localization signals. Our empirical results show that the model accurately predicts whether a protein is imported into the nucleus, surpassing the classification accuracy of similar predictors when evaluated on the mouse and yeast proteomes (area under the receiver operator characteristic curve of 0.84 and 0.80, respectively). The model also predicts the sequence position of a nuclear localization signal and whether it interacts with importin-α.

Availability:  http://pprowler.itee.uq.edu.au/NucImport

Contact:  m.boden@uq.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
Adaptations toin situfeeding: novel nutrient acquisition pathways in an ancient vertebrate
Authors: Glover Chris N. , Bucking Carol , Wood Chris M.
Published: March 2011

During feeding, hagfish may immerse themselves in the body cavities of decaying carcasses, encountering high levels of dissolved organic nutrients. We hypothesized that this feeding environment might promote nutrient acquisition by the branchial and epidermal epithelia. The potential for Pacific hagfish,Eptatretus stoutii, to absorb amino acids from the environment across the skin and gill was thus investigated.l-alanine and glycine were absorbed via specific transport pathways across both gill and skin surfaces, the first such documentation of direct organic nutrient acquisition in a vertebrate animal. Uptake occurred via distinct mechanisms with respect to concentration dependence, sodium dependence and effects of putative transport inhibitors across each epithelium. Significant differences in the absorbed amino acid distribution between the skin of juveniles and adults were noted. The ability to absorb dissolved organic matter across the skin and gill may be an adaptation to a scavenging lifestyle, allowing hagfish to maximize sporadic opportunities for organic nutrient acquisition. From an evolutionary perspective, hagfish represent a transitory state between the generalized nutrient absorption pathways of aquatic invertebrates and the more specialized digestive systems of aquatic vertebrates.
Horseshoe bats make adaptive prey-selection decisions, informed by echo cues
Authors: Koselj Klemen , Schnitzler Hans-Ulrich , Siemers Björn M.
Published: March 2011

Foragers base their prey-selection decisions on the information acquired by the sensory systems. In bats that use echolocation to find prey in darkness, it is not clear whether the specialized diet, as sometimes found by faecal analysis, is a result of active decision-making or rather of biased sensory information. Here, we tested whether greater horseshoe bats decide economically when to attack a particular prey item and when not. This species is known to recognize different insects based on their wing-beat pattern imprinted in the echoes. We built a simulation of the natural foraging process in the laboratory, where the bats scanned for prey from a perch and, upon reaching the decision to attack, intercepted the prey in flight. To fully control echo information available to the bats and assure its unambiguity, we implemented computer-controlled propellers that produced echoes resembling those from natural insects of differing profitability. The bats monitored prey arrivals to sample the supply of prey categories in the environment and to inform foraging decisions. The bats adjusted selectivity for the more profitable prey to its inter-arrival intervals as predicted by foraging theory (an economic strategy known to benefit fitness). Moreover, unlike in previously studied vertebrates, foraging performance of horseshoe bats was not limited by costly rejections of the profitable prey. This calls for further research into the evolutionary selection pressures that sharpened the species's decision-making capacity.
Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis
Authors: Yamashita Riu , Sathira Nuankanya P. , Kanai Akinori , Tanimoto Kousuke , Arauchi Takako , Tanaka Yoshiaki , Hashimoto Shin-ichi , Sugano Sumio , Nakai Kenta , Suzuki Yutaka
Published: March 2011

We performed a genome-wide analysis of transcriptional start sites (TSSs) in human genes by multifaceted use of a massively parallel sequencer. By analyzing 800 million sequences that were obtained from various types of transcriptome analyses, we characterized 140 million TSS tags in 12 human cell types. Despite the large number of TSS clusters (TSCs), the number of TSCs was observed to decrease sharply with increasing expression levels. Highly expressed TSCs exhibited several characteristic features: Nucleosome-seq analysis revealed highly ordered nucleosome structures, ChIP-seq analysis detected clear RNA polymerase II binding signals in their surrounding regions, evaluations of previously sequenced and newly shotgun-sequenced complete cDNA sequences showed that they encode preferable transcripts for protein translation, and RNA-seq analysis of polysome-incorporated RNAs yielded direct evidence that those transcripts are actually translated into proteins. We also demonstrate that integrative interpretation of transcriptome data is essential for the selection of putative alternative promoter TSCs, two of which also have protein consequences. Furthermore, discriminative chromatin features that separate TSCs at different expression levels were found for both genic TSCs and intergenic TSCs. The collected integrative information should provide a useful basis for future biological characterization of TSCs.
Which women default from follow‐up cervical cytology tests? A cohort study within the TOMBOLA trial
Authors: Sharp L. , Cotton S. , Thornton A. , Gray N. , Whynes D. , Smart L. , Waugh N. , Duncan I. , Cruickshank M. , Little J. ,   on behalf of the TOMBOLA Group
Published: March 2011

L. Sharp, S. Cotton, A. Thornton, N. Gray, D. Whynes, L. Smart, N. Waugh, I. Duncan, M. Cruickshank and J. Little, on behalf of the TOMBOLA Group

Which women default from follow‐up cervical cytology tests? A cohort study within the TOMBOLA trial

Objective:  To identify factors associated with default from follow‐up cervical cytology tests.

Methods:  A cohort study was conducted involving 2166 women, aged 20–59, with recent low‐grade cervical cytology taken within the NHS Cervical Screening Programmes in Scotland and England, and managed by 6‐monthly cytology in primary care. For the first (6‐month) and second (12‐month) surveillance cytology tests separately, women were categorized as ‘on‐time attendees’ (attended ≤6 months of test being due), ‘late attendees’ (attended greater than 6 months after test was due) or ‘non‐attendees’ (failed to attend). Multivariate odds ratios (ORs) were computed for factors associated with late and non‐attendance.

Results:  For the first surveillance test, risk of non‐attendance was significantly higher in younger women, those without post‐secondary education, and non‐users of prescribed contraception. Factors significantly associated with late attendance for the first test were the same as for non‐attendance, plus current smoking and having children. The most important predictor of non‐attendance for the second surveillance test was late attendance for the first test (OR = 9.65; 95% CI, 6.60–16.62). Non‐attendance for the second test was also significantly higher among women who were younger, smokers and had negative cytology on the first surveillance test. Late attendance for the second surveillance test was higher in women who were younger, smokers, had children and attended late for the first test.

Conclusions:  Women at highest risk of default from follow‐up cytology tend to be young, smoke, lack post‐secondary education, and have defaulted from a previous surveillance appointment. Tackling default will require development of targeted strategies to encourage attendance and research to better understand the reasons underpinning default.
Identification of components of fibroadenoma in cytology preparations using texture analysis: a morphometric study
Authors: Singh S. , Gupta R.
Published: March 2011

S. Singh and R. Gupta

Identification of components of fibroadenoma in cytology preparations using texture analysis: a morphometric study

Objectives:  To evaluate the utility of image analysis using textural parameters obtained from a co‐occurrence matrix in differentiating the three components of fibroadenoma of the breast, in fine needle aspirate smears.

Methods:  Sixty cases of histologically proven fibroadenoma were included in this study. Of these, 40 cases were used as a training set and 20 cases were taken as a test set for the discriminant analysis. Digital images were acquired from cytological preparations of all the cases and three components of fibroadenoma (namely, monolayered cell clusters, stromal fragments and background with bare nuclei) were selected for image analysis. A co‐occurrence matrix was generated and a texture parameter vector (sum mean, energy, entropy, contrast, cluster tendency and homogeneity) was calculated for each pixel. The percentage of pixels correctly classified to a component of fibroadenoma on discriminant analysis was noted.

Results:  The textural parameters, when considered in isolation, showed considerable overlap in their values of the three cytological components of fibroadenoma. However, the stepwise discriminant analysis revealed that all six textural parameters contributed significantly to the discriminant functions. Discriminant analysis using all the six parameters showed that the numbers of pixels correctly classified in training and tests sets were 96.7% and 93.0%, respectively.

Conclusion:  Textural analysis using a co‐occurrence matrix appears to be useful in differentiating the three cytological components of fibroadenoma. These results could further be utilized in developing algorithms for image segmentation and automated diagnosis, but need to be confirmed in further studies.
Down‐regulation of keratin 4 and keratin 13 expression in oral squamous cell carcinoma and epithelial dysplasia: a clue for histopathogenesis
Authors: Sakamoto Kei , Aragaki Tadanobu , Morita Kei‐ichi , Kawachi Hiroshi , Kayamori Kou , Nakanishi Shoichi , Omura Ken , Miki Yoshio , Okada Norihiko , Katsube Ken‐ichi , Takizawa Toichiro , Yamaguchi Akira
Published: March 2011

Sakamoto K, Aragaki T, Morita K‐i, Kawachi H, Kayamori K, Nakanishi S, Omura K, Miki Y, Okada N, Katsube K‐i, Takizawa T & Yamaguchi A (2011) Histopathology58, 531–542 Down‐regulation of keratin 4 and keratin 13 expression in oral squamous cell carcinoma and epithelial dysplasia: a clue for histopathogenesis

Aims:  This study aimed to identify relevant keratin subtypes that may associate with the pathogenesis of oral epithelial neoplasms.

Methods and results:  Expression of all the keratin subtypes was examined by cDNA microarray analysis of 43 oral squamous cell carcinoma (OSCC) cases. Immunohistochemical expression of the major keratins was examined in 100 OSCC and oral epithelial dysplasia (OED) cases. Many changes in keratin expression were observed and, significantly, consistent down‐regulation of keratin 4 (K4) and K13 expression was observed. Aberrant expression of K4 and K13 was associated with morphological changes in the affected oral epithelium. Experiments with cell cultures transfected with various keratin subtypes suggested that alterations in keratin subtype expression can cause changes in cell shape and movement.

Conclusions:  Aberrant expression of K4 and K13, which are the dominant pair of differentiation‐related keratins in oral keratinocytes, indicates dysregulation of epithelial differentiation in OSCC and OED. These keratins, especially K4, may be useful for pathological diagnosis. We propose that the aberrant expression of K4 and K13 and concomitant up‐regulation of the other keratins may be one of the causative factors for morphological alterations in the affected epithelium.
Elders and patient participation revisited – a discourse analytic approach to older persons’ reflections on patient participation
Authors: Foss Christina
Published: March 2011

Aim and objective.  This study focuses on how older persons’ accounts of participation might be framed and constructed based on their social and historical situatedness.

Background.  The picture emerging from contemporary research tends to portray older people as a group who prefer to leave decisions to the professionals during a hospital stay. Through an approach that sought to contextualise the respondents’ accounts of participation, different features of patient participation became visible.

Design.  The study is based on a postmodern framework using a discursive approach, informed by the works of Foucault and on works that have been developed in line with his main ideas.

Method.  Eighteen individual in‐depth interviews with older people (age 80+) were conducted between one to two weeks after discharge from hospital.

Results.  Findings indicate that older people actively position themselves in relation to various discourses at play in the hospital, and display a wide variety of strategies aimed at gaining influence. To the older persons in this study, participation was practised in a subtle and discreet way, as a matter of choosing a good strategy to interact with the personnel. Participation was also seen as a matter of balancing their own needs against the needs of others and as a behaviour that required self‐confidence.

Conclusion.  The accounts of patient participation given by the older persons differed from the dominant and taken‐for‐granted discourse of patient participation as a right.

Relevance to clinical practice.  As the older persons’ understanding and practice of patient participation do not ‘fit’ the contemporary idea of participation, it is in danger of being ignored or overlooked by care‐givers as well as by researchers. To identify older patients’ wish to participate, one must actively search for it.
Impaired Balance of Th17/Treg in Patients with Nasal Polyposis
Authors: Shen Y. , Tang X.‐Y. , Yang Y.‐C. , Ke X. , Kou W. , Pan C.‐K. , Hong S.‐L.
Published: March 2011

Nasal polyposis (NP) is a chronic inflammatory disease of the nasal cavity and sinuses that is regulated by T lymphocyte subsets. Imbalance of Th17/Treg has been considered critical in the development of inflammation and atopic reactions. To assess whether the balance of Th17/Treg is disrupted in patients with NP, we evaluated the distribution of Th17 and Treg cells among peripheral blood mononuclear cells (PBMCs) in atopic patients with NP, non‐atopic patients with NP and controls. We then determined mRNA levels of RORc and Foxp3 and protein levels of IL‐17, TGF‐β and IL‐10 in polyp tissue among the three groups. Finally, we investigated the correlation between Th17‐, Treg‐ and Th1‐, Th2‐related cytokines (INF‐γ, IL‐4, IL‐5). The results demonstrated that both atopic and non‐atopic patients with NP revealed significantly increased Th17 proportion and decreased Treg proportion in PBMCs, as well as significantly increased RORc and IL‐17 levels and decreased Foxp3 and TGF‐β levels in polyp tissue. Furthermore, these differences were significant between atopic and non‐atopic groups. The frequency of Treg in PBMCs was found to be negatively correlated with Th1 and Th2 cytokines in polyps. These results indicated that an impaired balance of Th17/Treg existed in patients with NP and was more severe in atopic patients, suggesting that the imbalance of Treg/Th17 may play an important role in the development of NP and that atopy may aggravate NP by promoting the imbalance of Th17/Treg.
Characterization of Catharanthus roseus Genes Regulated Differentially by Peanut Witches’ Broom Phytoplasma Infection
Authors: Chen Wuu‐Yang , Lin Chan‐Pin
Published: March 2011

The differential display (DD) strategy was applied to isolate periwinkle (Catharanthus roseus) cDNAs that were differentially expressed following infection with peanut witches’ broom (PnWB) phytoplasma. Sixty‐four clones were selected from differentially expressed cDNA fragments. Following screening by reverse Northern hybridization, ten transcripts were selected and sequenced. The expression level of each transcript was quantified by real‐time PCR, and seven DD transcripts were identified as truly differentially expressed following PnWB phytoplasma infection. Among these, one that was homologous with phi‐1 gene was up‐regulated, while the others were down‐regulated. Except two genes, other four down‐regulated genes shared homology with the genes encoding psaDa gene, ML domain protein gene, eukaryotic translation initiation factor SUI1 gene and plastidic aldolase NPALDP1 gene, respectively. The identities of homologous genes were further confirmed for three DD transcripts by isolating long cDNA fragments from the cDNA library that was established in this investigation. Verified genes were ML domain protein gene, translation initiation factor SUI1 gene and plastidic aldolase gene and were primarily involved in the innate immune response, the stress response and photosynthesis. The possible role of these genes in the periwinkle that was infected by PnWB phytoplasma is discussed.
Effect of trans‐10 cis‐12 conjugated linoleic acid on Bovine Oocyte Competence and Fatty Acid Composition
Authors: Lapa M , Marques CC , Alves SP , Vasques MI , Baptista MC , Carvalhais I , Silva Pereira M , Horta AEM , Bessa RJB , Pereira RM
Published: March 2011

Contents

The reproductive performance of dairy cows may be improved by feeding conjugated linoleic acid (CLA) supplements during early lactation. The mechanism of action of t10,c12 CLA is not clearly known. Our objective was to investigate the effect of t10,c12 CLA on oocyte maturation and lipid composition of cumulus oocyte complexes (COC). The developmental potential of oocytes incubated in in vitro maturation (IVM) medium supplemented with t10,c12 CLA to the blastocyst stage and embryo quality were also assessed. In experiment 1, abattoir‐derived oocytes were matured in TCM199 + 10% serum supplemented with 100 μM t10,c12 CLA (t10,c12 CLA n = 672) or without it (control n = 672). Mature oocytes were either stained for chromatin configuration or inseminated and cultured for embryo development assessment. In experiment 2, COC and IVM culture media were subjected to fatty acid (FA) analysis prior and after maturation with t10,c12 CLA or without it (control). Total lipids and FA profiles in oocytes, cumulus cells and culture media were determined by gas chromatography. t10,c12 CLA supplementation to IVM medium improved (p = 0.05) embryo quality evaluated morphologically. This effect was associated with t10,c12 CLA presence (3.1 ± 0.7%, p = 0.04) and lower levels of arachidonic acid in FA profile of t10,c12 CLA mature oocytes (immature oocytes = 4.4 ± 1.9%, t10,c12 CLA mature oocytes = 1.0 ± 0.7%, p = 0.05). Differences in myristic and eicotrienoic acids, saturated and unsaturated FA concentrations between oocytes and cumulus cells were detected (p ≤ 0.05). In conclusion, the presence of t10,c12 CLA during maturation interfered on lipid metabolism improving bovine oocyte competence to develop into higher quality embryos.
Prediction of Parturition Date in the Bitch and Queen
Authors: Michel E , Spörri M , Ohlerth S , Reichler IM
Published: March 2011

Contents

Assessment of gestational age and parturition date prediction is a challenging, yet common task in clinical management of the pregnant bitch or queen. Knowing the approximate parturition date is essential for a thorough pregnancy monitoring. Radiographic and ultrasonographic methods are suitable in bitches and queens. In the bitch, moreover, ovulation timing by means of LH or progesterone assay, determination of onset of vaginal dioestrus by means of examination of vaginal cytology, and recognition of impending parturition by monitoring prepartal progesterone levels and body temperature variation are practical methods. A combination of different methods increases the accuracy of parturition date prediction.
Computed tomography findings of sorafenib‐treated hepatic tumors in patients with advanced hepatocellular carcinoma
Authors: Kim Min Ju , Choi Joon‐Il , Lee Jong Seok , Park Joong‐Won
Published: March 2011

Background and Aim:  The purpose of this study was to describe the computed tomography (CT) findings of sorafenib‐treated hepatic tumors in patients with advanced hepatocellular carcinoma and to correlate the findings to the overall survival (OS).

Methods:  Twenty‐eight sorafenib‐treated patients who had advanced hepatocellular carcinoma (HCC) with viable hepatic tumors between August 2007 and February 2008 were enrolled in the study. Dynamic CT findings were analyzed with regard to the response of the tumor, based on the response evaluation criteria in solid tumor, version 1.1, and the attenuation values of the tumors during the late arterial and portal venous phases. Survival analyses according to early changes in the tumors were also performed.

Results:  In all patients, the tumor responses were stable disease or progressive disease on follow‐up CT scans. Prior to the treatment, the mean attenuation values of the tumors were 93.0 ± 20.0 Hounsfield unit (HU) at the late arterial phase, and 107.9 ± 23.0 HU at the portal venous phase. On the first follow‐up CT scans, the mean attenuation values of the late arterial and portal venous phases were 76.9 ± 26.5 HU and 94.2 ± 29.1 HU, respectively (P < 0.01). The median OS was better for the patients with the response of stable disease than the patients with progressive disease (P = 0.013).

Conclusions:  In patients with advanced HCC who were treated by sorafenib, the size of the hepatic tumors was not significantly reduced. However, the median survival was better for the patients with the response of stable disease. The attenuation values of the tumors became lower after treatment, as compared to the baseline CT scans.
An oxygen reduction chain in the hyperthermophilic anaerobe Thermotoga maritima highlights horizontal gene transfer between Thermococcales and Thermotogales
Authors: Le Fourn Céline , Brasseur Gaël , Brochier‐Armanet Céline , Pieulle Laetitia , Brioukhanov Andrei , Ollivier Bernard , Dolla Alain
Published: March 2011

The hyperthermophile Thermotoga maritima, although strictly anaerobic, is able to grow in the presence of low amounts of O2. Here, we show that this bacterium consumes O2 via a three‐partner chain involving an NADH oxidoreductase (NRO), a rubredoxin (Rd) and a flavo‐diiron protein (FprA) (locus tags: TM_0754, TM_0659 and TM_0755, respectively). In vitro experiments showed that the NADH‐dependent O2 consumption rate was 881.9 (± 106.7) mol O2 consumed min−1 per mol of FprA at 37°C and that water was the main end‐product of the reaction. We propose that this O2 reduction chain plays a central role in the O2 tolerance of T. maritima. Phylogenetic analyses suggest that the genes coding for these three components were acquired by an ancestor of Thermotogales from an ancestor of Thermococcales via a single gene transfer. This event likely also involved two ROS scavenging enzymes (neelaredoxin and rubrerythrin) that are encoded by genes clustered with those coding for FprA, NRO and Rd in the ancestor of Thermococcales. Such genomic organization would have provided the ancestor of Thermotogales with a complete set of enzymes dedicated to O2‐toxicity defence. Beside Thermotogales and Thermococcales, horizontal gene transfers have played a major role in disseminating these enzymes within the hyperthermophilic anaerobic prokaryotic communities, allowing them to cope with fluctuating oxidative conditions that exist in situ.
Benign prostatic hyperplasia: racial differences in treatment patterns and prostate cancer prevalence
Authors: Pettaway Curtis A. , Lamerato Lois E. , Eaddy Michael T. , Edwards Jessie K. , Hogue Susan L. , Crane Martin M.
Published: March 2011

Study Type – Prevalence (prospective cohort with good follow‐up)

Level of Evidence 1b

What’s known on the subject? and What does the study add?

Previous studies evaluating racial differences in BPH treatment and outcomes have concluded that more attention in the management of lower urinary tract symptoms should be directed at African Americans. Although the relationship between BPH and the development of prostate cancer is inconclusive, longitudinal studies have indicated racial disparities in the incidence of prostate cancer.

This is the first long‐term follow‐up study in a BPH population to assess the incidence of prostate cancer among African American and Caucasian men under “real‐world” clinical practice circumstances. This study suggests that African Americans with BPH have a much greater risk of developing prostate cancer than similar Caucasian men, highlighting the need for education, prevention and early detection.

OBJECTIVE

• To compare prostate cancer, prostate‐related surgery and acute urinary retention rates, as well as associated healthcare resource use over 11 years in African American and Caucasian men with benign prostatic hyperplasia (BPH).

PATIENTS AND METHODS

• The BPH‐related medical and surgical charges and events were determined for 398 African American men and 1656 Caucasian men followed for a mean of 10.2 years within a health maintenance organization.

• Racial differences in clinical outcomes were evaluated using time‐to‐event analysis, stratifying results by baseline prostate‐specific antigen (PSA) values.

RESULTS

• Risk of a prostate cancer diagnosis was 2.2 times greater in African American than Caucasian men (95% CI 1.48–3.35, P < 0.001) in analyses adjusting for serum PSA level.

• Although African Americans were more likely to receive medical therapy for symptoms of BPH than Caucasians (43.5% vs 37.2%, respectively; P= 0.029), there were no clinically meaningful differences with respect to subsequent acute urinary retention or BPH‐related surgery between them, or BPH‐related medical charges (US $407 vs US $405 per month).

CONCLUSION

• As evidenced by this analysis of ‘real‐world’ clinical practice, African Americans with BPH have a much greater risk of developing prostate cancer than similar Caucasian men highlighting the need for education and early detection in this population.
Globalization and modernization: an obesogenic combination
Authors: Huneault L. , Mathieu M.‐È. , Tremblay A.
Published: March 2011

Animal research has well established that a link exists between variations in corticosteroids and the proneness to excess body fat accumulation. Accordingly, it is known that adrenalectomy is an efficient approach to counteract weight gain in most animal models of obesity. In humans, the association between variations in corticosteroids, its stress‐related environmental effects and the predisposition to obesity is more difficult to demonstrate. In this paper, we propose that this relationship is accentuated by globalization and modernization which favour a labour context imposing additional stress and changes in life habits promoting a positive energy balance. Our main hypothesis is that the increase in knowledge‐based work, and the decrease of quality and duration of sleep both induce an increase in cortisolaemia and glycaemia instability, which results in an increase in food intake, a reduction in energy expenditure and body fat gain. The authors of this paper believe that, from a socioeconomic perspective, globalization leads every nation of the world in conflict with itself and may consequently represent a real problem. On one hand, there are preoccupations related to productivity and money making. On the other hand, people have to adopt a daily lifestyle leading to hyperphagia and decreased energy expenditure in order to maintain their economic competitiveness.