bluuebunny/crossref_metadata_2025 huggingface dataset:
Turbulence statistics and structures of drag-reducing turbulent boundary layer in homogeneous aqueous surfactant solutions
Authors: Tamano Shinji , Itoh Motoyuki , Inoue Takefumi , Kato Katsuo , Yokota Kazuhiko
Published: April 2009

In our earlier work [Itoh et al., Phys. Fluids 17, 075107 (2005)], the additional maximum of the streamwise turbulence intensity near the center of the drag-reducing turbulent boundary layer was found in the homogeneous dilute aqueous surfactant solution which was a mixture of cetyltrimethyl ammonium chloride with sodium salicylate as counterion. In this work, we systematically investigated the influence of the drag-reducing surfactant on the velocity fields of the turbulent boundary layer at various Reynolds numbers Reθ from 301 to 1437 and the drag reduction ratio DR from 8% to 74% under different streamwise locations and concentration and temperature of solutions using a two-component laser-Doppler velocimetry (LDV) system. It was revealed that all data on DR versus the wall-shear rate obtained here were collapsed on a single curve. We verified the existence of the additional maximum of the streamwise turbulence intensity near the center of the boundary layer which appeared at relatively large drag reduction ratios and small Reynolds numbers. It was found that the additional maximum of streamwise turbulence intensity and its wall-normal location were independent of the streamwise location, wall-shear rate, Reynolds number, and drag reduction ratio. The additional maximum could be explained by the bilayered structure model proposed, in which the flow in the near-wall region is in shear-induced structure (SIS) and viscoelastic, whereas the flow in the region away from the wall is in non-SIS and nonviscoelastic. This model was based on measurements of the shear viscosity. We also performed particle image velocimetry measurements, which revealed that the fluctuating velocity vector fields showed two situations, with low and high activity. In low activity, the velocity fluctuations were attenuated largely across the turbulent boundary layer. In high activity, fluctuating velocity vectors were almost parallel to the wall and relatively large in both regions near the wall and the center of the boundary layer, which seemed to be a bilayered structure and supported the bilayered structure model.
Poisson–Lie T-plurality with spectators
Authors: Hlavatý Ladislav , Petr Ivo , Štěpán Vojtěch
Published: April 2009

Using a suitable extension of Drinfel’d double we derive formulas for the Poisson–Lie T-plurality transformation with spectators, i.e., for σ-models whose group of generalized isometries does not act transitively on the target manifold. These formulas are further applied to transformations of the gluing matrices that define the boundary conditions of the σ-models.
Specific Na+ and K+ cation effects on the interfacial water molecules at the air/aqueous salt solution interfaces probed with nonresonant second harmonic generation
Authors: Bian Hong-tao , Feng Ran-ran , Guo Yuan , Wang Hong-fei
Published: April 2009

Here we report on the polarization dependent nonresonant second harmonic generation (SHG) measurement of the interfacial water molecules at the aqueous solution of the following salts: NaF, NaCl, NaBr, KF, KCl, and KBr. Through quantitative polarization analysis of the SHG data, the orientational parameter D (D=⟨cos θ⟩/⟨cos3 θ⟩) value and the relative surface density of the interfacial water molecules at these aqueous solution surfaces were determined. From these results, we found that addition of each of the six salts caused an increase in the thickness of the interfacial water layer at the surfaces to a certain extent. Noticeably, both the cations and the anions contributed to the changes, and the abilities to increase the thickness of the interfacial water layer were in the following order: KBr>NaBr>KCl>NaCl∼NaF>KF. Since these changes cannot be factorized into individual anion and cation contributions, there are possible ion pairing or association effects, especially for the NaF case. We also found that the orientational parameter D values of the interfacial water molecules changed to opposite directions for the aqueous solutions of the three sodium salts versus the aqueous solutions of the three potassium salts. These findings clearly indicated unexpected specific Na+ and K+ cation effects at the aqueous solution surface. These effects were not anticipated from the recent molecular dynamics simulation results, which concluded that the Na+ and K+ cations can be treated as small nonpolarizable hard ions and they are repelled from the aqueous interfaces. These results suggest that the electrolyte aqueous solution surfaces are more complex than the currently prevalent theoretical and experimental understandings.
Lubricant dynamics on a slider: “The waterfall effect”
Authors: Marchon B. , Guo X. C. , Moser A. , Spool A. , Kroeker R. , Crimi F.
Published: April 2009

In a modern disk drive, the total slider-to-disk distance, or magnetic spacing, needs to scale with the size of the recorded bit, and nowadays, it amounts to a mere 10nm or less. As disk lubricant often transfers to some extent to the slider surface, it can potentially increase the magnetic spacing. Therefore, it is important to quantify the thickness and flow dynamics of these molecularly thin films on the slider surface. In this paper, modeling, as well as experimental data, is shown that demonstrate the effect on recording performance of a subnanometer thin lubricant layer on the slider. Cleanup by air shear can be predicted reasonably well using the shear map calculated from an air-bearing solver, and reflow by surface diffusion highlights the importance of controlling lubricant transfer from the disk to the slider.
Structure and excited-state dynamics of anthracene: Ultrahigh-resolution spectroscopy and theoretical calculation
Authors: Baba Masaaki , Saitoh Motohisa , Taguma Kunio , Shinohara Keisuke , Yoshida Kazuto , Semba Yosuke , Kasahara Shunji , Nakayama Naofumi , Goto Hitoshi , Ishimoto Takayoshi , Nagashima Umpei
Published: April 2009

Rotationally resolved ultrahigh-resolution spectra of the S1 B12u←S0 A1g transition of anthracene-h10 and anthracene-d10 have been observed using a single-mode UV laser and a collimated supersonic jet. We have determined rotational constants of the zero-vibrational levels of the S0 and S1 states by analyzing the precisely calibrated transition wavenumbers of rotational lines. We measured Zeeman splitting of each rotational line in the external magnetic field, of which the magnitude was small and strongly dependent on the rotational quantum numbers. We have shown that the magnetic moment in the S1 B12u state arises from J-L coupling with the S2 B13u state and that mixing with the triplet state is negligibly small. We concluded that the main radiationless transition in the S1 state of anthracene is not intersystem crossing to the triplet state but internal conversion to the ground state. We also examined methods of ab initio theoretical calculation to determine which method most closely yielded the same values of rotational constants as the experimentally obtained ones. Moller–Plesset second-order perturbation method with a 6-31G(d,p) basis set yielded approximately the same values for the S0 A1g state with an error of less than 0.04%. Geometrical structure in the S0 A1g state of the isolated anthracene molecule has been accurately determined by this calculation. However, configurational-interaction with single excitations, time-dependent Hartree–Fock, and time-dependent density-function-theory methods did not yield satisfactory results for the excitation energy of the S1 B12u state. Symmetry-adapted-cluster configuration-interaction calculation was sufficiently good for the excitation energy and rotational constants.
Vacancy segregation in the initial oxidation stages of the TiN(100) surface
Authors: Zimmermann Janina , Finnis Mike W. , Ciacchi Lucio Colombi
Published: April 2009

The well-known corrosion resistance and biocompatibility of TiN depend on the structural and chemical properties of the stable oxide film that forms spontaneously on its surface after exposure to air. In the present work, we focus on the atomistic structure and stability of the TiN(100) surface in contact with an oxidizing atmosphere. The early oxidation stages of TiN(100) are investigated by means of first-principles molecular dynamics (FPMD). We observe selective oxidation of Ti atoms and formation of an ultrathin Ti oxide layer, while Ti vacancies are left behind at the metal/oxide interface. Within the formalism of ab initio thermodynamics we compute the segregation energies of vacancies and vacancy clusters at the metal/oxide interface, comparing the stability of the system obtained by FPMD simulations with ideally reconstructed models. We find that the localization of Ti vacancies in the thin oxide layer and at the TiN/oxide interface is thermodynamically stable and may account for the early removal of N atoms from the interface by segregation of N vacancies from the bulk reservoir. We suggest that superficial oxidation may proceed along two distinct possible pathways: a thermodynamically stable path along the potential energy minimum surface and a metastable, kinetically driven path that results from the high heat release during the dissociation of O2.
Magnetic anomaly in Ni51.5Fe21.5Ga27 single crystalline ferromagnetic shape memory alloy studied by ac impedance measurements
Authors: Corró M. L. , Kustov S. , Cesari E. , Chumlyakov Y. I.
Published: April 2009

A magnetic anomaly in the austenitic state of Ni51.5Fe21.5Ga27 single crystalline ferromagnetic shape memory alloy has been studied by means of ac impedance measurements. A much stronger effect of the degree of atomic order on the temperature of this anomaly (as compared to the temperature of the martensitic and para-ferromagnetic transitions) has been found. It has been shown that apart from the previously reported slight variation in the saturation magnetization, the magnetic anomaly results in a nearly one order of magnitude change in the value of initial magnetic permeability. The anomaly is not revealed in the resistive impedance at low frequencies, pointing likely to its purely magnetic origin.
NMR quadrupolar system described as Bose–Einstein-condensate-like system
Authors: Auccaise R. , Teles J. , Bonagamba T. J. , Oliveira I. S. , deAzevedo E. R. , Sarthour R. S.
Published: April 2009

This paper presents a description of nuclear magnetic resonance (NMR) of quadrupolar systems using the Holstein–Primakoff (HP) formalism and its analogy with a Bose–Einstein condensate (BEC) system. Two nuclear spin systems constituted of quadrupolar nuclei I=3/2 (N23a) and I=7/2 (C133s) in lyotropic liquid crystals were used for experimental demonstrations. Specifically, we derived the conditions necessary for accomplishing the analogy, executed the proper experiments, and compared with quantum mechanical prediction for a Bose system. The NMR description in the HP representation could be applied in the future as a workbench for BEC-like systems, where the statistical properties may be obtained using the intermediate statistic, first established by Gentile. The description can be applied for any quadrupolar systems, including new developed solid-state NMR GaAS nanodevices.
Critical slowing down of relaxation dynamics near the Curie temperature in the relaxor Pb(Sc0.5Nb0.5)O3
Authors: Ahart Muhtar , Hushur Anwar , Bing Yonghong , Ye Zuo-Guang , Hemley Russell J. , Kojima Seiji
Published: April 2009

Brillouin spectroscopy of Pb(Sc0.5Nb0.5)O3 single crystals reveals an order-disorder ferroelectric phase transition occurs at 110 °C upon cooling. A softening of the longitudinal acoustic (LA) mode is observed that can be attributed to the coupling between polar nanoregions and acoustic modes. A critical slowing down of the central peak, a feature of order-disorder ferroelectric phase transitions, is observed near Tc. The similarity in temperature dependences of the two kinds of relaxation times determined from the central peak and LA mode suggests that the changes in the central peak arise from local polarization fluctuations in the polar nanoregions.
Taking People Apart: Digitised Dissection and the Body at the Border
Authors: Amoore Louise , Hall Alexandra
Published: April 2009

The UK Home Office and the US Transportation Security Administration have made substantial recent investment in new Backscatter X-ray scanners to screen bodies at securitised border checkpoints. Promising to make the invisible visualisable, these devices project an image of a naked body onto a screen to identify concealed ‘risk’. Contemporary security practices which seek to fix identity at the border through biometrics, datamining, and profiling—of which the ‘whole body scanner’ is part—have their genealogy in efforts in aesthetics and medical science to mine the body for certainties and reveal something of the unknown future. The scan is revealed as a simultaneous partitioning and projection, the body ‘digitally dissected’ into its component parts, from which a specific, securitised visualisation is shaped. Drawing on the entangled histories of ‘body knowledge’ in art, science, and anatomy—their techniques of abstraction and technologies of visualisation—we explore what light may be shed on the Backscatter scan and, more importantly, what ramifications this may have for a critical response. Challenges to the biometric border have tended to centre on surveillance, making appeals to privacy and bodily integrity. However, if border disclosures which ‘take apart’ the body are more precisely understood as visualisations, then there are more fundamental issues than recourse to rights of privacy can counteract.
Riotous Sydney: Redfern, Macquarie Fields, and (My) Cronulla
Authors: Shaw Wendy S
Published: April 2009

This paper interrogates the reactions to three riotous events that occurred in 2004 and 2005 in neighbourhoods of Sydney, Australia. At Redfern and Cronulla, the riots appeared to be ‘race’ related, whereas the Macquarie Fields incidents represented an apparent ‘class war’. Parallels between Redfern and Macquarie Fields were also drawn because of the identification of similar circumstances of poverty and dispossession. By delving into the populist accounts of the three events and untangling their discursive threads, a different picture emerged. This paper unearths some of the strategies used to distinguish suburban Cronulla from the stigmatised Redfern and Macquarie Fields. I argue that this separation has served to reinforce the expectation that riotous activities remain the provenance of ‘ marginal’ (racialised, and/or classed) groups. Through a process of remembering—utilising my personal experiences of place—I found an entry point to challenge this understanding about riotous domains by reflecting on some of the underlying tensions and manifestations of wider historical geographies of a city, and a society. This paper traces the production of a societal fabric(ation) that has worked to reinforce and consolidate existing entitlements to urban space and amenity, which have led to violent turf protection in the past and present.
The neural origins of shell structure and pattern in aquatic mollusks
Authors: Boettiger Alistair , Ermentrout Bard , Oster George
Published: April 2009

We present a model to explain how the neurosecretory system of aquatic mollusks generates their diversity of shell structures and pigmentation patterns. The anatomical and physiological basis of this model sets it apart from other models used to explain shape and pattern. The model reproduces most known shell shapes and patterns and accurately predicts how the pattern alters in response to environmental disruption and subsequent repair. Finally, we connect the model to a larger class of neural models.
Igbo English in the Nigerian video film
Authors: Ezejideaku Emmanuel , Ugwu Esther Nkiru
Published: April 2009

This paper examines the use of Igbo English, one of the ethnic varieties of Nigerian English, in the Nigerian video film. By Nigerian video film, we mean video films produced in, and/or about Nigeria in English as opposed to those produced in Nigerian indigenous languages which are variously known as Igbo video films, Yoruba video films, or Edo video films, among others. The data for this study come from a random selection from video films produced in Nigeria between 2003 and 2006. In all the films studied, it is observed that Igbo English is essentially the medium of communication. Igbo English is one of the three major ethnic varieties of Nigerian English and is characterized by the fact that, while the vocabulary is mostly English, the sentence pattern is essentially Igbo. The choice of Igbo English as the medium for the films seems to be part of the efforts by the producers to retain, as much as possible, the “Nigerianness” of the films, which inevitably have to be produced in English to accommodate the international audience. This study observes that Igbo English, as used in the films studied, manifests itself in four forms: Igbo English proper, composed of English vocabulary in Igbo sentence structure; Engligbo, a form of code-mixing that is almost a fifty-fifty blend of English and Igbo; translation, in which Igbo idiomatic and other rhetorical expressions are transferred literally into English; and errors induced by the influence of the mother tongue (Igbo) on English.
CSL–MAML-dependent Notch1 signaling controls T lineage–specific IL-7Rα gene expression in early human thymopoiesis and leukemia
Authors: González-García Sara , García-Peydró Marina , Martín-Gayo Enrique , Ballestar Esteban , Esteller Manel , Bornstein Rafael , de la Pompa José Luis , Ferrando Adolfo A. , Toribio María L.
Published: April 2009

Notch1 activation is essential for T-lineage specification of lymphomyeloid progenitors seeding the thymus. Progression along the T cell lineage further requires cooperative signaling provided by the interleukin 7 receptor (IL-7R), but the molecular mechanisms responsible for the dynamic and lineage-specific regulation of IL-7R during thymopoiesis are unknown. We show that active Notch1 binds to a conserved CSL-binding site in the human IL7R gene promoter and critically regulates IL7R transcription and IL-7R α chain (IL-7Rα) expression via the CSL–MAML complex. Defective Notch1 signaling selectively impaired IL-7Rα expression in T-lineage cells, but not B-lineage cells, and resulted in a compromised expansion of early human developing thymocytes, which was rescued upon ectopic IL-7Rα expression. The pathological implications of these findings are demonstrated by the regulation of IL-7Rα expression downstream of Notch1 in T cell leukemias. Thus, Notch1 controls early T cell development, in part by regulating the stage- and lineage-specific expression of IL-7Rα.
Testing Behavioral Hypotheses Using an Integrated Model of Grocery Store Shopping Path and Purchase Behavior
Authors: Hui Sam K. , Bradlow Eric T. , Fader Peter S.
Published: April 2009

We examine three sets of established behavioral hypotheses about consumers' in-store behavior using field data on grocery store shopping paths and purchases. Our results provide field evidence for the following empirical regularities. First, as consumers spend more time in the store, they become more purposeful—they are less likely to spend time on exploration and more likely to shop/buy. Second, consistent with “licensing” behavior, after purchasing virtue categories, consumers are more likely to shop at locations that carry vice categories. Third, the presence of other shoppers attracts consumers toward a store zone but reduces consumers' tendency to shop there.
Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment
Authors: Peterson Eric L. , Kondev Jané , Theriot Julie A. , Phillips Rob
Published: April 2009

Motivation: Many proteins with vastly dissimilar sequences are found to share a common fold, as evidenced in the wealth of structures now available in the Protein Data Bank. One idea that has found success in various applications is the concept of a reduced amino acid alphabet, wherein similar amino acids are clustered together. Given the structural similarity exhibited by many apparently dissimilar sequences, we undertook this study looking for improvements in fold recognition by comparing protein sequences written in a reduced alphabet.

Results: We tested over 150 of the amino acid clustering schemes proposed in the literature with all-versus-all pairwise sequence alignments of sequences in the Distance mAtrix aLIgnment database. We combined several metrics from information retrieval popular in the literature: mean precision, area under the Receiver Operating Characteristic curve and recall at a fixed error rate and found that, in contrast to previous work, reduced alphabets in many cases outperform full alphabets. We find that reduced alphabets can perform at a level comparable to full alphabets in correct pairwise alignment of sequences and can show increased sensitivity to pairs of sequences with structural similarity but low-sequence identity. Based on these results, we hypothesize that reduced alphabets may also show performance gains with more sophisticated methods such as profile and pattern searches.

Availability: A table of results as well as the substitution matrices and residue groupings from this study can be downloaded from http://www.rpgroup.caltech.edu/publications/supplements/alphabets.

Contact:  phillips@pboc.caltech.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Enrichment constrained time-dependent clustering analysis for finding meaningful temporal transcription modules
Authors: Meng Jia , Gao Shou-Jiang , Huang Yufei
Published: April 2009

Motivation: Clustering is a popular data exploration technique widely used in microarray data analysis. When dealing with time-series data, most conventional clustering algorithms, however, either use one-way clustering methods, which fail to consider the heterogeneity of temporary domain, or use two-way clustering methods that do not take into account the time dependency between samples, thus producing less informative results. Furthermore, enrichment analysis is often performed independent of and after clustering and such practice, though capable of revealing biological significant clusters, cannot guide the clustering to produce biologically significant result.

Result:We present a new enrichment constrained framework (ECF) coupled with a time-dependent iterative signature algorithm (TDISA), which, by applying a sliding time window to incorporate the time dependency of samples and imposing an enrichment constraint to parameters of clustering, allows supervised identification of temporal transcription modules (TTMs) that are biologically meaningful. Rigorous mathematical definitions of TTM as well as the enrichment constraint framework are also provided that serve as objective functions for retrieving biologically significant modules. We applied the enrichment constrained time-dependent iterative signature algorithm (ECTDISA) to human gene expression time-series data of Kaposi's sarcoma-associated herpesvirus (KSHV) infection of human primary endothelial cells; the result not only confirms known biological facts, but also reveals new insight into the molecular mechanism of KSHV infection.

Availability: Data and Matlab code are available at http://engineering.utsa.edu/∼yfhuang/ECTDISA.html

Contact:  yufei.huang@utsa.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Rockfish sounds and their potential use for population monitoring in the Southern California Bight
Authors: Širović Ana , Cutter George R. , Butler John L. , Demer David A.
Published: April 2009

Širović, A., Cutter, G. R., Butler, J. L., and Demer, D. A. 2009. Rockfish sounds and their potential use for population monitoring in the Southern California Bight. – ICES Journal of Marine Science, 66: 981–990. Non-lethal methods are being developed to assess and monitor the depleted rockfish stocks off southern California. For example, data from multifrequency echosounders and underwater cameras have been combined to map the dispersions and estimate the abundances of rockfish at the historical fishing sites within this region. From August to October 2007, this ship-based technique was augmented with two passive-acoustic moored recorders. One collected data at the 43 Fathom Bank for 46 days, while the other was serially deployed at 13 locations for shorter periods (1–8 d). Passive-acoustic data were analysed for the presence of rockfish sounds. Potential sources of five pulsing sounds were identified from the optically estimated species compositions at each location, as well as from known rockfish recordings collected in aquaria. All sounds had a low frequency (<900 Hz). Some were short, individual pulses (≤0.1 s), others were repetitive. A repetitive pulsing from bocaccio (Sebastes paucispinis) was the most commonly recorded sound and it occurred mainly at night. The daily calling rates at each site were quantitatively compared with the rockfish abundance estimates obtained from the active-acoustic survey, and they were positively correlated. The feasibility of using passive-acoustic tools to monitor changes in rockfish populations efficiently is discussed.
The willingness to pay for dusky kob (Argyrosomus japonicus) restocking: using recreational linefishing licence fees to fund stock enhancement in South Africa
Authors: Palmer Ryan M. , Snowball Jen D.
Published: April 2009

Palmer, R. M., and Snowball, J. D. 2009. The willingness to pay for dusky kob (Argyrosomus japonicus) restocking: using recreational linefishing licence fees to fund stock enhancement in South Africa. – ICES Journal of Marine Science, 66: 839–843. The economic feasibility of stock enhancement of Argyrosomus japonicus in South Africa was investigated using a willingness-to-pay (WTP) survey. The pilot study provides a unique example of the use of the contingent valuation method as a valuation tool for a proposed stock enhancement programme. An increase in the cost of a recreational fishing permit is used as a potential vehicle of payment. The median value of the maximum that fishers were willing to pay for a recreational fishing permit was R155 (South African Rand) for frequent fishers and R100 for non-frequent fishers. Analysis showed that a fee of more than R100 excluded up to 50% of anglers from the fishery, but that a fee of R100 excluded only 28% of recreational anglers and would generate an additional R12 million annually from the sale of recreational fishing permits. The estimated costs of set-up and running of a stock enhancement programme are substantially lower than this, suggesting that stock enhancement may be an economically feasible management option that deserves more investigation. The WTP method itself produces robust results and is likely to be an effective tool in the management of the marine environment.
Clinical trial: the effects of the proton pump inhibitor dexlansoprazole MR on daytime and nighttime heartburn in patients with non‐erosive reflux disease
Authors: FASS R. , CHEY W. D. , ZAKKO S. F. , ANDHIVAROTHAI N. , PALMER R. N. , PEREZ M. C. , ATKINSON S. N.
Published: April 2009

Background  The proportion of patients who respond to proton pump inhibitor (PPI) therapy is about 20% lower in those with non‐erosive reflux disease (NERD) than in those with erosive oesophagitis.

Aim  To assess efficacy and safety of dexlansoprazole MR, a PPI using Dual Delayed Release technology, in NERD patients.

Methods  In this 4‐week, double‐blind, placebo‐controlled study, 947 NERD patients randomly received dexlansoprazole MR 30 mg, 60 mg or placebo once daily (QD). The percentages of 24‐h heartburn‐free days (primary) and nights without heartburn (secondary) were assessed from patients’ daily diaries. Investigators also assessed symptoms. Patients completed validated quality of life and symptom severity questionnaires.

Results  Dexlansoprazole MR provided significantly greater median percentages of 24‐h heartburn‐free days (54.9% and 50.0% for the 30‐ and 60‐mg doses vs. 17.5% for placebo, P < 0.00001) and nights without heartburn (80.8% and 76.9% vs. 51.7%, P < 0.00001 vs. placebo). Dexlansoprazole MR also reduced symptom severity. Quality of life improvements in patients receiving dexlansoprazole MR were consistent with clinical efficacy endpoints. Percentages of patients experiencing treatment‐emergent adverse events were similar among groups.

Conclusions  Dexlansoprazole MR 30 and 60 mg were superior to placebo in providing 24‐h heartburn‐free days and nights in NERD patients. Treatment was well tolerated.
Meta‐analysis: surveillance with ultrasound for early‐stage hepatocellular carcinoma in patients with cirrhosis
Authors: SINGAL A. , VOLK M. L. , WALJEE A. , SALGIA R. , HIGGINS P. , ROGERS M. A. M. , MARRERO J. A.
Published: April 2009

Background  A majority of studies investigating the accuracy of ultrasound for detecting hepatocellular carcinoma (HCC) do not reflect how this test is used for surveillance vs. diagnosis.

Aim  To determine the performance characteristics of surveillance with ultrasound for the detection of HCC, particularly early HCC as defined by the Milan criteria.

Methods  A systematic literature review using the MEDLINE and SCOPUS databases yielded six studies that evaluated the accuracy of ultrasound for HCC at any stage and 13 studies that were specific to early HCC.

Results  Surveillance ultrasound detected the majority of tumours before they presented clinically, with a pooled sensitivity of 94%. However, ultrasound was less effective for detecting early HCC with a sensitivity of 63%. Alpha‐fetoprotein provided no additional benefit to ultrasound. Meta‐regression analysis demonstrated a significantly higher sensitivity for early HCC with ultrasound every 6 months than with annual surveillance. Current studies have limitations such as verification bias and are of suboptimal quality.

Conclusions  Surveillance with ultrasound demonstrates limited sensitivity for early HCC, although this may be improved by testing at 6‐month intervals. Currently available evidence evaluating surveillance ultrasound has significant limitations and future studies are necessary to determine optimal surveillance methods for early HCC.
Variation in mitochondrial DNA and maternal genetic ancestry of Ethiopian cattle populations
Authors: Dadi H. , Tibbo M. , Takahashi Y. , Nomura K. , Hanada H. , Amano T.
Published: April 2009

This study describes complete control region sequences of mitochondrial DNA (mtDNA) from 117 Ethiopian cattle from 10 representative populations, in conjunction with the available cattle sequences in GenBank. In total, 79 polymorphic sites were detected, and these defined 81 different haplotypes. The haplotype and nucleotide diversity of Ethiopian cattle did not vary among the populations studied. All mtDNA sequences from Ethiopian cattle converged into one main maternal lineage (T1) that corresponds to African Bos taurus cattle. According to the results of this study, no zebu mtDNA haplotypes have been found in Ethiopia, where the most extensive hybridization took place on the African continent.
Genomic structure, chromosomal localization and expression profile of a porcine long non‐coding RNA isolated from long SAGE libraries
Authors: Ren H. , Li Y. , Tang Z. , Yang S. , Mu Y. , Cui W. , Ao H. , Du L. , Wang L. , Li K.
Published: April 2009

Long non‐coding RNA (long ncRNA) is a novel class of ncRNA that may be involved in critical cellular processes. A considerable number of mammalian long ncRNAs have now been isolated but only a small number of these nucleic acids have been functionally well characterized. In this study, to determine the structure, regulation and function of long ncRNA in pigs, TncRNA was isolated from this mammal and its potential function during pig foetus development was identified. We anticipated that this would provide new insights into functional genomic studies in the pig. Using LongSAGE libraries generated from Chinese indigenous Tongcheng and Landrace pigs at three prenatal stages, a novel porcine long ncRNA was identified, TncRNA, which was found to be differentially expressed during myogenesis. The full‐length cDNA for this gene is 3409 bp, and it harbours a typical polyadenylation signal sequence located 18 bp upstream from the 3′ poly (A) tail. Genomic sequence analysis showed that pig TncRNA is alternatively spliced and several transcripts were detected. Using the INRA–University of Minnesota porcine radiation hybrid panel, TncRNA was assigned to SSC2 and found to be closely linked to the microsatellite marker SW256. Porcine TncRNA was found to be expressed in all tissues examined but in variable amounts. Comparisons between the expression profiles of TncRNA at different development stages in Tongcheng and Landrace pigs revealed up‐regulation of this molecule in prenatal skeletal muscle, and differential expression in 90‐day‐old foetal skeletal muscle between these two pig breeds. This is the first report to describe a long ncRNA in pig. Moreover, the distinct expression pattern and structure of porcine TncRNA suggest that it performs complex and critical functions during foetal development.
Inhibitor of DASH proteases affects expression of adhesion molecules in osteoclasts and reduces myeloma growth and bone disease
Authors: Pennisi Angela , Li Xin , Ling Wen , Khan Sharmin , Gaddy Dana , Suva Larry J. , Barlogie Bart , Shaughnessy John D. , Aziz Nazneen , Yaccoby Shmuel
Published: April 2009

Dipeptidyl peptidase (DPP) IV activity and/or structure homologues (DASH) are serine proteases implicated in tumourigenesis. We previously found that a DASH protease, fibroblast activation protein (FAP), was involved in osteoclast‐induced myeloma growth. Here we further demonstrated expression of various adhesion molecules in osteoclasts cultured alone or cocultured with myeloma cells, and tested the effects of DASH inhibitor, PT‐100, on myeloma cell growth, bone disease, osteoclast differentiation and activity, and expression of adhesion molecules in osteoclasts. PT‐100 had no direct effects on viability of myeloma cells or mature osteoclasts, but significantly reduced survival of myeloma cells cocultured with osteoclasts. Real‐time PCR array for 85 adhesion molecules revealed upregulation of 17 genes in osteoclasts after coculture with myeloma cells. Treatment of myeloma/osteoclast cocultures with PT‐100 significantly downregulated 18 of 85 tested genes in osteoclasts, some of which are known to play roles in tumourigenesis and osteoclastogenesis. PT‐100 also inhibited osteoclast differentiation and subsequent pit formation. Resorption activity of mature osteoclasts and differentiation of osteoblasts were not affected by PT‐100. In primary myelomatous severe combined immunodeficient (SCID)‐hu mice PT‐100 reduced osteoclast activity, bone resorption and tumour burden. These data demonstrated that DASH proteases are involved in myeloma bone disease and tumour growth.
Immunogloblin E‐mediated immediate allergic reactions to dipyrone: value of basophil activation test in the identification of patients
Authors: Gómez E. , Blanca‐Lopez N. , Torres M. J. , Requena G. , Rondon C. , Canto G. , Blanca M. , Mayorga C.
Published: April 2009

BackgroundPyrazolones are a major cause of immediate IgE‐mediated reactions to drugs in many countries.

ObjectiveThe aim of the study was to evaluate a group of patients with this type of reaction by basophil activation test (BAT), focusing on the influence of the time since the reaction on the rate of positive results.

MethodsThe study included 51 patients with selective immediate allergic reactions to pyrazolones and 56 controls. Patients were defined by skin testing or a drug provocation test and BATs with pyrazolones were carried out in all cases. Patients who were BAT positive were followed‐up for 30 months to establish the rate of decline in positive tests.

ResultsBAT was positive in 28 (54.9%) cases. BAT sensitivity was higher in those who were skin‐test positive (85.7%) compared with those who were skin‐test negative (33.3%). The time between the initial reaction and this study was significantly shorter in those who were skin‐test positive (P=0.005) and those who were BAT positive (P=0.017). Follow‐up of the BAT‐positive patients showed a decrease over time, with 60% of these patients becoming negative after 6 months.

ConclusionsBAT is a useful complement to skin testing for the evaluation of immediate allergic reactions to pyrazolones. Although not optimal, BAT sensitivity was also positive in patients with a negative skin test and it is a reasonable alternative in patients with severe reactions who may develop symptoms after skin testing. The time of performance of the test is critical to obtain a positive response.
Allergen dose dependency of the early‐ and late‐phase cutaneous response in the cynomolgus monkey
Authors: Tomkinson A. , Morton M. , Stevens L. , Bowden A. , Tepper J.
Published: April 2009

Background
Cutaneous administration of allergen provides a means to confirm an allergic status, investigate the pathogenesis of allergic diseases, and/or provide a mechanism to evaluate the benefit of new potential therapeutics.

Objective
Studies were performed to characterize the allergen‐induced cutaneous early‐ and late‐phase response (EPR and LPR) in the cynomolgus monkey.

Methods
Following intradermal injections of Ascaris suum allergen, the cutaneous weal and flare EPR was measured 15 min post‐injection, and skin biopsies were collected at 8–24 h to determine the optimal time of LPR occurrence. Biopsies were analysed for epidermal and dermal inflammatory changes.

Results
The EPR was dose related with a reproducible, measurable response at 1 : 10 000 and maximal at a 1 : 100 allergen dilution. In contrast, the threshold dose required for a reproducible LPR was much greater requiring a dilution of 6 : 100, suggesting independent mechanisms for the EPR and LPR. The LPR 20 h post‐allergen injection induced an inflammatory response in the upper and deep dermis. The response was characterized by a moderate perivascular to diffuse inflammation consisting of mononuclear cells, neutrophils and eosinophils. Dexamethasone, while having no effect on the EPR, reduced dermal inflammation (upper dermis, P=0.004; deep dermis, P=0.03). Similarly, dermal eosinophilia was also reduced (upper dermis, P<0.001; deep dermis, P=0.02).

Conclusion
Collectively, the results indicate the dose dependency of the EPR and LPR. Furthermore, our observations indicate the value of the LPR response in the cynomolgus monkey to evaluate new therapeutics for the treatment of allergic diseases such as atopic dermatitis.
The rise and rise ofStaphylococcus aureus: laughing in the face of granulocytes
Authors: Anwar S , Prince L R , Foster S J , Whyte M K B , Sabroe I
Published: April 2009

Recent developments in the study of host–pathogen interactions have fundamentally altered our understanding of the nature of Staphylococcus aureus infection, and previously held tenets regarding the role of the granulocyte are being cast aside. Novel mechanisms of pathogenesis are becoming evident, revealing the extent to which S. aureus can evade neutrophil responses successfully by resisting microbicides, surviving intracellularly and subverting cell death pathways. Developing a detailed understanding of these complex strategies is especially relevant in light of increasing staphylococcal virulence and antibiotic resistance, and the knowledge that dysfunctional neutrophil responses contribute materially to poor host outcomes. Unravelling the biology of these interactions is a challenging task, but one which may yield new strategies to address this, as yet, defiant organism.
The effect of a mixotrophic chrysophyte on toxic and colony‐forming cyanobacteria
Authors: VAN DONK ELLEN , CERBIN SLAWEK , WILKEN SUSANNE , HELMSING NICO R. , PTACNIK ROBERT , VERSCHOOR ANTONIE M.
Published: April 2009

1. In order to test the effect of Ochromonas sp., a mixotrophic chrysophyte, on cyanobacteria, grazing experiments were performed under controlled conditions. We studied grazing on three Microcystis aeruginosa strains, varying in toxicity and morphology, as well as on one filamentous cyanobacterium, Pseudanabaena sp. Furthermore, we analysed the co‐occurrence of Ochromonas and Microcystis in natural systems in relation to various environmental parameters (TP, TN, DOC, temperature, pH), using data from 460 Norwegian lakes.

2. Ochromonas was able to feed on all four cyanobacterial strains tested, and grew quickly on all of them. The chrysophyte caused net growth reductions in all three Microcystis strains (the very toxic single‐celled strain PCC 7806; the less toxic colony‐forming Bear AC and the less toxic single‐celled Spring CJ). The effect of Ochromonas was strongest on the Spring CJ strain. Although the effect of Ochromonas grazing on the growth of Pseudanabaena was relatively smaller, it also reduced the net growth of this cyanobacterium significantly.

3. After 4 days of incubation with Ochromonas the total amount of cyanotoxins in the three Microcystis strains was reduced by 91.1–98.7% compared with the controls.

4. Ochromonas occurred in similar densities across all 460 Norwegian lakes. Microcystis occurred only at higher TN, TP, temperature and pH values, although its density was often several orders of magnitude higher than that of Ochromonas. Ochromonas co‐occurred in 94% of the samples in which Microcystis was present.

5. From our study it is not clear whether Ochromonas could control Microcystis blooms in natural lakes. However, our study does demonstrate that Ochromonas usually occurs in lakes with Microcystis, and our small scale experiments show that Ochromonas can strongly reduce the biomass of Microcystis and its toxin content.
Clusterin expression in cholestasis, hepatocellular carcinoma and liver fibrosis
Authors: Aigelsreiter Ariane , Janig Elke , Sostaric Julia , Pichler Martin , Unterthor Daniela , Halasz Judith , Lackner Carolin , Zatloukal Kurt , Denk Helmut
Published: April 2009

Aims:  Clusterin shares functional properties with small heat shock proteins. In contrast to other heat shock proteins, it is present in the extracellular space. Its expression is altered in various diseases. The aim was to evaluate the presence and distribution of clusterin in liver diseases associated with cholestasis, in fibrosis and in hepatocellular carcinoma.

Methods and results:  Tissue microarrays and biopsy materials were used to evaluate immunohistochemically the expression of clusterin in hepatocellular carcinoma, primary sclerosing cholangitis, primary biliary cirrhosis, mechanical cholestasis, drug‐induced cholestasis, liver fibrosis and cirrhosis. The presence of clusterin in human bile was assessed by Western blotting. Furthermore, real‐time reverse transcriptase‐polymerase chain reaction was performed on liver tissue with mechanical cholestasis. Clusterin colocalized with elastic fibres, but not with collagen, hepatocytes or bile duct epithelia. It was detected in bile plugs in cholestasis and hepatocellular carcinomas with pseudoglandular features within the lumina. Clusterin was demonstrated in bile by Western blotting and its mRNA was expressed in normal and cholestatic livers.

Conclusions:  Clusterin may protect bile duct epithelium against offensive biliary components or inhibit precipitation of biliary proteins. The association of clusterin with elastic fibres could reflect an extracellular chaperone function by either protecting elastic fibres or shielding abnormal elastic material.
Antigen retrieval and primary antibody type affect sensitivity but not specificity of CD117 immunohistochemistry
Authors: Wong Newton A C S , Melegh Zsombor
Published: April 2009

Aims:  To investigate the effects of antigen retrieval and primary antibody selection on specificity and sensitivity of CD117 immunohistochemistry.

Methods and results:  A survey and literature review were performed to determine the most commonly used CD117 antibodies. Of six such antibodies, three (Neomarkers polyclonal RB‐1518, Novocastra monoclonal T595 and Santa Cruz polyclonal C19) were rejected as only suboptimal immunoreactivity was produced despite the use of various immunohistochemical protocols. Immunohistochemistry using the three remaining antibodies (Cell Marque polyclonal CMC766, Dako polyclonal A4502 and Epitomics monoclonal YR145) was performed, with and without (for Dako and Epitomics antibodies) antigen retrieval, on 32 gastrointestinal stromal tumours (GISTs) and on 139 neoplasms (comprising 24 neoplasm types) that are differential diagnoses for GIST and/or have been reported to express CD117. Antigen retrieval generally increased the sensitivity but did not alter the specificity of immunoreactivity with the three antibodies. The different antibodies showed variations in sensitivity, but did not stain different spectrums of neoplasm type. A small number of neoplasms showed scattered nuclear immunopositivity (particularly seen without antigen retrieval), which was regarded as representing cross‐reactivity.

Conclusions:  Antigen retrieval and changing between the three antibodies tested affect sensitivity but not specificity of CD117 immunohistochemistry. Antigen retrieval does not produce false‐positive CD117 immunostaining.
Progressive cellular response in the lamina propria of the colorectal adenoma–carcinoma sequence
Authors: Cui Guanglin , Yuan Aping , Vonen Barthold , Florholmen Jon
Published: April 2009

Aims:  The lamina propria is inevitably involved in epithelial transformation. The aim was to evaluate the dynamic cellular changes in the tumour lamina propria throughout the colorectal adenoma–carcinoma sequence.

Methods and results:  Using immunohistochemistry and double immunohistochemistry, we examined lamina propria cellular changes in 41 colorectal adenomas, 25 colorectal cancers and 15 control tissues. The results showed that the proliferation labelling index in lamina propria cells began to increase in the precancerous lesions (adenomas) and became even higher in the colorectal cancers; these proliferative cells were primarily identified as myofibroblasts and lymphocytes. Phenotypic analysis revealed gradually increasing lymphocytic infiltration in both the lamina propria and adenomatous epithelium, as well as myofibroblasts in the lamina propria. However, the intraepithelial macrophage density also showed a tendency to increase gradually. Furthermore, cyclooxygenase‐2‐expressing cell density and microvessel density gradually increased in the tumour lamina propria throughout the adenoma–carcinoma sequence.

Conclusions:  Progressive cellular responses in the lamina propria could be involved in the adenoma–carcinoma transition.