bluuebunny/crossref_metadata_2025 huggingface dataset:
Growth and magnetic property of ζ-phase Mn2N1±x thin films by plasma-assisted molecular beam epitaxy
Authors: Liu Yajing , Xu Lingmin , Li Xinyu , Hu Ping , Li Shuwei
Published: May 2010

ζ -phase manganese nitride films were directly grown on sapphire substrates using plasma-assisted molecular beam epitaxy. Mn2N1.06, Mn2N0.98, and Mn2N0.86 films were synthesized by controlling the temperature of the effusion cell filled with highly pure manganese powder. The composition, structure, and morphology of the films were identified by x-ray photoelectron spectroscopy, x-ray diffraction and atomic force microscopy, and the magnetic properties of the films were characterized by a superconducting quantum interference device magnetometer at 5 and 300 K. The magnetic measurements reveal that Mn2N1±x exhibits weak ferromagnetism at 5 K, which is mainly ascribed to the weak interaction among the Mn cations induced by the nitrogen vacancies. Furthermore, the Mn2N0.86 single-crystalline films are found to have room-temperature ferromagnetism, which is attributed to the strain of the Mn2N0.86 films raised from lattice mismatch between the Mn2N0.86 films and the substrates.
High quality Ti-implanted Si layers above the Mott limit
Authors: Olea J. , Toledano-Luque M. , Pastor D. , San-Andrés E. , Mártil I. , González-Díaz G.
Published: May 2010

In this paper, we present a detailed characterization of high quality layers of Si implanted with Ti at high doses. These layers are intended to the formation of an intermediate band (IB) solar cell. The main requirement to obtain an IB material is to reach an impurity concentration beyond the Mott limit, which is, in this case, much higher than the solid solubility limit. To overcome this limit we used the combination of ion implantation and pulsed-laser melting as nonequilibrium techniques. Time-of-flight secondary ion mass spectrometry measurements confirm that Ti concentration exceeds the theoretical Mott limit in the implanted layer, and glancing incidence x-ray diffraction and transmission electron microscopy measurements prove that good crystallinity can be achieved. Sheet resistance and Hall effect mobility show uncommon characteristics that can only been explained assuming the IB existence.
Numerical analysis of mixing enhancement for micro-electroosmotic flow
Authors: Tang G. H. , He Y. L. , Tao W. Q.
Published: May 2010

Micro-electroosmotic flow is usually slow with negligible inertial effects and diffusion-based mixing can be problematic. To gain an improved understanding of electroosmotic mixing in microchannels, a numerical study has been carried out for channels patterned with wall blocks, and channels patterned with heterogeneous surfaces. The lattice Boltzmann method has been employed to obtain the external electric field, electric potential distribution in the electrolyte, the flow field, and the species concentration distribution within the same framework. The simulation results show that wall blocks and heterogeneous surfaces can significantly disturb the streamlines by fluid folding and stretching leading to apparently substantial improvements in mixing. However, the results show that the introduction of such features can substantially reduce the mass flow rate and thus effectively prolongs the available mixing time when the flow passes through the channel. This is a non-negligible factor on the effectiveness of the observed improvements in mixing efficiency. Compared with the heterogeneous surface distribution, the wall block cases can achieve more effective enhancement in the same mixing time. In addition, the field synergy theory is extended to analyze the mixing enhancement in electroosmotic flow. The distribution of the local synergy angle in the channel aids to evaluate the effectiveness of enhancement method.
Drift and reactions of positive tetratomic ions in dry, atmospheric air: Their effects on the dynamics of primary and secondary streamers
Authors: Bekstein A. , Yousfi M. , Benhenni M. , Ducasse O. , Eichwald O.
Published: May 2010

The ion swarm data, namely, the reduced mobility, diffusion, and reaction rates of the positive tetratomic ions O4+ and N2O2+ in N2 and O2 have been determined from a Monte Carlo simulation using calculated and fitted elastic and inelastic cross sections. The elastic momentum transfer cross sections have been determined from a semiclassical Jeffreys-Wentzell-Kramers-Brilouin (JWKB) approximation based on a rigid core potential model well adapted for polyatomic ions. The inelastic cross sections have been approximated from considerations based on the N4+/O2 and N4+/N2 systems. The validated cross section sets in pure N2 and O2 have been used to determine the O4+ and N2O2+ swarm data in dry air over a large E/N range up to 1000 Td. However, due to the lack of experimental ion transport coefficients necessary for a more rigorous cross section validation, the present data, validated only at low E/N, should be regarded as a first approximation, susceptible to improvements as soon as measurements of ion transport coefficients become available in the literature. Then, the present data are used in a two-dimensional discharge dynamics fluid model for the simulation of the primary and secondary streamers for the case of a positive point-to-plane corona discharge in dry air. Relevant characteristics such as discharge current, charged particle densities, space charge electric field and the variation in active species like N and O radicals (very useful in many nonthermal plasma applications) are analyzed and discussed with and without the consideration of three positive tetratomic ions (N4+, O4+, and N2O2+). More particularly, the non-negligible effect of O4+, in the dynamics of the primary and secondary streamers during the discharge propagation and relaxation stages is highlighted with an emphasis on the role of the related kinetic reactions occurring between the different charged particles.
Photoluminescence model for a hybrid aptamer-GaAs optical biosensor
Authors: Budz H. A. , Ali M. M. , Li Y. , LaPierre R. R.
Published: May 2010

The present work describes the development of a hybrid GaAs-aptamers biosensor for the label-free detection of adenosine 5′-triphosphate (ATP). The implemented sensing strategy relies on the sensitivity of the GaAs photoluminescence (PL) emission to the local environment at its surface. Specifically, GaAs substrates were chemically modified with thiol-derivatized oligonucleotide aptamers following conventional condensed-phase deposition techniques and exposed to the target ATP molecules. The resulting modification in the PL intensity is attributed to a specific biorecognition interaction between the aptamer receptors and the ATP target and, more importantly, the accompanying ligand-induced structural change in the aptamer conformation. Since the negatively charged aptamer probes are covalently anchored to the substrate surface, the sensing mechanism can be understood in terms of a change in the surface charge distribution and thereby, the width of the nonemissive GaAs surface depletion layer. Biosensors fabricated with aptamer probes of various lengths indicate a strand length-dependent nature of the luminescence response to the biorecognition events, with longer aptamers yielding a greater PL enhancement. Results provided by several control experiments demonstrate the sensitivity, specificity, and selectivity of the proposed biosensor in accurately identifying ATP. Modeling the performance data by means of Poisson–Boltzmann statistics in combination with the GaAs depletion layer model shows a good correlation between the structural conformation of the aptamers and the PL yield of the underlying substrate. Collectively, the results described within indicate the promise of the prospective luminescence-based GaAs-aptamer biosensor for use in real-time sensing assays requiring a straightforward and efficient means of label-free analytical detection.
Note: X-ray radiography for measuring chemical diffusion in metallic melts
Authors: Griesche A. , Zhang B. , Solórzano E. , Garcia-Moreno F.
Published: May 2010

A x-ray radioscopy technique for measuring in situ chemical diffusion coefficients in metallic melts is presented. The long-capillary diffusion measurement method is combined with imaging techniques using microfocus tubes and flat panel detectors in order to visualize and quantitatively analyze diffusive mixing of two melts of different chemical composition. The interdiffusion coefficient as function of temperature and time is obtained by applying Fick’s diffusion laws. Tracking the time dependence of the mean square penetration depth of the mixing process allows to detect changes in the mass transport caused by convective flow. The possibility to sort out convective mass transport contributions from analysis enhances significantly the accuracy compared to the conventional long-capillary diffusion measurement method with postmortem analysis. The performance of this novel diffusion measurement method with x-ray radiography technique is demonstrated by a diffusion experiment in an Al–Ni melt.
Infrared and Raman line shapes for ice Ih. I. Dilute HOD in H2O and D2O
Authors: Li F. , Skinner J. L.
Published: May 2010

Vibrational spectroscopy of ice Ih provides information about structure, dynamics, and vibrational coupling in this important substance. Vibrational spectra are simplified for HOD in either H2O or D2O, as in these instances the OD or OH stretch, respectively, functions as a local chromophore. As a first step in providing a theoretical treatment of the vibrational spectroscopy for the fully coupled system (H2O or D2O), herein we calculate the infrared and Raman spectra for the isotopically substituted systems. The calculation involves a classical molecular dynamics simulation using a new water model, an initial proton-disordered ice configuration, and ab initio based transition frequency, dipole, and polarizability maps. Our theoretical results are in reasonable agreement with experiment, and from our results we provide molecular and physical interpretations for the spectral features.
Particle-size effects on the terahertz transmittance of metallic particle ensembles: Comparison with effective medium theory
Authors: Zheng Y. , Johnson A. , Pyde E. , Chau K. J.
Published: May 2010

We investigate the transmittance of fixed-length ensembles of spherical particles having average radii ranging over two orders of magnitude. The transmittance is interrogated at discrete frequencies in the terahertz regime where the particle radius is subwavelength by at least an order of magnitude. A nonmonotonic dependence of the transmittance on particle radius is observed. As a function of increasing particle size, the transmittance increases to a peak value and then decreases toward zero. Calculations of the complex effective permittivity of the ensemble yield predicted transmittance curves that accurately describe the transmittance decrease as a function of increasing particle size.
Homogeneous water nucleation and droplet growth in methane and carbon dioxide mixtures at 235 K and 10 bar
Authors: Holten V. , van Dongen M. E. H.
Published: May 2010

Homogeneous nucleation rates and droplet growth rates of water in pure methane and mixtures of methane and carbon dioxide were measured in an expansion wave tube at 235 K and 10 bar. The nucleation rate in pure methane is three orders of magnitude higher than literature nucleation rates of water in low-pressure helium or argon. Addition of carbon dioxide to the carrier gas mixture increases the rates even more. Specifically, rates in a mixture of methane and 3% carbon dioxide are a factor of 10 higher than the rates in pure methane. With 25% carbon dioxide, the rates are four orders of magnitude higher than the rates in pure methane. An application of the nucleation theorem shows that the critical cluster consists of 22 water molecules and 5 methane molecules, for nucleation in pure methane. Growth rates of water droplets were measured in methane and in methane-carbon dioxide mixtures at 243 K and 11.5 bar. At equal temperature, pressure and water vapor fraction, the growth rate of the squared droplet radius is about 20% lower in the mixture with 25% carbon dioxide than in pure methane. The lower growth rate is caused by a smaller diffusion coefficient of water in the mixture with carbon dioxide; the difference of the diffusion coefficients is qualitatively reproduced by the empirical Fuller correlation combined with Blanc’s law.
Enhanced dissociation of charge-transfer states in narrow band gap polymer:fullerene solar cells processed with 1,8-octanedithiol
Authors: Moet D. J. D. , Lenes M. , Morana M. , Azimi H. , Brabec C. J. , Blom P. W. M.
Published: May 2010

The improved photovoltaic performance of narrow band gap polymer:fullerene solar cells processed from solutions containing small amounts of 1,8-octanedithiol is analyzed by modeling of the experimental photocurrent. In contrast to devices that are spin coated from pristine chlorobenzene, these cells do not produce a recombination-limited photocurrent. Modeling of the experimental data reveals that a sixfold reduction in the decay rate of photogenerated bound electron–hole pairs can account for the marked increase in short-circuit current density and fill factor. At short-circuit conditions, the dissociation probability of bound pairs is found to increase from 48% to 70%.
Stress control in polycrystalline thin films—reduction in adatoms diffusion into grain boundaries via surfactants
Authors: Yang Yi , Huang Hanchen , Xiang S. K. , Chason Eric
Published: May 2010

The diffusion of adatoms into grain boundaries (GBs) of polycrystalline thin film during vapor deposition affects the stress that develops and the film’s subsequent performance. This Letter reports a proposed mechanism of modifying the stress by controlling adatom diffusion into GBs through the use of surfactants. Based on polycrystalline kinetic Monte Carlo simulations of Cu⟨111⟩ thin films with In surfactant, the authors demonstrate that the proposed mechanism is feasible. Further, the authors show that the reduction is due to the decrease in effective adatom diffusivity, which dominates over the increase in adatom concentration.
Resonance behavior of single ultrathin slot antennas on finite dielectric substrates in terahertz regime
Authors: Park H. R. , Koo S. M. , Suwal O. K. , Park Y. M. , Kyoung J. S. , Seo M. A. , Choi S. S. , Park N. K. , Kim D. S. , Ahn K. J.
Published: May 2010

We investigate resonance behaviors of optically thin metallic slot antennas on finite substrates in terahertz frequency regime. By carefully analyzing theoretical and experimental results, we observe that slot antennas fabricated in a gold film with a thickness below the skin depth of gold show blueshifted resonance frequencies for the increasing slot width, while the opposite resonance behaviors appear when the slot antennas are perforated in perfectly electric conductor. In addition, we find that for slot antenna sustained by a finite substrate its thickness and the slot width are additional crucial factors determining the resonance frequency of slot antennas.
Pathologies of Migrant Place-Making: The Case of Polish Migrants to the UK
Authors: Gill Nick
Published: May 2010

The author argues that migrant place-making can become counterproductive for migrant communities for a variety of reasons. Existing place-making literature is often optimistic about the ability of places to offer migrants common identities and means of mobilising collectively. The author constructs a four-stage general model of migrant place-making to examine the potential pathologies of migrant organisational strategies at each of these four stages. In order to demonstrate the use of this model, an analysis of post-2004 Polish migration to the UK, drawing upon forty-two semistructured interviews with Polish migrants and domestic service providers, is presented. Although earlier migration displayed a number of the ideal characteristics of positive place-making described in the ideal four-stage model, centring around the Polish Catholic churches of England and Wales, post-2004 migration has introduced a series of problems that illustrate the various pathologies that can occur. The author concludes by calling for (i) a greater appreciation of the role of host organisations in the production of successful and unsuccessful place-making, and (ii) a recognition that place-making as a migrant settlement strategy is deeply fallible at various stages of its development.
Crisis and Institutional Change in Urban Governance
Authors: Fuller Crispian
Published: May 2010

Recent studies of new institutional spaces typically underplay the uneven and contested process of institutional change by undervaluing the role of inherited institutions and discourses. This is a critical issue as neoliberal networked forms of governance interact with inherited institutional arrangements, characterised by important path dependencies that guide actors. Contradiction and tensions can emerge, culminating in crisis tendencies, and producing both discursive and material contestation between actors. It is with an understanding of path dependencies, ideas (structured into discourses), and (perceived and actual) crisis tendencies that this paper examines contested institutional change through a case-study analysis of one city, and a critical engagement with neoinstitutionalism. The purpose is to examine, firstly, the significance of inherited path-dependent arrangements in fostering conflict and crisis tendencies during interaction with emergent state action; secondly, the extent to which crisis is evident in processes of institutional change and the form that this takes; and, thirdly, the importance of ideas in producing institutional transformation. It is found that institutional conflict is evident between inherited institutions and emergent state action, and stems both from the way agents are organised by the state and from certain path dependencies, but that this does not lead to an actual material crisis. Rather, the nation-state, in partnership with senior city government actors, use ideational/discursive ‘crisis talk’ as a means by which to induce institutional change. The role of ideas has been in critical in this process as the nation-state frames problems and solutions in line with its existing policy paradigm and institutional arrangements, and with discourses further reinforcing existing material power relations.
The Death of Great Ships: Photography, Politics, and Waste in the Global Imaginary
Authors: Crang Mike
Published: May 2010

The iconic images heralding an age of connectivity are the plane and the trace of digital flows bearing information. However, not far behind has been the cumbrous yet essential ‘big box’ of containerization, shipping all manner of goods across the planet on great vessels remorselessly circling the globe. Critiques of global trade have latched upon the counterimage of these mighty ships' ruinous carcasses beached and being broken in South Asia. Here then is the antipode of globalization—ships, once carrying cargoes, now themselves sold around the globe for scrap and ending up broken up according to the very logics of cheap locations that their routes made possible. This paper interrogates these counterimages of global capitalism. Looking at the works of various photographers it examines how waste ships are made to work aesthetically. It examines the photo-documentary and traditions of the industrial sublime to find ‘time-images’ that speak to the material and labour worlds of global capital.
COMPASSS (COMplex PAttern of Sequence Search Software), a simple and effective tool for mining complex motifs in whole genomes
Authors: Maccari Giuseppe , Gemignani Federica , Landi Stefano
Published: May 2010

Motivation: The complete sequencing of the human genome shows that only 1% of the entire genome encodes for proteins. The major part of the genome is made up of non-coding DNA, regulatory elements and junk DNA. Transcriptional regulation plays a central role in a multitude of critical cellular processes and responses, and it is a central force in the development and differentiation of multicellular organisms. Identifying regulatory elements is one of the major tasks in this challenge. To accomplish this task, we developed a solid and simple suite that allows direct access to genomic database and immediate result check. We introduce COMPASSS (COMplex PAttern of Sequence Search Software), a simple and effective tool for motif search in entire genomes. Motifs can be partially degenerated and interrupted by spacers of variable length.

Results: We demonstrate through real biological data mining the simplicity and robustness of this tool. The test was performed on two well-known protein domains and a highly variable cis-acting element. COMPASSS successfully identifies both protein domains and cis-acting semi-conserved elements.

Availability: The COMPASSS suite is available for Windows free of charge from our web sites: compasss.sourceforge.net/; www.stefanolandi.eu/

Contact:  gpmaccari@gmail.com; slandi@biologia.unipi.it

Supplementary information:  Supplementary data are available at Bioinformatics online.
A quality control algorithm for filtering SNPs in genome-wide association studies
Authors: Pongpanich Monnat , Sullivan Patrick F. , Tzeng Jung-Ying
Published: May 2010

Motivation: The quality control (QC) filtering of single nucleotide polymorphisms (SNPs) is an important step in genome-wide association studies to minimize potential false findings. SNP QC commonly uses expert-guided filters based on QC variables [e.g. Hardy–Weinberg equilibrium, missing proportion (MSP) and minor allele frequency (MAF)] to remove SNPs with insufficient genotyping quality. The rationale of the expert filters is sensible and concrete, but its implementation requires arbitrary thresholds and does not jointly consider all QC features.

Results: We propose an algorithm that is based on principal component analysis and clustering analysis to identify low-quality SNPs. The method minimizes the use of arbitrary cutoff values, allows a collective consideration of the QC features and provides conditional thresholds contingent on other QC variables (e.g. different MSP thresholds for different MAFs). We apply our method to the seven studies from the Wellcome Trust Case Control Consortium and the major depressive disorder study from the Genetic Association Information Network. We measured the performance of our method compared to the expert filters based on the following criteria: (i) percentage of SNPs excluded due to low quality; (ii) inflation factor of the test statistics (λ); (iii) number of false associations found in the filtered dataset; and (iv) number of true associations missed in the filtered dataset. The results suggest that with the same or fewer SNPs excluded, the proposed algorithm tends to give a similar or lower value of λ, a reduced number of false associations, and retains all true associations.

Availability: The algorithm is available at http://www4.stat.ncsu.edu/˜jytzeng/software.php

Contact:  jytzeng@stat.ncsu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Mind the gaps: a state-space model for analysing the dynamics of North Sea herring spawning components
Authors: Payne Mark R.
Published: May 2010

Payne, M. R. 2010. Mind the gaps: a state-space model for analysing the dynamics of North Sea herring spawning components. – ICES Journal of Marine Science, 67: 1939–1947. The North Sea autumn-spawning herring (Clupea harengus) stock consists of a set of different spawning components. The dynamics of the entire stock have been well characterized, but although time-series of larval abundance indices are available for the individual components, study of the dynamics at the component level has historically been hampered by missing observations and high sampling noise. A simple state-space statistical model is developed that is robust to these problems, gives a good fit to the data, and proves capable of both handling and predicting missing observations well. Furthermore, the sum of the fitted abundance indices across all components proves an excellent proxy for the biomass of the total stock, even though the model utilizes information at the individual-component level. The Orkney–Shetland component appears to have recovered faster from historic depletion events than the other components, whereas the Downs component has been the slowest. These differences give rise to changes in stock composition, which are shown to vary widely within a relatively short time. The modelling framework provides a valuable tool for studying and monitoring the dynamics of the individual components of the North Sea herring stock.
Cutaneous endometriosis in the umbilical region: The usefulness of CD10 in identifying the interstitium of ectopic endometriosis
Authors: FUKUDA Hidetsugu , MUKAI Hideki
Published: May 2010

Endometriosis is a condition in which endometrium or endometrium‐like tissue grows in areas other than the endometrium and is often found within the pelvis such as in the uterus or ovary, but occasionally develops ectopically in the skin. In this paper, we report a case of cutaneous endometriosis in the umbilical region found in a 37‐year‐old woman with no history of pregnancy. The lesion was a brown, firm and elastic nodule, 9 mm × 7 mm in size, and caused bleeding as well as pain which increased during menstruation. Histopathological findings revealed that there were small and large glandular cavity structures in the dermis and the edematous interstitium around it. On immunohistochemical staining for estrogen and progesterone receptors, the cellular nuclei of glandular cavity walls were mainly found to be positive for both, and cells in the edematous interstitium around the glandular cavity were positive for CD10. Consequently, we diagnosed this case as cutaneous endometriosis in the umbilical region. CD10 was initially described as a tumor‐specific antigen found in acute lymphoblastic leukemia. Recently, the usefulness of CD10 in diagnosing endometriosis in addition to various types of lymphoma or blood cancer has been confirmed, and in our case it also proved to be as useful as estrogen receptor or progesterone receptor in the definitive diagnosis of endometriosis.
Amelanotic vulvar melanoma with intratumor histological heterogeneity
Authors: OISO Naoki , YOSHIDA Masuki , KAWARA Shigeru , KAWADA Akira
Published: May 2010

Amelanotic vulvar melanoma is a rare type of malignant melanoma. This paper describes a case of an asymptomatic ulcerated nodule 20 mm in size. The tumor cells from the nodular lesion showed positive staining immunohistochemically for Melan‐A, but negative staining with HMB‐45. The cells showed negative reactivity to S‐100 except in one region. The melanoma cells in the epidermis were detected in one of the specimens from the excised tumor nodule. The cells in the epidermis showed positive staining for Melan‐A and S‐100 and partial staining with HMB‐45. The tumor was diagnosed as malignant melanoma of the vulva and immunohistochemically shown to have intratumor histological heterogeneity. This case suggests the importance of viewing non‐pigmented nodules on the vulva of elderly females as potentially malignant melanoma, and that a combination of immunohistochemical stains may be useful for recognizing the stage of the melanosomes in the melanoma cells.
Whitening efficacy of plant extracts including orchid extracts on Japanese female skin with melasma and lentigo senilis
Authors: TADOKORO Taketsugu , BONTÉ Frédéric , ARCHAMBAULT Jean C. , CAUCHARD Jean H. , NEVEU Michèle , OZAWA Kentaro , NOGUCHI Fumihito , IKEDA Aya , NAGAMATSU Maki , SHINN Sachiko
Published: May 2010

The purpose of this study was to assess thein vivoefficacy of a cosmetic formulation containing plant extracts including orchid extracts, compared to 3% vitamin C derivative formulated with the same excipient, in Japanese female adult volunteers with melasma and/or lentigo senilis. The ethics committee of Osaka National Hospital approved the protocol of the study. Before recruitment, selection and inclusion of a volunteer in this study, signed informed consent was obtained from each volunteer after she was given clear and precise information on the study, enabling her to appreciate the aim of the study and the consequences of her consent. Forty‐eight female volunteers aged 30–60 years applied the plant extracts and vitamin C derivative to one side of the face. After repeated application for 8 weeks, efficacy was evaluated clinically by colorimetric measurements and subjectively using a questionnaire. After 8 weeks of treatment, both the clinical evaluations by a dermatologist and the questionnaire surveys by volunteers indicated that the cosmetic formulation containing plant extracts was significantly effective in improving the size, brightness, color intensity, clarity, visibility and global appearance of the pigmented spots, and also the luminosity complexion and skin clarity of the face. The good agreement between the results of clinical evaluations and those of questionnaire surveys showed that the orchid‐rich plant extracts possess efficacy similar to vitamin C derivative in whitening the skin as well as melasma and lentigo senilis on the face of Japanese women.
Rapid clonal shifts in response to kinase inhibitor therapy in chronic myelogenous leukemia are identified by quantitation mutation assays
Authors: Yin C. Cameron , Cortes Jorge , Galbincea John , Reddy Neelima , Breeden Megan , Jabbour Elias , Luthra Rajyalakshmi , Jones Dan
Published: May 2010

Treatment of CML with the tyrosine kinase inhibitor (TKI) imatinib mesylate results in the emergence of point mutations within the kinase domain (KD) of the BCR‐ABL1 fusion transcript. The introduction of next‐generation TKIs that can overcome the effects of some BCR‐ABL1 KD mutations requires quantitative mutation profiling methods to assess responses. We report the design and validation of such quantitative assays, using pyrosequencing and mutation‐specific RT‐PCR techniques, to allow sequential monitoring and illustrate their use in tracking specific KD mutations (e.g. G250E, T315I, and M351T) following changes in therapy. Pyrosequencing and mutation‐specific RT‐PCR allows sequential monitoring of specific mutations and identification of rapid clonal shifts in response to kinase inhibitor therapy in CML. Rapid reselection of TKI‐resistant clones occurs following therapy switch in CML. (Cancer Sci 2010)
Review article: the role of rapid virological response in determining treatment duration for chronic hepatitis C
Authors: POORDAD F. F.
Published: May 2010

Aliment Pharmacol Ther 31, 1251–1267

Background  For patients with chronic hepatitis C, attaining rapid virological response (RVR) is highly predictive of attaining SVR.

Aim  To consider the predictive value of RVR in terms of SVR and relapse.

Methods  Data were collected from published clinical trials to define the predictive value of RVR for SVR and evaluate the proposed continuum linking RVR to relapse.

Results  These data support a 24‐week regimen among genotype (G)1 patients who attain RVR with positive predictive values (PPVs) of 77.8% and 85.7% in patients with G1 infection treated for 24 and 48 weeks. Conversely, failure to attain RVR among G1 patients should not be viewed as a criterion for extending treatment duration beyond 48 weeks: negative predictive values (NPVs) were 60.9% and 52.7% in G1 patients without RVR treated for 48 and 72 weeks. Among G2/3 patients, RVR has a high PPV; however, the NPV varied with treatment duration indicating that a 24‐week treatment regimen is warranted in G2/3 patients who fail to attain RVR.

Conclusions  The present analysis confirms RVR as a strong predictor of SVR that can be used to tailor treatment duration, but which also should be appreciated in the context of treatment duration and regimen.
A model of healing of Los Angeles grades C and D reflux oesophagitis: is there an optimal time of acid suppression for maximal healing?
Authors: Katz P. O. , Johnson D. A. , Levine D. , Röhss K. , Junghard O. , Åstrand M. , Nagy P.
Published: May 2010

Aliment Pharmacol Ther 2010; 32: 443–447

Background  In patients with Los Angeles (LA) grade C or D oesophagitis, a positive relationship has been established between the duration of intragastric acid suppression and healing.

Aim  To determine whether there is an apparent optimal time of intragastric acid suppression for maximal healing of reflux oesophagitis.

Methods  Post hoc analysis of data from a proof‐of‐concept, double‐blind, randomized study of 134 adult patients treated with esomeprazole (10 or 40 mg od for 4 weeks) for LA grade C or D oesophagitis. A curve was fitted to pooled 24‐h intragastric pH (day 5) and endoscopically assessed healing (4 weeks) data using piecewise quadratic logistic regression.

Results  Maximal reflux oesophagitis healing rates were achieved when intragastric pH >4 was achieved for approximately 50–70% (12–17 h) of the 24‐h period. Acid suppression above this threshold did not yield further increases in healing rates.

Conclusion  After 4 weeks’ acid‐suppressive therapy for LA grade C or D oesophagitis, successful healing appears to reach a threshold above which improvements are unlikely to be achieved despite an increase in number of hours with intragastric pH >4.
Coronary artery calcification and cardiovascular risk: the role of RANKL/OPG signalling
Authors: Quercioli Alessandra , Montecucco Fabrizio , Bertolotto Maria , Ottonello Luciano , Pende Aldo , Mach François , Dallegri Franco
Published: May 2010

Eur J Clin Invest 2010; 40 (7): 645–654

Background  Coronary artery disease (CAD) represents the most relevant cause of death and morbidity in the adult population of developed and developing countries. During the last decades, a strong research effort has been performed to identify more selective markers and better assess the cardiovascular risk in both primary and secondary prevention.

Materials and methods  This review updates current knowledge regarding the pathophysiological relevance as possible markers of coronary calcification of the receptor activator of nuclear factor‐kappa ligand (RANKL)/osteoprotegerin (OPG) system. Furthermore, the potential clinical use of both RANKL/OPG and coronary calcium score (CAC) to assess cardiovascular vulnerability has been discussed.

Results  Emerging evidence indicates that atherosclerotic plaque calcification is positively correlated with vulnerability. Several inflammatory mediators have been shown to modulate arterial calcification, thus increasing the risk of plaque rupture. Among these factors, RANKL/OPG axis might be of particular interest as a promising biomarker of plaque vulnerability in subjects with diffuse coronary calcification.

Conclusion  Together with clinical parameters of coronary calcification (such as CAC), circulating RANKL/OPG levels could contribute to better assess and predict cardiac events.
Discrimination of wild and hatchery trout by natural chronological patterns of elements and isotopes in otoliths using LA‐ICP‐MS
Authors: ZITEK A. , STURM M. , WAIDBACHER H. , PROHASKA T.
Published: May 2010

Abstract  The potential to discriminate between wild and hatchery trout [Salmo trutta f. fario L. and Oncorhynchus mykiss (Walbaum)] by chronological microchemical patterns of different otolith regions was tested. Central and rim regions of otoliths were analysed for life stage specific elemental patterns of strontium (Sr), sodium (Na) and calcium (Ca) as well as of 87Sr/86Sr ratios using laser ablation inductively coupled plasma mass spectrometry (LA‐ICP‐MS). Classification to life stage specific habitats was achieved with 100% accuracy by 88Sr/43Ca, 23Na/43Ca and 87Sr/86Sr ratios resulting in a discrimination of hatchery fish from wild fish. 87Sr/86Sr ratios and Sr concentration in otoliths were positively correlated with the ratio and amount in the water. Na content in otoliths did not directly reflect the concentration in the water, although the 23Na/43Ca ratio in otoliths contributed to the discrimination. Clear differences in otolith chemistry were found for fish experiencing different geological units or a groundwater‐fed environment in a hatchery. Natural chronological microchemical patterns in otoliths proved to be a valuable tool for discriminating wild and hatchery fish without the necessity to use marking methods. LA‐ICP‐MS is well suited for this application because of its limited need for sample preparation, its potentially high sample throughput and the possibility of simultaneous measurement of multiple elemental and isotopic fingerprints.
Current practice in the management of muscle haematomas in patients with severe haemophilia
Authors: BEYER R. , INGERSLEV J. , SØRENSEN B.
Published: May 2010

Summary.  Muscle haematomas (MH) represent 10–25% of all bleeds in patients with severe haemophilia. We performed a cross‐sectional survey on current practice in the management of MH with participation from 22 consultants. The respondents reported 492 MH/year, corresponding an average of 25/centre, mostly associated with trauma. Iliopsoas (55%), calf (18%) and thigh (18%) bleeds were scored as most serious. Half of the respondents distinguished between contusion and strains, whereas the majority (68.2%) did not categorize bleedings as intra‐ or intermuscular, although 77.3% routinely used ultrasound. Half of the respondents used a standard protocol for the management of MH. Twenty of 22 (90.9%) respondents offered physiotherapy in the hospital following MH, with no clear consensus on timing and type of treatment. In a theoretical case, for a 70‐kg patient with a soleus triceps haematoma, the average initial dose of factor VIII was 2730 U (range: 1750–4000) twice daily for 3–5 days. In a similar case of a patient with inhibitors, 31.8% reported first‐line and only use of either recombinant factor VIIa (rFVIIa) or activated prothrombin complex concentrate (APCC), while 36.4% switched between bypassing agents. Using rFVIIa, the median dose was 100 μg/kg (range: 85–270) and with APCC, the median dose was 70 U kg−1 (range: 50–100). The majority (68.2%) did not use antifibrinolytics. Resolution of pain (81.8% & 77.3%) was regarded as the key clinical marker of arrest of bleeding as compared with diminished swelling and improved range of motion. The survey outlines limited consensus in the management of MH in patients with haemophilia and highlights potential topics for future studies.
Gene expression profiles of the incisor pulp tissue during fluorosis
Authors: Wu Y. , Hao Y.‐Q. , Li J.‐Y. , Zhou X.‐D.
Published: May 2010

Wu Y, Hao Y‐Q, Li J‐Y, Zhou X‐D. Gene expression profiles of the incisor pulp tissue during fluorosis. International Endodontic Journal.

Aim  To examine gene expression levels within the cells of dental pulp tissue in fluorotic rats and normal subjects and to identify fluoride‐susceptible genes.

Methodology  Female wistar rats were given 0.16 (control) or 100 parts per 106 fluoride ion in their drinking water. After 3 months, the teeth in the fluoride‐exposed animals showed signs of fluorosis. The animals were killed, and RNA was extracted from incisor pulp tissue and pooled into three fluorosis and three control pools. The females were analysed for gene expression profiles using microarray analysis and semi‐quantitative reverse transcriptase polymerase chain reaction (Sq‐RT‐PCR).

Results  Of the 26 962 probe sets, duplicate hybridisation data indicated that 5443 genes were detected as being present by both targets. Two hundred and forty seven genes, that is 4.53% of detected genes, were 1.5‐fold or greater differentially expressed after fluoride treatment. Three interesting genes, dentine matrix protein 1, dentine sialophosphoprotein and Cadherin‐11, were confirmed as being down‐regulated by Sq‐RT‐PCR.

Conclusions  The gene expression levels in rat pulp tissue changed during fluorosis. The gene expression profiles between the fluorotic model and the normal group will help to understand the multiple pathogenic mechanisms for the altered mineralization patterns observed in fluorotic dentine.
Fell‐Muir Lecture: Cartilage 2010 – The Known Unknowns
Authors: Hardingham Timothy E.
Published: May 2010

Over the past 40 years there have been giant steps forward in our understanding of cellular and molecular biology that have given us the framework by which to understand tissue organization and tissue function on a range of scales. However, although the progress has been great, the more we have discovered, the more we are aware of what we don’t yet know. In this article, I would like to flag up some issues of cartilage biology, function and pathology where we still have significant ignorance. As scientists we all provide contributions to add to the greater understanding of science and progress is on a broad front, but gaps are left where particular difficulty is encountered and in life sciences it is no different. Progress is fast where new knowledge and techniques pave the way, but where study is complex and relevant techniques poorly developed the gaps are left behind. In cartilage research and matrix biology, the gaps can particularly be seen at interfaces between disciplines and where technology development has lagged behind and in the particular challenges of understanding how molecular properties can explain tissue macro properties.
Effects of low dose gamma irradiation on microbial inactivation and physicochemical properties of fried shrimp (Penaeus vannamei)
Authors: Wang He , Yang Ruijin , Liu Yanning , Zhang Weibin , Zhao Wei , Zhang Yanpeng , Hua Xiao
Published: May 2010

Changes in microbiological, physicochemical and sensory properties of shrimp gamma irradiated with 60Co at doses of 0, 1, 3, 6, 9 kGy were investigated. Irradiation at 6 kGy eliminated most of the spoilage microorganisms and did not affect sensory quality. The L* value increased as irradiation dose increased, while a* value decreased as irradiation dose increased. Irradiation had no significant effect on the texture of shrimp samples; however, increasing the dose up to 9 kGy significantly increased the amount of volatile compounds, such as, alcohols, ketones, aldehydes, furans, and oxides. According to the total sensory points, the appearance and flavour of the shrimp product was considered as acceptable by sensory evaluation when irradiated at doses of 0–6 kGy. These results showed that gamma irradiation processing (<6 kGy) had the potential to extend the shelf life of fried shrimp.
Palynological and physicochemical data characterisation of honeys produced in the Entre‐Douro e Minho region of Portugal
Authors: Feás Xesús , Pires José , Estevinho María Letícia , Iglesias Antonio , De Araujo José Pedro Pinto
Published: May 2010

Honey legislation has been addressed to establish the minimum marketing level of the product and the need for consumer protection through correct denominations. Research oriented toward assessment of floral origin and physicochemical properties may increase the commercial value of these products. The characteristics of thirty‐one honeys produced in the Entre‐Douro e Minho region in Portugal were studied. Pollen features and some physicochemical parameters (moisture, ash, pH, free acidity, electrical conductivity, hydroxymethylfurfural contain, apparent sucrose, reducing sugars and diastase activity) were determined. The samples were found to meet international honey specifications. The present study found a linear regression between the ash content of honeys and their specific conductivity. Five samples are listed as Eucalyptus honey, one sample as Citrus honey, and twenty‐five samples as multifloral honeys. Of the total, 87.1% exceeded the quality parameters and should be labelled as ‘virgin’ honey.
Quality assessment of dehydrated red bell pepper using tempering drying cycles
Authors: Carrillo Montes Juan Pablo , Cruz y Victoria María Teresa , Anaya Sosa Irasema , Santiago Pineda Teodoro
Published: May 2010

Quality assessment of red bell pepper dices preserved through batch dehydration introducing tempering cycles were performed in this work. The parameters considered were: the percentages of ascorbic acid and final antioxidant activity retention, as well as the influence of calcium chloride on diffusivity and colour values. Although, a similar final moisture content was reached through different red bell pepper dehydration processes, but the one with tempering cycles had better qualities than those without tempering. Ascorbic acid and final antioxidant activity retention showed higher values and so were colour intensities compared to control samples in all cases. In respect to the effective diffusivity coefficients, there was an increment as the calcium chloride concentration increased. As of the treatments with tempering cycles, the best scheme was 15 min drying time and 30 min tempering time at 60 °C.
Main variables affecting the lactic acid fermentation of table olives
Authors: Medina Eduardo , Gori Chiara , Servili Maurizio , De Castro Antonio , Romero Concepción , Brenes Manuel
Published: May 2010

Among the olive varieties, Manzanilla is the most employed as table olives worldwide. Inoculation of the brines of Manzanilla and Gordal olives, which were not treated with alkali, with a strain of Lactobacillus pentosus was carried out and results indicated that variety is one of the main factors to be considered when fermenting olives, even more important than the salt level. This conclusion was based on the presence of a high concentration of antimicrobial compounds, namely the dialdehydic form of decarboxymethyl elenolic acid, either free or linked to hydroxytyrosol in the brines of the Manzanilla variety, as compared to the low level of these substances in the Gordal brines. Likewise, it was also observed that the inhibitory activity of Manzanilla olives against lactic acid bacteria could be counteracted by the addition of nitrogenous supplements such as MRS and yeast extract to their brines. Results obtained from this work are of great interest for the table olive industry in order to develop lactic acid fermentation in olives non‐treated with alkali.
Effect of muscle type and cooking temperature on liver‐like off‐flavour of five beef chuck muscles
Authors: Wadhwani Ranjeeta , Murdia Lalit K. , Cornforth Daren P.
Published: May 2010

Steaks (1.9 cm thick) from the US Department of Agriculture (USDA) Select grade beef chuck muscles (Infraspinatus, Longissimus dorsi, Serratus ventralis, Supraspinatus and Terres major) were cooked to two temperatures commonly applied in US restaurants (71 °C and 82 °C) and evaluated for liver‐like off‐flavour by trained panel. Pigment content of raw muscles were determined to establish its effect on liver‐like off‐flavour. Mean myoglobin content of Serratus (9.26 mg g−1) was significantly lower than other beef chuck muscles analysed in this study. Infraspinatus had highest (P < 0.05) mean liver flavour of 2.08 where other muscles had <2. Rancid flavour was slightly but significantly increased from 1.34 to 1.58 as internal cook temperature increased from 71 °C to 82 °C; however mean thiobarbituric acid (TBA) values were not affected by cooking temperature. Infraspinatus had small but significant incidence of liver‐like off‐flavour. Cooking temperature had a clear impact on rancidity as evaluated by trained panel but no direct impact on liver‐like off flavour was observed.