bluuebunny/crossref_metadata_2025 huggingface dataset:
Delays in diagnosis and bladder cancer mortality
Authors: Hollenbeck Brent K. , Dunn Rodney L. , Ye Zaojun , Hollingsworth John M. , Skolarus Ted A. , Kim Simon P. , Montie James E. , Lee Cheryl T. , Wood David P. , Miller David C.
Published: July 2010

BACKGROUND:

Mortality from invasive bladder cancer is common, even with high‐quality care. Thus, the best opportunities to improve outcomes may precede the diagnosis. Although screening currently is not recommended, better medical care of patients who are at risk (ie, those with hematuria) has the potential to improve outcomes.

METHODS:

The authors used the Surveillance, Epidemiology, and End Results‐Medicare linked database for the years 1992 through 2002 to identify 29,740 patients who had hematuria in the year before a bladder cancer diagnosis and grouped them according to the interval between their first claim for hematuria and their bladder cancer diagnosis. Cox proportional hazards models were fitted to assess relations between these intervals and bladder cancer mortality, adjusting first for patient demographics and then for disease severity. Adjusted logistic models were used to estimate the patient's probability of receiving a major intervention.

RESULTS:

Patients (n = 2084) who had a delay of 9 months were more likely to die from bladder cancer compared with patients who were diagnosed within 3 months (adjusted hazard ratio [HR], 1.34; 95% confidence interval [CI], 1.20‐1.50). This risk was not markedly attenuated after adjusting for disease stage and tumor grade (adjusted HR, 1.29; 95% CI, 1.14‐1.45). In fact, the effect was strongest among patients who had low‐grade tumors (adjusted HR, 2.11; 95% CI, 1.69‐2.64) and low‐stage disease (ie, a tumor [T] classification of Ta or tumor in situ; adjusted HR, 2.02; 95% CI, 1.54‐2.64).

CONCLUSIONS:

A delay in the diagnosis of bladder cancer increased the risk of death from disease independent of tumor grade and or disease stage. Understanding the mechanisms that underlie these delays may improve outcomes among patients with bladder cancer. Cancer 2010. © 2010 American Cancer Society.
Methylphenidate for fatigue in ambulatory men with prostate cancer
Authors: Roth Andrew J. , Nelson Christian , Rosenfeld Barry , Scher Howard , Slovin Susan , Morris Michael , O'Shea Noelle , Arauz Gabrielle , Breitbart William
Published: July 2010

BACKGROUND:

Fatigue is a highly prevalent and clinically significant symptom of advanced prostate cancer. To date, however, there are no published controlled trials of interventions for fatigue in men with prostate cancer.

METHODS:

This 6‐week, randomized, double‐blind, placebo‐controlled design evaluated the efficacy of methylphenidate to treat fatigue in prostate cancer patients. Inclusion criteria included men with advanced prostate cancer and the presence of moderate to severe fatigue. Patients with major depression, hypothyroidism, uncontrolled hypertension, arrhythmia, or anemia were excluded. Fatigue levels, blood pressure, pulse, and other safety concerns were monitored regularly.

RESULTS:

Thirty‐two subjects were randomized to methylphenidate (n = 16) or placebo (n = 16). Brief Fatigue Inventory total scores significantly decreased for both groups; however, the methylphenidate group, as compared with placebo, reported greater decrease on Brief Fatigue Inventory severity scores (P = .03) and a trend toward greater decrease on Brief Fatigue Inventory total scores (P = .07). A significantly greater number of subjects in the methylphenidate group versus the placebo group demonstrated clinically significant improvement in fatigue on total Brief Fatigue Inventory scores (7 of 10 vs 3 of 13) and Brief Fatigue Inventory severity scores (8 of 10 vs 3 of 13). Importantly, 6 subjects in the methylphenidate group discontinued because of increased blood pressure or tachycardia. There were no serious adverse events.

CONCLUSIONS:

Methylphenidate is effective in treating fatigue in men with prostate cancer; however, oncologists need to monitor for possible pulse and blood pressure elevations. Cancer 2010. © 2010 American Cancer Society.
Use of white blood cell growth factors and risk of acute myeloid leukemia or myelodysplastic syndrome among elderly patients with non‐Hodgkin lymphoma
Authors: Gruschkus Stephen K. , Lairson David , Dunn J. Kay , Risser Jan , Du Xianglin L.
Published: July 2010

BACKGROUND.

The current study was conducted to evaluate the association between colony‐stimulating factor (CSF) use and the risk of developing therapy‐related myelodysplastic syndromes or acute myeloid leukemia (t‐MDS/AML) among a large cohort of elderly patients with non‐Hodgkin lymphoma (NHL) who were treated with chemotherapy.

METHODS.

A total of 13,203 NHL patients were identified from the Surveillance, Epidemiology, and End Results‐Medicare database who were diagnosed from 1992 through 2002. Patients were followed from their initial chemotherapy date until the date they were diagnosed with t‐MDS/AML, death, or last follow‐up (October 31, 2006), whichever occurred first.

RESULTS.

Overall, 40% (n = 5266) of patients received CSF. During the follow‐up period (median follow‐up, 2.9 years [range, 1‐14.7 years]), 272 (5.2%) patients who were treated with CSF developed t‐MDS/AML, compared with 230 (2.9%) patients who did not (P < .0001, log‐rank test). The 5‐year incidence of t‐MDS/AML for patients receiving CSF was 14.1 per 1000 person‐years compared with 8.3 per 1000 person‐years for patients not receiving CSF. In a multivariable Cox regression analysis adjusted for gender, histology, stage, comorbidities, radiotherapy, and chemotherapy agent, CSF use was found to be independently associated with a 53% increased risk of t‐MDS/AML (hazard ratio [HR], 1.53; 95% confidence interval [95% CI], 1.26‐1.84). The observed association between CSF use and t‐MDS/AML persisted across histologic subgroups (ie, diffuse large B‐cell lymphoma, follicular lymphoma, and others). Patients who received both CSF and antimetabolite chemotherapy were found to have a 2.5‐fold increased risk of t‐MDS/AML (HR, 2.49; 95% CI, 1.91‐3.26) compared with patients who received neither agent.

CONCLUSIONS.

The current study, which to our knowledge is the first large population‐based study published to date, demonstrated that the administration of CSF among elderly NHL patients receiving chemotherapy was associated with an increased risk of t‐MDS/AML, although the absolute risk was low. Cancer 2010. © 2010 American Cancer Society.
One‐ and Two‐Dimensional Inorganic Crystals inside Inorganic Nanotubes
Authors: Hong Sung You , Kreizman Ronen , Rosentsveig Rita , Zak Alla , Sloan Jeremy , Enyashin Andrey N. , Seifert Gotthard , Green Malcolm L. H. , Tenne Reshef
Published: July 2010

Various inorganic salts can be encapsulated inside the comparatively narrow (0.8–2 nm) hollow core of single‐walled carbon nanotubes (SWNTs) by molten phase capillary wetting. A new synthetic strategy is presented allowing the formation of one dimensional (1D) inorganic crystals or core–shell nanotubular structures by using multiwall WS2 nanotubes as host templates. Molten phase wetting with CsIresults in the formation of 1D crystal structures inside WS2 nanocapillaries with a Moiré pattern. The relatively large diameter of the WS2 nanotube (with inner and outer diameters of ca. 10 and 20 nm, respectively), allows a conformal folding of the guest PbI2 layers (PbI2@WS2 core–shell nanotubes) on the interior wall of the WS2 nanotube‐template, thus leading to relatively defect‐free core–shell inorganic nanotubular structures, which have not been previously observed within carbon nanotubes (CNTs). Core–shell WS2@MoS2 nanotubes can be obtained by the gas‐phase reaction of MoCl5 with sulfur in the presence of WS2 nanotubes. The mechanism of imbibition/solidification of the molten salt into the hollow cores of MoS2 nanotubes has been studied by molecular dynamics simulations, showing major differences between layered compounds and those with quasi‐isotropic structure. Theoretical considerations also show the conditions for the stability of such core–shell 1D nanostructures. These new strategies can open up many possibilities for the synthesis of new nanotubular structures.
Explicit finite‐element analysis for the in‐plane cyclic behavior of unreinforced masonry structures
Authors: Karapitta Lucia , Mouzakis Harris , Carydis Panayotis
Published: July 2010

A simple constitutive model is proposed for an in‐plane numerical analysis of unreinforced masonry structures, which are subject to cyclic loading, by using explicit dynamic procedures. The proposed model is implemented by using two‐dimensional plane‐stress finite elements. Three different constitutive relations that are based on the total strain in the global material system are used. Cracking and crushing are controlled through normal strains, whereas shear is controlled through shear strain. Separate hysteretic rules are adopted for each mode of damage. A numerical analysis of masonry walls that are subject to cyclic loading has demonstrated that the use of explicit procedures in conjunction with the proposed model results in an acceptable accuracy when compared with the experimental results. Copyright © 2010 John Wiley & Sons, Ltd.
Effects of interface material on the performance of free rocking blocks
Authors: ElGawady Mohamed A. , Ma Quincy , Butterworth John W. , Ingham Jason
Published: July 2010

This paper presents the results of an experimental investigation on the rocking behavior of rigid blocks. Two types of test specimens have been tested, namely M and C types. Nine blocks of the M type and two blocks of the C type with different aspect ratios were tested with varying initial rotational amplitudes and with different materials at the contact interface, namely concrete, timber, steel, and rubber. The results showed that the interface material has significant influence on the free rocking performance of the blocks. Blocks tested on rubber had the fastest energy dissipation followed by concrete and timber bases, respectively. Analysis of the test results has shown that the energy dissipation in the case of tests on a rubber base is a continuous mechanism whereas in the case of tests on rigid bases, i.e. timber and concrete, energy dissipation is a discrete function. Finally, the rocking characteristics of the blocks were calculated using piecewise equations of motion and numerical analysis. It was possible to predict the correct free rocking amplitude response when a reliable value for the coefficient of restitution was used. Copyright © 2010 John Wiley & Sons, Ltd.
Neurogranin, a link between calcium/calmodulin and protein kinase C signaling in synaptic plasticity
Authors: Díez‐Guerra F. Javier
Published: July 2010

Neurogranin (Ng) (also named RC3, p17 or BICKS) is a small protein originally identified in rat brain and abundantly expressed in several telencephalic areas, such as the cerebral cortex, hippocampus, amygdala, and striatum. In neurons, it is found concentrated at dendritic spines where it participates in synaptic signaling events through the regulation of calmodulin (CaM) availability. Ng features an IQ motif that mediates its interaction with CaM and phosphatidic acid (PA) and that is phosphorylated by protein kinase C (PKC) at serine 36 (Ser36). Ser36‐phosphorylated Ng is unable to bind either CaM or PA. Ng knockout mice display an apparently normal phenotype; however, they show severe deficits in spatial and emotional learning and a decrease in LTP induction, mostly due to the attenuation of the signaling that depends on calcium/CaM kinase II (CaMKII), PKC, and protein kinase A (PKA) activation. The present review is an update on the most relevant information about Ng expression, localization, interactions, and modifications as well as on its role in synaptic plasticity. © 2010 IUBMB IUBMB Life, 62(8): 594–606, 2010.
WNT unrelated activities in commercially available preparations of recombinant WNT3a
Authors: Cajanek Lukas , Adlerz Linda , Bryja Vitezslav , Arenas Ernest
Published: July 2010

WNT signaling pathways play an important role in both development and disease. By analyzing the signaling capabilities of commercially available WNT3a preparations towards the PI3K/AKT/GSK3 signaling pathway, we discovered unexpected inconsistencies from lot to lot of recombinant WNT3a. We provide evidence that: (1) The ability to trigger AKT/GSK3 signaling varies dramatically between different lots of WNT3a, without any variation in their ability to activate the canonical WNT/β‐catenin signaling. (2) sFRP1, a WNT signaling inhibitor, is unable to interfere with the activation of AKT/GSK3 signaling induced by some of the WNT3a lots. (3) Pharmacological inhibition of AKT/GSK3 phosphorylation by PI3K inhibitors fails to affect the stabilization of β‐catenin, the central effector of the canonical WNT/β‐catenin signaling pathway. In summary, while all tested lots of recombinant WNT3a activated WNT/β‐catenin pathway, our results suggest that individual lots of recombinant WNT3a activate the PI3K/AKT/GSK3 pathway in a WNT‐independent manner, hampering thus the analysis of regulation of PI3K/AKT/GSK3 by WNT ligand. J. Cell. Biochem. 111: 1077–1079, 2010. © 2010 Wiley‐Liss, Inc.
Electrochemical photovoltaic cells—review of recent developments
Authors: Wei Di , Andrew Piers , Ryhänen Tapani
Published: July 2010

Photoelectrochemistry is attracting extensive attention from scientists worldwide for its use in converting light energy into electricity in electrochemical photovoltaic cells, the most common form of which, dye sensitized solar cells (DSSCs), can offer both flexibility and transparency. Their efficiencies are now comparable with amorphous silicon solar cells but at a much lower cost. This review covers not only the fundamentals of electrochemical photovoltaic cell operation but also recent advances in research and development for industrial applications. The most recent research topics relating to DSSCs, for example, applications of nanostructured n‐type semiconducting electrodes, ionic liquid electrolytes and graphene and carbon nanotube electrodes are all included. In addition, the storage of electrochemical energy by electrochemical photovoltaic cells has also been reviewed. Copyright © 2010 Society of Chemical Industry
Characterisation of fine wall and eggshell Roman pottery by Raman spectroscopy
Authors: Olivares M. , Zuluaga M. C. , Ortega L. A. , Murelaga X. , Alonso‐Olazabal A. , Urteaga M. , Amundaray L. , Alonso‐Martin I. , Etxebarria N.
Published: July 2010

Roman pottery from the Oiasso harbour (nowadays Irun, Basque Country) was thoroughly studied by micro‐Raman spectroscopy and X‐ray diffraction (XRD) analysis in order to identify and characterise the mineralogical composition of those samples and to get a deeper insight into the technologies involved in the elaboration of the ceramic artefacts. The diffraction pattern of the ceramic body shows the presence of mullite and trydimite, which suggests firing temperatures above 1100 °C, and alumina‐rich raw materials. Additionally, the presence of pseudowollastonite and diopside observed by the XRD and Raman spectroscopy is explained by the high firing temperatures of lime‐rich raw materials. Raman microscopy has also provided further information about the heating temperature and composition of the raw materials. The presence of rutile instead of anatase also suggests a strong heating process. Moreover, the presence of hematite (α‐Fe2O3) and maghemite (γ‐Fe2O3) instead of magnetite (Fe3O4) suggests the oxidising conditions during ceramics firing. The comparison of the minerals found in the different Roman potteries with the characteristic mineralogy of the archaeological site suggests the use of raw material coming from different source areas, opening up an interesting discussion about the commercial networks. Copyright © 2010 John Wiley & Sons, Ltd.
Electrospun Magnetic Fibrillar Polystyrene Nanocomposites Reinforced with Nickel Nanoparticles
Authors: Chen Xuelong , Wei Suying , Gunesoglu Cem , Zhu Jiahua , Southworth Cara S. , Sun Luyi , Karki Amar B. , Young David P. , Guo Zhanhu
Published: July 2010

The morphology and thermal stability of bead‐free and uniform electrospun pure polystyrene (PS) and PS/Ni nanocomposite fibers are investigated by SEM and TGA/DSC. A higher thermal stability is observed after introducing the nanoparticles in the polymer fibers. FT‐IR analysis indicates a physical entanglement rather than chemical bonding between the nanoparticles and the polystyrene matrix. The nanoparticles still exhibit superparamagnetic properties even after dispersing in the polymer matrix, different from the reported enhanced coercivity as a result of the enlarged particle distance. However, the magnetic field required to saturate the magnetization is significantly reduced. A further oxidation is deduced after the high voltage electrospinning process.

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Electrospinning: A Novel Method to Incorporate POSS Into a Polymer Matrix
Authors: Cozza Erika Simona , Monticelli Orietta , Marsano Enrico
Published: July 2010

The effectiveness of electrospinning as a simple approach to disperse POSS into a polymer matrix at a nm‐level has been assessed. Electrospun and cast films were prepared by dissolving CA and epoxycyclohexylisobutyl POSS in the solvent mixture acetone/DMAc. The membranes were characterized by SEM, TEM and WAXD. Whereas films produced by casting showed µm‐sized POSS crystals, thus suggesting a small affinity between the polymer matrix and the POSS molecules, those prepared by electrospinning were characterized by a nanometric POSS distribution. This is explained by considering the peculiar solvent evaporation mechanism, occurring during the electrospinning process, which allows to produce nanofibers characterized by a silsesquioxane dispersion similar to that present in solution.

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Investigation on RAFT Polymerization of a Y‐Shaped Amphiphilic Fluorinated Monomer and Anti‐Fog and Oil‐Repellent Properties of the Polymers
Authors: Wang Yun , Dong Qibao , Wang Yanxue , Wang Hu , Li Guang , Bai Ruke
Published: July 2010

A Y‐shaped amphiphilic fluorinated monomer, 1‐(1H,1H,2H,2H‐perfluorodecyloxy)‐3‐(3,6,9‐trioxadecyloxy)‐propan‐2‐yl acrylate has been synthesized and its polymerization by reversible addition–fragmentation chain transfer (RAFT) homopolymerization has been investigated. The results show that the molecular weights of the polymers are controlled and all the molecular weight distributions are lower than 1.4. Well‐defined copolymers with 2‐(N,N‐dimethylamino)ethyl methacrylate have been prepared by RAFT polymerization, and the surface properties of the block and random copolymers have been examined by contact angle measurement for water and hexadecane. It has been found that the surfaces of the block copolymers simultaneously exhibit excellent anti‐fog and oil‐repellent properties.

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Time‐dependent effects of pre‐conditioning activation on muscle fiber conduction velocity and twitch torque
Authors: Kamavuako Ernest Nlandu , Farina Dario
Published: July 2010

In this study we investigate the range of interstimulus intervals influencing the recovery functions for conduction velocity (velocity recovery function, or VRF) and twitch torque (twitch torque recovery function, or TRF) of muscle fibers. We studied the tibialis anterior muscle of 8 healthy men by varying the time interval between a pair of stimuli in the range of 4–1000 ms, with (triplet) and without (doublet) a preconditioning stimulus. For triplet stimulations, the interval between the first and second stimulus or between the second and third stimulus was fixed, and the other interval was varied. VRF and TRF were influenced by a preconditioning stimulus only when it was delivered within 125 ms and 30 ms, respectively, before the doublet stimulation. The results provide evidence of the range of preconditioning intervals influencing the VRF and TRF; this is relevant for understanding the mechanisms of force generation and for standardizing compound action potential measurements. Muscle Nerve, 2010
Intracellular β‐amyloid accumulation leads to age‐dependent progression of Ca2+ dysregulation in skeletal muscle
Authors: Lopez Josè R. , Shtifman Alexander
Published: July 2010

Intramyofiber accumulation of β‐amyloid fragments (Aβ) is a pathologic hallmark of inclusion‐body myositis (IBM), a progressive skeletal muscle disorder. We investigated the temporal pattern of alterations in the resting cytoplasmic [Ca2+] ([Ca2+]i) as well as the depolarization‐evoked Ca2+ release from the sarcoplasmic reticulum in skeletal muscle from transgenic mice expressing human βAPP (MCK‐βAPP). MCK‐βAPP mice show an age‐dependent increase in [Ca2+]i along with a reduction in depolarization‐evoked Ca2+ release, which appear well before the other reported aspects of IBM, such as inclusion formation, inflammation, centralized nuclei, atrophy, and skeletal muscle weakness. In the young MCK‐βAPP animals the increase in resting [Ca2+]i can be attributed largely to Ca2+ influx through nifedipine‐sensitive Ca2+ channels. In the adult MCK‐βAPP mice, in addition to the nifedipine‐sensitive pathway, there is also a substantial contribution by the intracellular compartments to the increase in [Ca2+]i. These results suggest that β‐amyloid‐induced disuption of Ca2+ handling may represent an early event in the pathogenesis of IBM. Muscle Nerve, 2010
Microwave promoted synthesis and characterization of isomeric poly(ether ether ketone)s
Authors: Li Man , Zhang Aiqing , Yin Jun , Liew Kong Yong
Published: July 2010

A series of isomeric poly(ether ether ketone)s were synthesized using microwave‐assisted method by nucleophilic substitution reaction of hydroquinone and 4,4′‐biphenol with 4,4′‐difluorobenzophenone (DFBP) or 2,4′‐DFBP in the presence of anhydrous K2CO3. The polymers with inherent viscosities in the range of 0.20–0.71 dlg−1 were obtained in quantitative yields and had excellent thermal stability as shown by the temperature of 5% weight loss in nitrogen above 410°C. X‐ray diffraction patterns confirmed the semicrystalline character of some of the polymers. The results also indicate that the reaction time was shortened remarkably and the reaction temperature could be controlled easily. POLYM. ENG. SCI., 2011. © 2010 Society of Plastics Engineers
Comparative antioxidant activity of an extract of Lithraea molleoides and an isolated 5‐alkyl resorcinol derivative. Effects on the proliferation of normal and tumoral lymphocytes
Authors: López Paula , Ferraro Graciela , Anesini Claudia
Published: July 2010

Lithraea molleoides (Vell.) Engl. (Anacardiaceae), is known in South America for its medicinal properties: antiarthritic, haemostatic, diuretic, tonic and useful for the treatment of respiratory diseases. Previously the isolation of a new cytotoxic 5‐alkyl resorcinol derivative, 1,3‐dihydroxy‐5‐(tridec‐4′,7′‐dienyl) benzene, from a dichloromethane extract (DM) was reported. The aim of this work was to determine and to compare the antioxidant activity of DM and the isolated compound, 1,3‐dihydroxy‐5‐(tridec‐4′,7′‐dienyl) benzene. Moreover, the activity of both on the proliferation of tumoral and normal lymphocytes was determined. The compound was isolated and quantified by HPLC. The compound represented 0.036% of DM. The extract and the compound exerted antioxidant activity by DPPH and FTC methods. On tumoral cells, both exerted antiproliferative action but the compound was more active (EC50: 17.4 ± 1 µg/mL). On normal lymphocytes, both exerted a stimulatory effect on cell proliferation inversely related to concentration, the extract was more active than the compound (maximum effect: 300 ± 20% of stimulation). Most of the effects observed with the extract were independent of the isolated compound. DM could be an important source of antioxidant and immunomodulatory compounds to be studied on cancer diseases. Copyright © 2010 John Wiley & Sons, Ltd.
Reversible adsorption change of 2‐amino‐4,5‐imidazoledicarbonitrile on Ag electrode surfaces by potential‐dependent surface‐enhanced Raman scattering
Authors: Jang Yun Hee , Hwang Sungu , Cho Keunchang , Lim Manho , Joo Taiha , Choi Suhee , Kim Jongwon , Joo Sang‐Woo
Published: July 2010

The potential‐induced adsorption change of 2‐amino‐4,5‐imidazoledicarbonitrile (AIDCN) on Ag electrode surfaces has been examined by surface‐enhanced Raman scattering (SERS) in an applied potential range between −1.0 and 0.2 V. Upon adsorption, AIDCN has a substantial interaction with the Ag metal surfaces via its two nitrile groups. The CN stretching peaks at ∼2200 cm−1 appeared to be more intensified and redshifted at a negative potential. The deconvolution peak analysis of the CN bands at various voltages suggests that there should be a change in binding modes of AIDCN on Ag surfaces. This potential‐dependent orientation change appeared to be reversible. The density functional theory (DFT) calculation of AIDCN on Ag cluster atoms is used to explain its potential‐dependent adsorption. Copyright © 2010 John Wiley & Sons, Ltd.
Microstructure and surface residual stress of plasma sprayed nanostructured and conventional ZrO2‐8wt%Y2O3 thermal barrier coatings
Authors: Wang L. , Wang Y. , Sun X. G. , Pan Z. Y. , He J. Q. , Zhou Y. , Wu P. L.
Published: July 2010

The nanostructured agglomerate feedstock which can be used for plasma spraying was obtained successfully by the reconstituting nanoparticle technique. Nanostructured and conventional ZrO2‐8wt%Y2O3 (8YSZ) thermal barrier coatings (TBCs) have been prepared by atmospheric plasma spraying (APS) on NiCoCrAlY coated 45# steel substrates. The microstructure and phase composition of feedstock and corresponding coating were characterized by SEM and XRD. The elastic modulus was tested by the nanoindenter instrument. The surface residual stresses were examined by XRD stress test equipment. The numerical value probability statistics of surface residual stress by the Weibull distribution theory was implemented under different thermal spray parameters. The value of residual stresses increased with increasing the thickness of the ceramic coating. The surface residual stress of nanostructured 8YSZ coating is lower than that of the conventional 8YSZ coating. A physical mechanical model is put forward to explain the causation of the variation of residual stresses. At the same time, the variation characteristic of surface residual stress is discussed by introducing the closed form solution of residual stress of laminar layer plate. Copyright © 2010 John Wiley & Sons, Ltd.
SELENIUM FORTIFICATION AND PRO/ANTI OXIDANT RESPONSES IN ALLIUM CEPA (ONION) CULTIVATED IN Se SUPPLEMENTED SOILS
Authors: PRAKASH N. TEJO , SHARMA NEETU , PRAKASH RANJANA , NATHANIEL T. N. , ACHARYA R. , REDDY A. V. R.
Published: July 2010

Native plantlets of Allium cepa (onion) were cultivated in selenium (Se)-supplemented soils to observe dose- and time-dependent uptake and associated pro/anti-oxidant activity. Allium plantlets were grown in soils supplemented with Se at 2.5, 5.0 and 7.5 mg kg−1 as selenite (Na2SeO3) and selenate (Na2SeO4) for 40–120 days. The effect of different concentrations of Se oxyanions on the growth and accumulation profile in plants in relation to glutathione peroxidase activity and thiobarbituric acid reactive substances was studied. Total Se concentrations in plantlets were determined by instrumental neutron activation analysis. The accumulation of Se in plant was observed to be dose dependent in the case of selenite, but, no definite correlation between accumulation levels and exposed concentration was observed. The changes in pro/anti-oxidant properties were observed to be dependent on the accumulation of Se in plant.
Periodic spacing between consecutive equatorial plasma bubbles
Authors: Makela J. J. , Vadas S. L. , Muryanto R. , Duly T. , Crowley G.
Published: July 2010

We analyze three‐years of data collected by a field‐aligned airglow imaging system located at the Cerro Tololo Inter‐American Observatory near La Serena, Chile to determine the occurrence of equatorial plasma bubbles (EPBs). On 317 of the 552 predominately clear nights of observations, structure indicative of EPBs is present. On 123 of these nights, multiple EPBs with periodic spacings were recorded with 88 nights showing 3 or more consecutive bubbles. We suggest that the periodic spacing of EPBs could be related to the properties of an underlying seed mechanism, namely gravity waves (GWs). The distribution of spacings compares favorably to the spectrum of GW induced traveling ionospheric disturbances (TIDs) measured by Vadas and Crowley (2010) from a similar geographic latitude in the northern hemisphere. Furthermore, the distribution of spacings decreases from 2006 through 2009, tracking the corresponding decrease in the thermospheric neutral temperature, Tn. As Tn decreases, GWs with larger horizontal wavelengths have smaller initial amplitudes and cannot propagate as easily to EPB seeding altitudes. Thus, our observations are consistent with GW theory.
BigWig and BigBed: enabling browsing of large distributed datasets
Authors: Kent W. J. , Zweig A. S. , Barber G. , Hinrichs A. S. , Karolchik D.
Published: July 2010

Summary: BigWig and BigBed files are compressed binary indexed files containing data at several resolutions that allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser. The visualization is implemented using a multi-layered software approach that takes advantage of specific capabilities of web-based protocols and Linux and UNIX operating systems files, R trees and various indexing and compression tricks. As a result, only the data needed to support the current browser view is transmitted rather than the entire file, enabling fast remote access to large distributed data sets.

Availability and implementation: Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/. Source code for the creation and visualization software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. The UCSC Genome Browser is available at http://genome.ucsc.edu

Contact:  ann@soe.ucsc.edu

Supplementary information: Supplementary byte-level details of the BigWig and BigBed file formats are available at Bioinformatics online. For an in-depth description of UCSC data file formats and custom tracks, see http://genome.ucsc.edu/FAQ/FAQformat.html and http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html
Predictive models for population performance on real biological fitness landscapes
Authors: Rowe William , Wedge David C. , Platt Mark , Kell Douglas B. , Knowles Joshua
Published: July 2010

Motivation: Directed evolution, in addition to its principal application of obtaining novel biomolecules, offers significant potential as a vehicle for obtaining useful information about the topologies of biomolecular fitness landscapes. In this article, we make use of a special type of model of fitness landscapes—based on finite state machines—which can be inferred from directed evolution experiments. Importantly, the model is constructed only from the fitness data and phylogeny, not sequence or structural information, which is often absent. The model, called a landscape state machine (LSM), has already been used successfully in the evolutionary computation literature to model the landscapes of artificial optimization problems. Here, we use the method for the first time to simulate a biological fitness landscape based on experimental evaluation.

Results: We demonstrate in this study that LSMs are capable not only of representing the structure of model fitness landscapes such as NK-landscapes, but also the fitness landscape of real DNA oligomers binding to a protein (allophycocyanin), data we derived from experimental evaluations on microarrays. The LSMs prove adept at modelling the progress of evolution as a function of various controlling parameters, as validated by evaluations on the real landscapes. Specifically, the ability of the model to ‘predict’ optimal mutation rates and other parameters of the evolution is demonstrated. A modification to the standard LSM also proves accurate at predicting the effects of recombination on the evolution.

Contact:  william.rowe@manchester.ac.uk
Towards optimal alignment of protein structure distance matrices
Authors: Wohlers Inken , Domingues Francisco S. , Klau Gunnar W.
Published: July 2010

Motivation: Structural alignments of proteins are important for identification of structural similarities, homology detection and functional annotation. The structural alignment problem is well studied and computationally difficult. Many different scoring schemes for structural similarity as well as many algorithms for finding high-scoring alignments have been proposed. Algorithms using contact map overlap (CMO) as scoring function are currently the only practical algorithms able to compute provably optimal alignments.

Results: We propose a new mathematical model for the alignment of inter-residue distance matrices, building upon previous work on maximum CMO. Our model includes all elements needed to emulate various scoring schemes for the alignment of protein distance matrices. The algorithm that we use to compute alignments is practical only for sparse distance matrices. Therefore, we propose a more effective scoring function, which uses a distance threshold and only positive structural scores. We show that even under these restrictions our approach is in terms of alignment accuracy competitive with state-of-the-art structural alignment algorithms, whereas it additionally either proves the optimality of an alignment or returns bounds on the optimal score. Our novel method is freely available and constitutes an important promising step towards truly provably optimal structural alignments of proteins.

Availability: An executable of our program PAUL is available at http://planet-lisa.net/

Contact:  Inken.Wohlers@cwi.nl

Supplementary information:  Supplementary data are available at Bioinformatics online.
REVIEW: Rye Arabinoxylans: Molecular Structure, Physicochemical Properties and Physiological Effects in the Gastrointestinal Tract
Authors: Knudsen Knud Erik Bach , Lærke Helle Nygaard
Published: July 2010

Arabinoxylans (AX) are the main dietary fiber (DF) polysaccharides in rye where they represent ≈55% of the total polysaccharides. Rye AX consist of a backbone of (1→4)‐β‐d‐xylopyranosyl residues (X) mainly substituted with α‐l‐arabinofuranosyl residues (A) to varying degrees at the O‐2 position, the O‐3 position, or both. The A/X ratio of total AX is 0.49–0.82 and extractable AX ratio is 0.34–0.85 in different studies. AX also contain small amounts of ferulate residues bound to arabinose as esters at its O‐5 position. The weight average molecular weight varies from 40,000 to 900,000 with an average of ≈200,000. AX influence physiology in different segments of the gastrointestinal tract. The complex molecular structure of rye AX makes them resistant against microbial modification in the small intestine; consequently, rye AX have a much higher influence on the viscosity in the small intestinal digesta than does β‐glucan from oats and barley. In spite of that, it has not been possible in studies with AX‐rich foods such as bread to demonstrate a significant effect on the postprandial glucose response, however, a significantly reduced insulin response has been seen. Nevertheless, addition of 6 g and 12 g of AX‐rich wheat fiber to a breakfast meal has significantly lowered postprandial glucose and insulin response. Studies with hypercholesterolemic pigs fed rye buns rich in AX have resulted in dramatic reductions in plasma total and LDL cholesterol, whereas a gender difference was seen in studies on the effect of AX on plasma lipids in humans. Only certain species of bacteria from the human gut produce the enzymes needed for the degradation of AX. Nevertheless, wheat AX stimulate prebiotic bacteria presumably brought about by cross feeding of lactobacilli and bifidobacteria with degradation products from versatile carbohydrate‐degrading bacteria. Soluble AX are readily fermented in the large intestine, the majority is broken down between the ileum and the cecum. AX, characterized by a low degree of substitution and virtually no doubly substituted xylose, are slowly degraded at more distal locations. The remaining AX, characterized by a high degree of substitution, are not degraded at all. Although the fermentation pattern of AX may vary in different experimental models, in vitro fermentation studies and in vivo intervention studies with animals and humans point to AX as substrates that enhance the formation of butyrate in the large intestine.
Dyschromatosis symmetrica hereditaria associated with neurological disorders
Authors: KONDO Taisuke , SUZUKI Tamio , ITO Shiro , KONO Michihiro , NEGORO Tamiko , TOMITA Yasushi
Published: July 2010

Dyschromatosis symmetrica hereditaria (DSH) is a pigmentary genodermatosis of autosomal dominant inheritance caused by a mutation of adenosine deaminase acting on the RNA 1 gene (ADAR1). It is characterized by a mixture of hyper‐ and hypopigmented macules on the back of the hands and feet. The pathomechanism by which the ADAR1 gene mutation induces DSH has not been clarified yet. We experienced an 11‐year‐old male DSH patient associated with dystonia, mental deterioration and brain calcification, who had a mutation of p.G1007R in the ADAR1 gene. This mutation had already been reported in a patient with similar neurological symptoms by Tojo et al. Additionally, a patient with DSH associated with torsion dystonia was reported by Patrizi et al., but gene analysis was not carried out. Only three cases with neurological disorders have been reported, although more than 50 mutations of the ADAR1 gene causing DSH have been reported and none of them had any neurological symptoms. Therefore, we suggest that neurological disorders rarely develop in DSH.
Evolutionary conservation of the linkage between the structural loci for serum albumin and vitamin D binding protein (Gc) in cattle
Authors: BOUQUET Y. , VAN DE WEGHE A. , VAN ZEVEREN A. , VAREWYCK H.
Published: July 2010

Summary. Evidence is presented for close genetic linkage between the structural loci for serum albumin and the vitamin D binding protein (Gc) in Belgian Blue and White cattle. Five recombinants were observed in a total of 342 informative offspring. The recombination frequency between the two loci was estimated as 1.5%± 0.9. The observed distribution of the haplotypes deviated from the expected one in the population, probably due to selection and significant linkage disequilibrium.
Joint Report of the Third International Bovine Lymphocyte Antigen (BoLA) Workshop, Helsinki, Finland, 27 July 1986
Authors: BULL R. W. , LEWIN H. A. , WU M. C. , PETERBAUGH K. , ANTCZAK D. , BERNOCO D. , CWIK S. , DAM L. , DAVIES C. , DAWKINS R. L. , DUFTY J. H. , GERLACH J. , HINES H. C. , LAZARY S. , LEIBOLD W. , LEVEZIEL H. , LIE Ø. , LINDBERG P. G. , MEGGIOLARO D. , MEYER E. , OLIVER R. , ROSS M. , SIMON M. , SPOONER R. L. , STEAR M. J. , TEALE A. J. , TEMPLETON J. W.
Published: July 2010

Summary.Two hundred and eighty‐two alloantisera were submitted by 20 participating laboratories from 13 countries and tested against lymphocytes of 1298 cattle. The cell panel consisted of samples from 38Bos taurusbreeds, 11Bos tauruscrossbreeds, 4Bos indicusbreeds, 6Bos taurus X Bos indicus, and a variety of other crossbred populations. Using a standardized lymphocytotoxicity test, all 17 previously identified BoLA specificities were confirmed. The workshop produced agreement on 16 new lymphocyte alloantigenic specificities. Three of the new specificities behaved as splits of previously identified BoLA specificities. Four of the new specificities behaved as alleles at the agreed BoLA‐A locus. Seven new specificities are tentatively assigned to the BoLA‐A locus but require further definition. Two new specificities may represent products of a second closely‐linked BoLA locus.
Evidence for a third allele at the β‐lactoglobulin (β‐Lg) locus of sheep milk and its occurrence in different breeds
Authors: ERHARDT G.
Published: July 2010

Summary. Milk samples from 189 Merinoland Sheep, 145 Black Faced Mutton Sheep, 89 East Friesian Milk Sheep, 36 Rhön, 36 Pleven, 23 Tsigaja, 25 Black Razka and 86 Hungarian Merino x Pleven (F1) sheep were analysed by polyacrylamide gel electrophoresis under acid conditions and isoelectric focusing in ultrathin layer polyacrylamide gels with carrier ampholytes. Six different β‐lactoglobulin (β‐Lg) phenotypes (A, AB, B, AC, BC and C) were observed by both methods. The occurrence of three codominant alleles (β‐LgA, β‐LgB, β‐Lgc) at an autosomal locus (β‐Lg) was supported by family and population data on genetic equilibrium. Differences in gene frequencies between the breeds were observed.
DNA fingerprints of farm animals generated by microsatellite and minisatellite DNA probes
Authors: HABERFELD A. , CAHANER A. , YOFFE O. , PLOTSKY Y. , HILLEL J.
Published: July 2010

Summary. A multi‐locus DNA probe, R18.1, derived from a bovine genomic library, detected DNA fingerprints of highly polymorphic loci in hybridization to genomic DNA from poultry and sheep, and of moderate polymorphic loci in cattle and human DNA. The average numbers of detected bands in chickens and sheep were 27.8 and 21.4, and the average band sharing levels were 0.25 and 0.33, respectively. In hybridization to cattle and human DNA, the results were less polymorphic; nevertheless, individual identification is feasible using probe R18.1. The results obtained by R18.1 were compared to results obtained by Jeffreys minisatellite probe 33.6 and two microsatellite oligonucleotides, (GT)12 and (GTG)5. The total number of detected loci using probes R18.1 and 33.6 were estimated in chickens through family analysis of broilers and the maximal number of detectable loci was calculated.
Nucleotide sequence and Northern analysis of a bovine major histocompatibility class II DRß‐like cDNA
Authors: BURKE M. G. , STONE R. T. , MUGGLI‐COCKETT N. E.
Published: July 2010

Summary. A1.2‐kb bovine DRß‐like cDNA clone (BoLA‐DRB3) was isolated from a peripheral blood lymphocyte cDNA library utilizing a human DRß cDNA as a probe. BoLA‐DRB3 was found to have a high degree of nucleotide sequence similarity (96.8%) with a previously sequenced bovine DRß‐like gene (Al). It is believed that BoLA‐DRB3 and A1 represent distinct alleles of one of the three bovine DRß‐like loci. Sequence comparison of BoLA‐DRB3 with genes representing the other two bovine DRß‐like loci. resulted in moderate degrees of sequence similarities (83.1% and 86.3%, respectively). Comparison of the relative abundance of RNA transcripts of the three bovine DRß‐like loci by Northern analysis of lymphocyte RNA indicated that BoLA‐DRB3 is the most actively transcribed of the three bovine DRß‐like genes. Based on these results we suggest that of the three DRß‐like loci thus far identified in the bovine, only one is actively transcribed.
Cloning and sequencing of the porcine lactoferrin cDNA
Authors: ALEXANDER L. J. , LEVINE W. B. , TENG C. T. , BEATTIE C. W.
Published: July 2010

Summary. cDNA clones encoding the entire porcine lactoferrin protein were isolated and sequenced. The porcine lactoferrin cDNA sequence presented here is 2259 bp in length and encodes a leader peptide of 19 amino acids and a mature protein of 684 amino acids. Comparisons with other lactoferrins indicate a single glycosylation site. The iron‐ and anion‐binding sites, and the cysteine residues involved in disulphide bonds, are conserved between the lactoferrin proteins.
The sex‐determining region Y (SRY) gene is mapped to p12‐p13 of the Y chromosome in pig (Sus scrofa domestica) by in situ hybridization
Authors: Yang H. , Fries R. , Stranzinger G.
Published: July 2010

The sex‐determining region Y is a gene located in the distal portion of the short arm of human (SRY) and mouse (Sry) Y chromosomes and considered to be the best candidate for the testis determining factor (TDF/Tdy). The gene is believed to be the key factor in sex differentiation in mammals and is conserved across mammalian species. We report herein that the SRY/Sry gene has been assigned to pi 2‐p13 on the short arm of the Y chromosome in pig by in situ hybridization. The result confirms interspecies conservation of this chromosomal segment in the evolution of mammalian chromosomes, and suggests further use of this gene probe in genomic studies in other mammals. The assignment of the Sry gene is the second physical gene mapping data available for the Y chromosome in pigs. Such data can be used in the effort of constructing the pig gene map and for further establishment of a comparison of sex chromosome morphology in different mammalian species concerning sex‐specific and pseudoautosomal regions.
Polymerase chain reaction analysis of mitochondrial DNA polymorphism in N'Dama and Zebu cattle
Authors: Suzuki R. , Kemp S. J. , Teale A. J.
Published: July 2010

A study of polymorphisms of mitochondrial DNA (mtDNA) of West African N'Dama (Bos taurus) and East African Zebu (B. indicus) cattle was carried out to obtain information on maternal phylogenetic relationships between these breeds. A relatively large sample size was made possible by using polymerase chain reaction (PCR) amplification of DNA prepared from small blood samples to generate fragments of two known polymorphic mtDNA regions, one within the gene encoding subunit 5 of NADH dehydrogenase and one encompassing the entire D‐loop. This approach allowed us to achieve a higher resolution restriction analysis on mtDNA from more animals than would have been possible by conventional methods. PCR‐amplified mtDNA of 58 animals from five populations was examined at 26 restriction sites by 16 enzymes. In this way 154 nucleotides of mtDNA were scanned for polymorphism. Six polymorphic sites were located by this means, five of which were within the D‐loop and one of which was within the NADH dehydrogenase 5 gene. None of the polymorphisms observed could be con sidered typical of breed or type.
Mapping of MYF5, GlR, MYHL, TPIl, IAPP, A2MR and RNR onto sheep chromosome 3q
Authors: Broad T. E. , Lewis P. E. , Ansari H. A. , Pearce P. D. , Burkin D. J. , Jones C.
Published: July 2010

Five new loci, myogenic factor 5 (MYF5), complement 1 receptor (CIR), myosin‐like heavy chain (MYHL), islet amyloid polypeptide (IAPP), and alpha‐2‐macroglobulin receptor (A2MR), were mapped onto sheep chromosome 3q by Southern hybridization to a panel of chro‐mosomally characterized sheep × hamster cell hybrid lines. The location of the triose phosphate isomerase (TPI1) gene and one of the nucleolar organizer regions (RNR) on sheep 3q was confirmed by Southern analysis. This study provides further evidence for the existence of a large conserved chromosomal segment comprising much of sheep chromosome 3q, cattle chromosome 5, and human chromosome 12. The distal evolutionary breakpoint on human chromosome 12, producing the chromosomal segment U23 in cattle marked by aldehyde dehydrogenase (ALDH2), also produces a separate segment in sheep. Neither ALDH2 nor pancreatic lipase (PLA2), which is also distally located on human chromosome 12, were mapped onto sheep chromosome 3q.
A new αS1‐casein allele in bovine milk and its occurrence in different breeds
Authors: Erhardt G
Published: July 2010

A new asi‐casein variant (αS1‐CN F) with a frequency of 0.009 was demonstrated in a genetic resource of German Black and White Cattle by isoelectric focusing in polyacrylamide gels and by polyacrylamide gel electrophoresis under alkaline conditions. αs1‐CN F was not present either in German Holstein Friesians, which originate from crossing Holstein Friesians with German Black and White Cattle, or in milk samples from eight other breeds in Germany.