bluuebunny/crossref_metadata_2025 huggingface dataset:
The effects of interface design and age on children's information processing of Web sites
Authors: Rose Mei , Rose Gregory M. , Blodgett Jeffrey G.
Published: December 2008

Children increasingly utilize the Internet as a primary medium, a source of consumer information, and an important source of entertainment. This article investigates the influence of Web site design on children's information processing performance. A model is advanced that integrates theories from a variety of disciplines, including developmental psychology, human computer interaction (HCI), and consumer behavior. This study found that age moderates the relationship between Web site design and spatial (search) and learning (recall) performance. Younger children, between the ages of 7 and 9, recalled more content when using a map (as compared to a content list) and when learning cues were employed. Older children, between the ages of 10 and 12, performed equally as well with either a map or a content list, and with or without learning cues. Implications for business, education, and public policy are discussed and guidelines are provided for designing more child‐friendly Web sites. © 2008 Wiley Periodicals, Inc.
Prostate cancer and vegetable consumption
Authors: Chan Ruth , Lok Kris , Woo Jean
Published: December 2008

Epidemiological studies have shown marked variations in prostate cancer incidence and mortality across different geographic regions, leading to the rising interest in the role of nutrition in prostate cancer risk. There is also a large body of evidence that a diverse diet, rich in vegetables, can reduce the risk of prostate cancer. In this review, the role of various kinds of vegetables and their bioactive compounds associated with prostate cancer risk, and the underlying mechanisms of these associations are summarized. There is accumulating evidence to support the consumption of lycopene, in particular tomato and tomato‐based products, as protective factors against prostate cancer. Evidence on the protective role of β‐carotene was inconsistent from cohort and case–control studies. Evidence on the effect of pulses or soy consumption on prostate cancer risk was limited but suggestive of decreased risk with increased pulses or soy consumption. However, the role of vitamin C, vitamin E, allium vegetables, and cruciferous vegetables on prostate cancer risk remains to be determined due to limited evidence. Although the impact on prostate cancer risk differs among various vegetables and their constituent nutrients, the overall benefits of plant based diet on cancer prevention and other diet‐related diseases should be promoted.
A new smoothed aggregation multigrid method for anisotropic problems
Authors: Gee Michael W. , Hu Jonathan J. , Tuminaro Raymond S.
Published: December 2008

A new prolongator is proposed for smoothed aggregation (SA) multigrid. The proposed prolongator addresses a limitation of standard SA when it is applied to anisotropic problems. For anisotropic problems, it is fairly standard to generate small aggregates (used to mimic semi‐coarsening) in order to coarsen only in directions of strong coupling. Although beneficial to convergence, this can lead to a prohibitively large number of non‐zeros in the standard SA prolongator and the corresponding coarse discretization operator. To avoid this, the new prolongator modifies the standard prolongator by shifting support (non‐zeros within a prolongator column) from one aggregate to another to satisfy a specified non‐zero pattern. This leads to a sparser operator that can be used effectively within a multigrid V‐cycle. The key to this algorithm is that it preserves certain null space interpolation properties that are central to SA for both scalar and systems of partial differential equations (PDEs). We present two‐dimensional and three‐dimensional numerical experiments to demonstrate that the new method is competitive with standard SA for scalar problems, and significantly better for problems arising from PDE systems. Copyright © 2008 John Wiley & Sons, Ltd.
Phase I study of SU5416, a small molecule inhibitor of the vascular endothelial growth factor receptor (VEGFR) in refractory pediatric central nervous system tumors
Authors: Kieran Mark W. , Supko Jeffrey G. , Wallace Dana , Fruscio Robert , Poussaint Tina Young , Phillips Peter , Pollack Ian , Packer Roger , Boyett James M. , Blaney Susan , Banerjee Anu , Geyer Russ , Friedman Henry , Goldman Stewart , Kun Larry E. , MacDonald Tobey ,   on behalf of the Pediatric Brain Tumor Consortium
Published: December 2008

SU5416 is a novel small molecule tyrosine kinase inhibitor of the VEGF receptors 1 and 2. A phase I dose escalation study stratified by concurrent use (stratum II) or absence (stratum I) of enzyme‐inducing anticonvulsant drugs was undertaken to estimate the maximum‐tolerated dose (MTD) and to describe the toxicity profile of SU5416 in pediatric patients with refractory brain tumors. Dose escalations were conducted independently for stratum I starting at 110 mg/m2while stratum II started at 48 mg/m2. Thirty‐three eligible patients were treated on stratum I (n = 23) and stratum II (n = 10). Tumor types included 23 glial tumors, 4 neural tumors, 4 ependymomas, and 2 choroid plexus carcinomas. The MTD in stratum I was initially estimated to be 110 mg/m2. The protocol was amended to determine the MTD after excluding transient AST elevation. Re‐estimation of the MTD began at the 145 mg/m2dose level but due to development of SU5416 being stopped by the sponsor, the trial was closed before completion. The most serious drug‐related toxicities were grade 3 liver enzyme abnormalities, arthralgia, and hallucinations. The plasma pharmacokinetics of SU5416 was not significantly affected by the concurrent administration of enzyme‐inducing anticonvulsant drugs. Mean values of the total body clearance, apparent volume of distribution, and terminal phase half‐life of SU5416 for the 19 patients in stratum I were 26.1 ± 12.5 l/hr/m2, 41.9 ± 21.4 l/m2, and 1.11 ± 0.41 hr, respectively. The plasma pharmacokinetics of SU5416 in children was similar to previously reported findings in adult cancer patients. Prolonged disease stabilization was observed in 4 of 16 stratum I patients. Pediatr Blood Cancer 2009;52:169–176. © 2008 Wiley‐Liss, Inc.
Ionic and radical fragmentations of alkoxyhalocarbenes – a perspective
Authors: Moss Robert A.
Published: December 2008

Fragmentations of secondary or tertiary alkoxyhalocarbenes in polar solvents generate carbocations as components of ion pairs. A variety of carbocations can be produced including acyclic, alicyclic, benzyl, bridgehead, cyclopropyl, cyclopropylcarbinyl, and norbornyl examples. Laser flash photolysis (LFP) studies provide kinetics and activation parameters for the carbene fragmentations, which are orders of magnitude faster, and require considerably reduced activation energies, compared to analogous solvolytic carbocation‐generative processes. In some cases, the time required for solvent and anion equilibration of the ion pairs can be estimated. In nonpolar solvents, the gas phase, or cryogenic matrices, homolytic carbene fragmentation may, in certain cases, supplant heterolytic fragmentation. Copyright © 2008 John Wiley & Sons, Ltd.
Tracing pathway activities with kinase inhibitors and reverse phase protein arrays
Authors: van Oostrum Jan , Calonder Claudio , Rechsteiner Daniel , Ehrat Markus , Mestan Jürgen , Fabbro Doriano , Voshol Hans
Published: December 2008

Controlling aberrant protein kinase activity is a promising strategy for a variety of diseases, particularly cancer. Hence, the development of kinase inhibitors is currently a focal point for pharmaceutical research. In this study we utilize a chip‐based reverse phase protein array (RPA) platform for profiling of kinase inhibitors in cell‐based assays. In combination with the planar wave‐guide technology the assay system has an absolute LOD down to the low zeptomole range. A431 cell lysates were analyzed for the activation state of key effectors in the epidermal growth factor (EGF) and insulin signaling pathways to validate this model for compound screening. A microtiter‐plate format for growing, treating, and lysing cells was shown to be suitable for this approach, establishing the value of the technology as a screening tool for characterization of large numbers of kinase inhibitors against a wide variety of cellular signaling pathways. Moreover, the reverse array format allows rapid development of site‐specific phosphorylation assays, since in contrast to ELISA type systems only a single antigen‐specific antibody is required.
The proteome of the human breast cancer cell line MDA‐MB‐231: Analysis by LTQ‐Orbitrap mass spectrometry
Authors: Strande Vaïk , Canelle Ludovic , Tastet Christophe , Burlet‐Schiltz Odile , Monsarrat Bernard , Hondermarck Hubert
Published: December 2008

We have used a combination of SDS‐PAGE and LTQ‐Orbitrap MS to explore the proteome of the highly invasive MDA‐MB‐231 breast cancer cell line. Based on about 520 000 MS/MS spectra, a total of 3481 proteins were identified and subsequently classified according to their cellular distribution and molecular function. Interestingly, a large proportion of proteins (38%) were from cellular membranes and we were able to characterize numerous proteins involved in cancer initiation and progression such as the tumor suppressor p53 and the epidermal growth factor receptor. Together, this study represents the largest proteome database of breast cancer cells realized to date and demonstrates the value of using Orbitrap MS for deeper proteome analysis.
A method for the analysis of domain movements in large biomolecular complexes
Authors: Poornam Guru Prasad , Matsumoto Atsushi , Ishida Hisashi , Hayward Steven
Published: December 2008

A new method for the analysis of domain movements in large, multichain, biomolecular complexes is presented. The method is applicable to any molecule for which two atomic structures are available that represent a conformational change indicating a possible domain movement. The method is blind to atomic bonding and atom type and can, therefore, be applied to biomolecular complexes containing different constituent molecules such as protein, RNA, or DNA. At the heart of the method is the use of blocks located at grid points spanning the whole molecule. The rotation vector for the rotation of atoms from each block between the two conformations is calculated. Treating components of these vectors as coordinates means that each block is associated with a point in a “rotation space” and that blocks with atoms that rotate together, perhaps as part of the same rigid domain, will have colocated points. Thus a domain can be identified from the clustering of points from blocks that span it. Domain pairs are accepted for analysis of their relative movements in terms of screw axes based upon a set of reasonable criteria. Here, we report on the application of the method to biomolecules covering a considerable size range: hemoglobin, liver alcohol dehydrogenase, S‐Adenosylhomocysteine hydrolase, aspartate transcarbamylase, and the 70S ribosome. The results provide a depiction of the conformational change within each molecule that is easily understood, giving a perspective that is expected to lead to new insights. Of particular interest is the allosteric mechanism in some of these molecules. Results indicate that common boundaries between subunits and domains are good regions to focus on as movement in one subunit can be transmitted to another subunit through such interfaces. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Isoform‐specific variation in the intrinsic disorder of the ecdysteroid receptor N‐terminal domain
Authors: Nocula‐Ługowska Małgorzata , Rymarczyk Grzegorz , Lisowski Marek , Ożyhar Andrzej
Published: December 2008

The Drosophila melanogaster ecdysteroid receptor (EcR) is a member of the nuclear hormone receptor superfamily. EcR controls animal development and metamorphosis by activating or repressing the transcription of target genes. There are three EcR isoforms, EcRA, EcRB1, and EcRB2 that exhibit diverse spatial and temporal distributions within various tissues and reveal essential functional differences. These differences can be attributed to the isoform‐specific N‐terminal domains (NTDs), which differ in length and primary structure. To lay a foundation for understanding of the molecular mechanism underlying functional diversity of the isoforms, we have carried out a comprehensive biochemical and biophysical analysis of purified hexahistidine‐tagged EcRA and EcRB1 NTDs (EcRA‐NTD and EcRB1‐NTD). The results, along with in silico examinations of the primary structures indicate that the EcR NTDs exhibit properties of premolten globule‐like intrinsically disordered proteins. Furthermore, we demonstrate for the first time that NTDs of isoforms of a particular nuclear hormone receptor exhibit distinct structural properties. In silico analysis revealed that the EcRA‐NTD sequence has a bigger tendency for disorder than the EcRB1‐NTD sequence. Accordingly, the circular dichroism experiments demonstrated that EcRA‐NTD has lower regular secondary structure content than EcRB1‐NTD and the size‐exclusion chromatography showed that EcRA‐NTD is less compact than EcRB1‐NTD. Furthermore, the limited proteolysis analysis revealed that the C‐terminal region common to both NTDs is more susceptible to the enzymatic cleavage in EcRA‐NTD than in EcRB1‐NTD. We postulate that unique conformational states of EcRA‐NTD and EcRB1‐NTD might act as the starting points for the functional diversity of EcRA and EcRB1 isoforms. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Spot the Hazard! A cultural extension of hazard identification training
Authors: Wasileski Robert F.
Published: December 2008

Hazard identification training (HIT) programs have been used in the chemical processing industry to raise awareness with employees on what constitutes a process hazard and techniques for identifying these hazards. Quite often these HIT programs will deliver the course material to the participants as classroom instruction, computer‐based training, organized field reviews, or a combination of these formats. These presentations tend to be one‐time efforts or cyclic programs that reach the target audience on some periodic basis (e.g., triennially). Although the content of the course material may be educational, these programs often have limited success because of their inability to make a lasting impression with the participants. Organizational and personnel changes, employee turnover, vanishing corporate memory, and shifting priorities can all have an undermining effect on the well‐intended efforts of traditional HIT programs. The challenge thus becomes finding ways to keep the knowledge both relevant and current, to effect lasting cultural change in a dynamic environment.

This article presents a unique HIT program known as “Spot the Hazard,” which uses the facility's intranet to reinforce the concepts taught in the classroom. Spot the Hazard blends photographic examples and technical knowledge with aspects of behavior modification. The photographs that are presented have not been staged and thus are germane to the employees. The inherent on‐going nature of the program ensures the knowledge remains current, while at the same time it provides a platform for making a positive cultural change.

The concepts of Spot the Hazard are explained in greater detail in the current article, along with a representative number of actual examples. © 2008 American Institute of Chemical Engineers Process Saf Prog, 2009
Superconductivity in diamond induced by boron doping at high pressure
Authors: Ekimov E. A. , Sidorov V. A. , Zoteev A. , Lebed' Yu. , Thompson J. D. , Bauer E. D. , Stishov S. M.
Published: December 2008

The application of hydrostatic pressure to boron‐doped diamond samples produces a linear decrease in the superconducting transition temperature Tc. The values d ln Tc/dP obtained for samples with different Tc's collapse near an average value –2 × 10–2 GPa–1, which is in reasonable agreement with theoretical predictions based on an electron–phonon mechanism of superconductivity in diamond within the virtual crystal approximation [Y. Ma et al., Phys. Rev. B 72, 014306 (2005)]. For the first time, superconducting boron‐doped diamond samples were synthesized with 10B and 13C isotopes. Isotopic substitution permits us to relate almost all bands in the Raman spectra of heavily boron‐doped diamond with the vibrations of carbon atoms. The “500 cm–1” Raman band shifts with both carbon and boron isotope substitutions and is associated with vibrations of clustered boron. We claim the presence of a carbon isotope effect in superconducting diamond. This fact supports the importance of the electron–phonon interaction as the mechanism of superconductivity in diamond. The value of the isotope effect coefficient is β0 = –d ln Tc/d ln M = 0.5 ± 0.3. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electronic and optical properties of III‐nitrides under pressure
Authors: Christensen N. E. , Gorczyca I. , Laskowski R. , Svane A. , Albers R. C. , Chantis A. N. , Kotani T. , van Schilfgaarde M.
Published: December 2008

Results of theoretical studies of electronic and optical properties of III–V nitride compound semiconductors under pressure are presented. As representatives InN and AlN have been chosen, and for InN the pressure effects on the fundamental gap as well as the role of conduction‐band filling are examined. Both the fundamental gap and the electron effective mass increase with pressure, but due to the strong non‐parabolicity of the conduction band, the pressure coefficient of the mass decreases with electron concentration. Particular attention is paid to the electronic states in the gap region. The “local‐density gap error” is avoided by performing Quasi Particle self‐consistent GW calculations, which produce slightly too large gaps. Including in addition the missing electron–hole excitonic states and the gap renormalization due to electron–phonon interaction a gap reduction is obtained. The e–h correlations are deduced from solutions of the Bethe‐Salpeter equation. These are further used to study excitonic states in the gap of AlN under pressure, and for the rocksalt phase a pressure induced delocalized → localized transition is predicted. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Study of UV excited white light‐emitting diodes for optimization of luminous efficiency and color rendering index
Authors: Cho Jaehee , Kim Hyungkun , Sone Cheolsoo , Park Yongjo , Kim Young Sic , Kubota Shunichi , Yoon Euijoon
Published: December 2008

Wavelength down‐converted white‐light sources excited by near ultraviolet light‐emitting diodes require specific phosphor properties in order to generate high‐quality white light (namely, light with good color rendition and stability of color coordinate). Simulation and experimental results are discussed, with particular emphasis on the spectral distribution property of red phosphor required to realize high values of luminous efficiency and color rendition. A peak wavelength of 610 nm and an FWHM of 80 nm for the spectral power distribution were proposed, and co‐doped phosphate materials were synthesized successfully. This can contribute to a white‐light source with a luminous efficiency of 45 lm/W and color rendering index greater than 90 at a color temperature of 5600 K and an operational current of 20 mA. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Exploring Equisetum arvense L., Equisetum ramosissimum L. and Equisetum telmateia L. as sources of natural antioxidants
Authors: Štajner Dubravka , Popović Boris M. , Čanadanović‐Brunet Jasna , Anačkov Goran
Published: December 2008

The antioxidant and scavenging activities of above ground parts of Equisetum arvense L., Equisetum ramosissimum L. and Equisetum telmateia L. phosphate buffer (pH 7) extracts were investigated. Activities of antioxidant enzymes (superoxide dismutase, catalase, guaiacol peroxidase and glutathione peroxidase), quantities of reduced glutathione, malonyldialdehyde, superoxide and hydroxyl radicals and flavonoid, soluble protein, chlorophyll a, b and carotenoid contents were determined. The total antioxidant capacity was determined by ferric reducing antioxidant power (FRAP) assay. The Equisetum telmateia extract demonstrated scavenging and antioxidant properties better than Equisetum ramosissimum and Equisetum arvense. The ESR signal of DMPO‐OH radical adducts in the presence of Equisetum telmateia phosphate buffer (pH 7) extract was reduced by 98.9% indicating that Equisetum telmateia could be a useful source of antioxidants with huge scavenging ability. Copyright © 2008 John Wiley & Sons, Ltd.
Effects of hydroxytyrosol‐20 on carrageenan‐induced acute inflammation and hyperalgesia in rats
Authors: Gong Dezheng , Geng Chengyan , Jiang Liping , Cao Jun , Yoshimura Hiroyuki , Zhong Laifu
Published: December 2008

Hydroxytyrosol (HT) is a simple phenol compound extracted from olive leaves. The content of HT in the studied preparation was about 20%, and the preparation was called hydroxytyrosol‐20 (HT‐20). HT has antioxidant and antiinflammatory activities. There has been no report so far on the efficacy of HT‐20 in carrageenan‐induced acute inflammation and hyperalgesia in rats. Therefore, the aim of this study was to assess the inhibitory role of HT‐20 on carrageenan‐induced swelling and hyperalgesia of rat paw. Paw inflammation was assessed by the increase in paw volume and hyperalgesia. The rat paws were cut out under ether anesthesia at 270 min after administration of carrageenan. The tissue of the right paw was isolated separately from the individual rat. The levels of the tumor necrosis factor‐alpha (TNF‐α), interleukin 1β(IL‐1β) and interleukin 10 (IL‐10) mRNA in the tissue were estimated by reverse transcription‐polymerase chain reaction (RT‐PCR). The results showed that the paw pressure thresholds of rats orally administered HT‐20 significantly increased at 210, 240 and 270 min after administration of carrageenan, compared with corresponding basal paw pressure thresholds; the degree of swelling of the right hind paw showed a statistically significant reduction, compared with rats in the carrageenan‐treated control. In this model, HT‐20 appears to decrease pro‐inflammatory cytokines IL‐1βand TNF‐αand not to increase the antiinflammatory cytokine mRNA expression of IL‐10. Copyright © 2008 John Wiley & Sons, Ltd.
Using degradation data to assess reliability: a case study on train wheel degradation
Authors: Freitas Marta A. , de Toledo Maria Luíza G. , Colosimo Enrico A. , Pires Magda C.
Published: December 2008

Degradation experiments are usually used to assess the lifetime distribution of highly reliable products, which are not likely to fail under the traditional life tests or accelerated life tests. In such cases, if there exist product characteristics whose degradation over time can be related to reliability, then collecting ‘degradation data’ can provide information about product reliability. In general, the degradation data are modeled by a nonlinear regression model with random coefficients. If we can obtain the estimates of parameters under the model, then the failure‐time distribution can be estimated. In order to estimate those parameters, three basic methods are available, namely, the analytical, numerical and the approximate. They are chosen according to the complexity of the degradation path model used in the analysis. In this paper, the numerical and the approximate methods are compared in a simulation study, assuming a simple linear degradation path model. A comparison with traditional failure‐time analysis is also performed. The mean‐squared error of the estimated 100pth percentile of the lifetime distribution is evaluated for each one of the approaches. The approaches are applied to a real degradation data set. Copyright © 2008 John Wiley & Sons, Ltd.
Characterizing future large, rapid changes in aggregated wind power using Numerical Weather Prediction spatial fields
Authors: Cutler Nicholas J. , Outhred Hugh R. , MacGill Iain F. , Kay Merlinde J. , Kepert Jeffrey D.
Published: December 2008

A critical limiting factor to the successful deployment of a large proportion of wind power in power systems is its predictability. Power system operators play a vital role in maintaining system security, and this task is greatly aided by useful characterizations of future system operations. A wind farm power forecast generally relies on the forecast output from a Numerical Weather Prediction (NWP) model, typically at a single grid point in the model to represent the wind farm's physical location. A key limitation of this approach is the spatial misplacement of weather features often found in NWP forecasts. This paper presents a methodology to display wind forecast information from multiple grid points at hub height around the wind farm location. If the raw forecast wind speeds at hub height at multiple grid points were to be displayed directly, they would be misleading as the NWP outputs take account of the estimated local surface roughness and terrain at each grid point. Hence, the methodology includes a transformation of the wind speed at each grid point to an equivalent value that represents the surface roughness and terrain at the chosen single grid point for the wind farm site. The chosen‐grid‐point‐equivalent wind speeds for the wind farm can then be transformed to available wind farm power. The result is a visually‐based decision support tool which can help the forecast user to assess the possibilities of large, rapid changes in available wind power from wind farms. A number of methods for displaying the field for multiple wind farms are discussed. The chosen‐grid‐point‐equivalent transformation also has other potential applications in wind power forecasting such as assessing deterministic forecast uncertainty and improving downscaling results. Copyright © 2008 John Wiley & Sons, Ltd.
Continuous Monitoring of Adverse Events: Influence on the Quality of Care and the Incidence of Errors in General Surgery
Authors: Rebasa Pere , Mora Laura , Luna Alexis , Montmany Sandra , Vallverdú Helena , Navarro Salvador
Published: December 2008

Background

This study was designed to determine the incidence of adverse events and errors in the care of surgical patients and to demonstrate that continuous prospective collection of data on adverse events can improve quality of care and reduce the number of errors. Retrospective studies find adverse events in approximately 5% of patients admitted. Prospective studies publish figures of approximately 30%. No studies to date have tried to use continuous collection of data on adverse events to reduce the incidence of errors.

Methods

Longitudinal prospective surveillance of adverse events in patients admitted to the Surgery Service during a 22‐month period. Sequelae after discharge and errors during hospital stay were evaluated by peer review.

Results

A total of 3,807 patients were controlled: 1,177 patients presented 2,193 adverse events (30.9% of admissions); 330 adverse events due to errors were detected in 258 patients (6.9% of admissions). Thirty‐four deaths were considered due to adverse events (0.89% of admissions), and in 11 cases mortality was deemed avoidable (0.29% of admissions). The incidence of adverse events remained constant during the study period, but errors decreased from 11.1% to 4.5% (P = 0.005).

Conclusions

This is the first attempt to determine the prevalence of errors in surgery. Introducing systematic programs for recording adverse events can reduce error rates and promote a culture of patient safety in a General Surgery Department.
Sequencing the Full‐Length of the Phosphatase and Tensin Homolog (PTEN) Gene in Hepatocellular Carcinoma (HCC) Using the 454 GS20 and Illumina GA DNA Sequencing Platforms
Authors: Rodriguez Joel A. , Guiteau Jacfranz J. , Nazareth Lynne , Reid Jeff G. , Goss John A. , Gibbs Richard A. , Gingras Marie‐Claude
Published: December 2008

Background

Phosphatase and tensin homolog (PTEN) is a tumor‐suppressor gene that is mutated in cancer of the liver, pancreas, endometrium, and prostate. PTEN‐dependent pathways are involved in mediating cell growth and invasion. To sequence the whole gene (including introns and exons), we have taken advantage of new technologies that allow for rapid, inexpensive sequencing to great depth.

Methods

DNA from 15 HCC specimens were pooled, and long‐range PCR was performed by using the GeneAmp XL PCR kit. Primer parameters included: length of 20–30 base pairs (bp), melting temperature of −68°C, and G/C content of 50–60%. PCR products were then column‐purified and pooled, and DNA libraries were prepared for “shotgun sequencing” on both the 454 GS and Illumina GA sequencing platforms.

Results

We successfully amplified approximately 98.9% of the PTEN gene by using one long‐range PCR protocol applied to 24 primer sets, resulting in 20 amplicons ~6.5 kilobases (kb) in length, 2 amplicons ~10 kb in length, and 2 amplicons ~2.5 kb in length. Sequencing of fragmented PCR products on both sequencing platforms identified six high‐frequency SNPs that were catalogued in dbSNP as known variants.

Conclusions

Shotgun sequencing based on a single long‐range PCR protocol in pooled samples is an efficient and relatively inexpensive way to sequence an entire gene.
Hammering K-Wires is Superior to Drilling with Irrigation
Authors: Franssen Bas B. G. M. , Schuurman Arnold H. , Brouha Pascal C. R. , Kon Moshe
Published: December 2008

Cooling during drilling Kirschner wires is not always effective in preventing thermal related damage. In this study, we used a human in vitro model and compared temperature elevation, insertion time, and extraction force between three Kirschner wire insertion methods–drilling with and without irrigation and pneumatic hammering. Forty five Kirschner wires were inserted into 15 fresh human cadaver metacarpals. All three insertion methods were applied in each metacarpal. Drilling without irrigation resulted in a temperature elevation of 67.25±5.4°C with significantly lower values for drilling with irrigation (4.15±0.6°C) and pneumatic hammering (31.52±3.4°C). The insertion time for pneumatic hammering (47.63±8.8 s) was significantly lower compared to drilling without irrigation (263.16±36.5 s) and drilling with irrigation (196.10±28.5 s). Extraction forces after drilling without irrigation, drilling with irrigation, and pneumatic hammering were 39.85±4.1 N, 57.81±6.5 N, and 62.23±6.7 N, respectively. Pneumatic hammering is superior to drilling without irrigation, especially when irrigation is not possible.
The impact of floral resources and omnivory on a four trophic level food web
Authors: Jonsson M. , Wratten S.D. , Robinson K.A. , Sam S.A.
Published: December 2008

Omnivory is common among arthropods, but little is known about how availability of plant resources and prey affects interactions between species operating at the third and fourth trophic level. We used laboratory and field cage experiments to investigate how the provision of flowers affects an omnivorous lacewing, Micromus tasmaniae (Hemerobiidae) and its parasitoid Anacharis zealandica (Figitidae). The adult lacewing is a true omnivore that feeds on both floral resources and aphids, whereas the parasitoid is a life-history omnivore, feeding on lacewing larvae in the larval stage and floral nectar as an adult. We showed that the effect of floral resources (buckwheat) on lacewing oviposition depends on prey (aphid) density, having a positive effect only at low prey density and that buckwheat substantially increases the longevity of the adult parasitoid. In field cages, we tested how provision of flowering buckwheat affects the dynamics of a four trophic level system, comprising parasitoids, lacewings, pea aphids and alfalfa. We found that provision of buckwheat decreased the density of lacewings in the first phase of the experiment when the density of aphids was high. This effect was probably caused by increased rate of parasitism by the parasitoid, which benefits from the presence of buckwheat. Towards the end of the experiment when the aphid populations had declined to low levels, the effect of buckwheat on lacewing density became positive, probably because lacewings were starving in the no-buckwheat treatment. Although presence of buckwheat flowers did not affect aphid populations in the field cages, these findings highlight the need to consider multitrophic interactions when proposing provision of floral resources as a technique for sustainable pest management.
Inter-seasonal population dynamics and pest status of Bemisia tabaci (Gennadius) biotype B in an Australian cropping system
Authors: Sequeira R.V. , Shields A. , Moore A. , De Barro P.
Published: December 2008

Bemisia tabaci, biotype B, commonly known as the silverleaf whitefly (SLW) is an alien species that invaded Australia in the mid-90s. This paper reports on the invasion ecology of SLW and the factors that are likely to have contributed to the first outbreak of this major pest in an Australian cotton cropping system. Population dynamics of SLW within whitefly-susceptible crop (cotton and cucurbit) and non-crop vegetation (sowthistle, Sonchus spp.) components of the cropping system were investigated over four consecutive growing seasons (September–June) 2001/02–2004/05 in the Emerald Irrigation Area (EIA) of Queensland, Australia. Based on fixed geo-referenced sampling sites, variation in spatial and temporal abundance of SLW within each system component was quantified to provide baseline data for the development of ecologically sustainable pest management strategies. Parasitism of large (3rd and 4th instars) SLW nymphs by native aphelinid wasps was quantified to determine the potential for natural control of SLW populations. Following the initial outbreak in 2001/02, SLW abundance declined and stabilised over the next three seasons. The population dynamics of SLW is characterised by inter-seasonal population cycling between the non-crop (weed) and cotton components of the EIA cropping system. Cotton was the largest sink for and source of SLW during the study period. Over-wintering populations dispersed from weed host plant sources to cotton in spring followed by a reverse dispersal in late summer and autumn to broad-leaved crops and weeds. A basic spatial source-sink analysis showed that SLW adult and nymph densities were higher in cotton fields that were closer to over-wintering weed sources throughout spring than in fields that were further away. Cucurbit fields were not significant sources of SLW and did not appear to contribute significantly to the regional population dynamics of the pest. Substantial parasitism of nymphal stages throughout the study period indicates that native parasitoid species and other natural enemies are important sources of SLW mortality in Australian cotton production systems. Weather conditions and use of broad-spectrum insecticides for pest control are implicated in the initial outbreak and on-going pest status of SLW in the region.
Immune responses to polyethylenimine delivered plasmid DNA encoding aFasciola giganticafatty acid binding protein in mice and rabbits
Authors: Raina O.K. , Tripathy A. , Sriveny D. , Gupta P.K. , Samanta S. , Gupta S.C. , Singh R. , Tewari A.K. , Banerjee P.S. , Kumar S. , Yadav S.C.
Published: December 2008

Fasciola giganticafatty acid binding protein (FABP) was evaluated for evoking an effective immune response in mice and rabbits, when delivered as a DNA vaccine in muscle cells. Polyethylenimine (PEI), 25 kDa, branched cationic polymer was used as a delivery vehicle for this DNA in the muscle cells of mice and rabbits. Naked DNA evoked mixed Th1 and Th2 responses in mice. PEI condensed DNA, at amine nitrogen over DNA phosphate (N/P) ratios of 4, 6 and 8 and with various DNA concentrations, failed to evoke a significantly higher antibody response compared to naked DNA in mice. Similarly, the humoral immune response to naked DNA administration in rabbit thigh muscles was poor and no boosting of this antibody response on administration of DNA complexed to PEI was observed. On metacercarial challenge, rabbits failed to show any significant protective immune response in both the naked DNA and PEI–DNA immunized groups. Administration of PEI alone (12.5 μg) in mouse thigh muscles caused significant muscle cytotoxicity but condensation of DNA with PEI had less of a toxic effect on muscle cells, which was inversely related to the N/P ratio. Delivery of plasmid DNA encodingF. giganticaFABP by high molecular weight polyethylenimine (branched, 25 kDa) did not boost the effective immune response in both the animal species, which could either be attributed to cytotoxicity associated with this cationic polymer or muscle cells being unsuitable target cells for PEI condensed DNA delivery.
AdultBrugia malayimitochondrial and nuclear fractions impart Th1-associated sizeable protection against infective larval challenges inMastomys coucha
Authors: Shakya S. , Srivastava A.K. , Misra-Bhattacharya S.
Published: December 2008

Protective immunity to the subperiodic human filariid,Brugia malayi, was explored in the rodent host,Mastomys couchaafter vaccination with subcellular fractions derived from the adult stage of the parasite. The highest level of protection was conferred in animals vaccinated with the ‘mitochondria rich’ (MT) fraction, in which microfilaraemia and worm burden were markedly reduced by 67.2 and 65.9%, respectively, followed by the ‘nucleus rich’ (NR) fraction, showing reductions of 62 and 52.3%, respectively, over the non-immunized control group. Mastomys vaccinated with MT and NR, displayed a significant increase in the level of antigen-specific serum immunoglobulin G (IgG). The levels of IgG2a, IgG2b and IgM antibody isotypes were remarkably elevated in both the MT and NR immunized groups, while IgG1 and IgG3 levels were low. Apart from antibodies, both these fractions also led to marked antigen-specific lymphoproliferationin vitro, along with enhanced release of nitric oxide by peritoneal macrophages. There was an increased population of CD4+ and CD8a+T-cells in MT immunized animals, as measured by flow cytometry, accompanied by elevated levels of proinflammatory cytokines; interferon gamma (IFN-γ), tumour necrosis factor alpha (TNF-α) and interleukin-1 beta (IL-1β) in the culture supernatants of the activated splenocytes. The results suggest that both NR and MT contain proinflammatory molecules which evoke a protective Th1 type of immune response.
Detecting stress patterns is related to children's performance on reading tasks
Authors: GUTIÉRREZ-PALMA NICOLÁS , RAYA-GARCÍA MANUEL , PALMA-REYES ALFONSO
Published: December 2008

This paper investigates the relationship between the ability to detect changes in prosody and reading performance in Spanish. Participants were children aged 6–8 years who completed tasks involving reading words, reading pseudowords, stressing pseudowords, and reproducing pseudoword stress patterns. Results showed that the capacity to reproduce pseudoword stress patterns accounted for a unique portion of the variance in text reading, after controlling for phonological awareness, phoneme sensitivity, and working memory. In addition, stress sensitivity predicted children's performance in stressing pseudowords. These results suggest that stress sensitivity may affect fluency in reading as well as word stress learning.
The use of voice onset time by early bilinguals to distinguish homorganic stops in Canadian English and Canadian French
Authors: MACLEOD ANDREA A. N. , STOEL-GAMMON CAROL
Published: December 2008

The goal of this study was to examine the extent to which bilingual speakers maintain language-specific phonological contrasts for homorganic stops when a cue is shared across both languages. To this end, voice onset time (VOT) was investigated in three groups of participants: early bilinguals speakers of Canadian French and Canadian English (n = 8), monolingual speakers of Canadian English (n = 8), and monolingual speakers of Canadian French (n = 7). Three questions were targeted: What are the general patterns of VOT production in bilingual and monolinguals? Do bilingual speakers produce different mean VOT than monolinguals? Do bilingual speakers produce different variability in VOT than monolinguals? Acoustic measurements of VOT were made from monosyllabic English and French words with word-initial bilabial or coronal stop consonants. The results indicate that the early bilingual speakers maintain monolingual-like phonemic contrasts, but that they exhibit more variation within categories than monolingual speakers.
When study-abroad experience fails to deliver: The internal resources threshold effect
Authors: SUNDERMAN GRETCHEN , KROLL JUDITH F.
Published: December 2008

Some second language (L2) learners return from study-abroad experiences (SAEs) with seemingly no change in their L2 ability. In this study we investigate whether a certain level of internal cognitive resources is necessary in order for individuals to take full advantage of the SAE. Specifically, we examine the role of working memory resources in lexical comprehension and production for learners who had or had not studied abroad. Participants included native English learners of Spanish. Participants completed a translation recognition task and a picture-naming task. The results suggest that individuals who lack a certain threshold of working memory resources are unable to benefit from the study-abroad context in terms of being able to produce accurately in the L2.
Children's spoken word recognition and contributions to phonological awareness and nonword repetition: A 1-year follow-up
Authors: METSALA JAMIE L. , STAVRINOS DESPINA , WALLEY AMANDA C.
Published: December 2008

This study examined effects of lexical factors on children's spoken word recognition across a 1-year time span, and contributions to phonological awareness and nonword repetition. Across the year, children identified words based on less input on a speech-gating task. For word repetition, older children improved for the most familiar words. There was a competition effect for the word repetition task, but this effect was present only for the most familiar words on the gating task. Recognition for words from sparse neighborhoods predicted phonological awareness 1 year later, and children poorer at recognizing these words in Year 1 scored lower on word reading in Year 2. Spoken word recognition also accounted for unique variance in nonword repetition across the 1-year time span. Findings are discussed in terms of understanding the effects of vocabulary growth on spoken word recognition, phonological awareness, and nonword repetition.
Embeddings of dynamical systems into cellular automata
Authors: MÜLLER JOHANNES , SPANDL CHRISTOPH
Published: December 2008

We prove that general topological dynamical systems on metric Cantor spaces can be embedded into cellular automata defined on Cayley graphs. Furthermore, we prove that it is possible to construct this embedding in such a way that topological entropy is preserved.
An asymptotic-numerical approach for examining global solutions to an ordinary differential equation
Authors: ROBINSON MICHAEL
Published: December 2008

Purely numerical methods do not always provide an accurate way to find all the global solutions to nonlinear ordinary differential equations on infinite intervals. For example, finite-difference methods fail to capture the asymptotic behavior of solutions, which might be critical for ensuring global existence. We first show, by way of a detailed example, how asymptotic information alone provides significant insight into the structure of global solutions to a nonlinear ordinary differential equation. Then we propose a method for providing this missing asymptotic data to a numerical solver, and show how the combined approach provides more detailed results than either method alone.
Chaotic period doubling
Authors: CHANDRAMOULI V. V. M. S. , MARTENS M. , DE MELO W. , TRESSER C. P.
Published: December 2008

The period doubling renormalization operator was introduced by Feigenbaum and by Coullet and Tresser in the 1970s to study the asymptotic small-scale geometry of the attractor of one-dimensional systems that are at the transition from simple to chaotic dynamics. This geometry turns out not to depend on the choice of the map under rather mild smoothness conditions. The existence of a unique renormalization fixed point that is also hyperbolic among generic smooth-enough maps plays a crucial role in the corresponding renormalization theory. The uniqueness and hyperbolicity of the renormalization fixed point were first shown in the holomorphic context, by means that generalize to other renormalization operators. It was then proved that, in the space ofC2+αunimodal maps, forα>0, the period doubling renormalization fixed point is hyperbolic as well. In this paper we study what happens when one approaches from below the minimal smoothness thresholds for the uniqueness and for the hyperbolicity of the period doubling renormalization generic fixed point. Indeed, our main result states that in the space ofC2unimodal maps the analytic fixed point is not hyperbolic and that the same remains true when adding enough smoothness to geta prioribounds. In this smoother class, calledC2+∣⋅∣, the failure of hyperbolicity is tamer than inC2. Things get much worse with just a bit less smoothness thanC2, as then even the uniqueness is lost and other asymptotic behavior becomes possible. We show that the period doubling renormalization operator acting on the space ofC1+Lipunimodal maps has infinite topological entropy.
Normal forms for almost periodic differential systems
Authors: LI WEIGU , LLIBRE JAUME , WU HAO
Published: December 2008

In this paper we prove smooth conjugate theorems of Sternberg type for almost periodic differential systems, based on the Lyapunov exponents of the corresponding reduced systems.
Induction and restriction of cellular automata
Authors: CECCHERINI-SILBERSTEIN TULLIO , COORNAERT MICHEL
Published: December 2008

We analyze in detail the notions of induction and restriction for cellular automata. As a by-product we extend a few classical and recent theorems on cellular automata to uncountable groups.
Transitive Anosov flows and Axiom-A diffeomorphisms
Authors: BONATTI CHRISTIAN , GUELMAN NANCY
Published: December 2008

Let M be a smooth compact Riemannian manifold without boundary, and ϕ:M×ℝ→M a transitive Anosov flow. We prove that if the time-one map of ϕ is C1-approximated by Axiom-A diffeomorphisms with more than one attractor, then ϕ is topologically equivalent to the suspension of an Anosov diffeomorphism.
Dynamics and geometry of the Rauzy–Veech induction for quadratic differentials
Authors: BOISSY CORENTIN , LANNEAU ERWAN
Published: December 2008

Interval exchange maps are related to geodesic flows on translation surfaces; they correspond to the first return maps of the vertical flow on a transverse segment. The Rauzy–Veech induction on the space of interval exchange maps provides a powerful tool to analyze the Teichmüller geodesic flow on the moduli space of Abelian differentials. Several major results have been proved using this renormalization. Danthony and Nogueira introduced in 1988 a natural generalization of interval exchange transformations, namely linear involutions. These maps are related to general measured foliations on surfaces (whether orientable or not). In this paper we are interested by such maps related to geodesic flow on (orientable) flat surfaces with ℤ/2ℤ linear holonomy. We relate geometry and dynamics of such maps to the combinatorics of generalized permutations. We study an analogue of the Rauzy–Veech induction and give an efficient combinatorial characterization of its attractors. We establish a natural bijection between the extended Rauzy classes of generalized permutations and connected components of the strata of meromorphic quadratic differentials with at most simple poles, which allows us, in particular, to classify the connected components of all exceptional strata.