bluuebunny/crossref_metadata_2025 huggingface dataset:
Neuroproteomics and systems biology‐based discovery of protein biomarkers for traumatic brain injury and clinical validation
Authors: Kobeissy Firas H. , Sadasivan Shankar , Oli Monika W. , Robinson Gillian , Larner Stephen F. , Zhang Zhiqun , Hayes Ronald L. , Wang Kevin K. W.
Published: August 2008

The rapidly growing field of neuroproteomics has expanded to track global proteomic changes underlying various neurological conditions such as traumatic brain injury (TBI), stroke, and Alzheimer's disease. TBI remains a major health problem with approximately 2 million incidents occurring annually in the United States, yet no affective treatment is available despite several clinical trials. The absence of brain injury diagnostic biomarkers was identified as a significant road‐block to therapeutic development for brain injury. Recently, the field of neuroproteomics has undertaken major advances in the area of neurotrauma research, where several candidate markers have been identified and are being evaluated for their efficacy as biological biomarkers in the field of TBI. One scope of this review is to evaluate the current status of TBI biomarker discovery using neuroproteomics techniques, and at what stage we are at in their clinical validation. In addition, we will discuss the need for strengthening the role of systems biology and its application to the field of neuroproteomics due to its integral role in establishing a comprehensive understanding of specific brain disorder and brain function in general. Finally, to achieve true clinical input of these neuroproteomic findings, these putative biomarkers should be validated using preclinical and clinical samples and linked to clinical diagnostic assays including ELISA or other high‐throughput assays.
Evaluation of a bio‐coating as a solution to improve barrier, friction and optical properties of plastic films
Authors: Farris Stefano , Introzzi Laura , Piergiovanni Luciano
Published: August 2008

The present research dealt with evaluating barrier, friction and optical properties of three different plastic films after deposition of a gelatin‐based bio‐coating. The composite films showed improved barrier properties against oxygen and UV radiation. The oxygen transmission rate decreased in the order of 73% for oriented polypropylene (OPP), 56% for low‐density polyethylene (LDPE) and 40% for polyethylene terephthalate (PET). The increased UV barrier characteristics ranged from 20% for OPP to 12% for both LDPE and PET. Static and kinetic coefficients of friction significantly decreased both in the film‐to‐film and in the film‐to‐metal tests, leading to a desirable value for many applications. However, bio‐coated films showed lower optical performances in terms of transparency and haze. Transparency decreased mainly for LDPE (36%), whereas the haze index increased especially for OPP (85%). Non‐significant differences were observed as far as the water vapour permeability was concerned, except for a slight reduction for PET (from 15.78 to 13.53 cm3/m2/day at 23°C and 90% of relative humidity), suggesting that non‐meaningful effects arose from the addition of a hydrophobic component in the original formulation. Finally, the solubility of the coating in water was around 25% for all the three plastic substrates. The obtained data suggest that the lipid protein coating tested in this study, in spite of its great potential for enhancing some characteristics of plastic packaging films, still exhibits negative aspects which necessitate further improvement. Copyright © 2008 John Wiley & Sons, Ltd.
Ion mobility adds an additional dimension to mass spectrometric analysis of solution‐phase hydrogen/deuterium exchange
Authors: Iacob Roxana E. , Murphy James P. , Engen John R.
Published: August 2008

The goal of this study was to determine the utility of adding ion mobility spectrometry to studies probing the solution‐phase hydrogen/deuterium exchange (HX) of proteins. The HX profile of the Hck SH3 domain was measured at both the intact protein and the peptic peptide levels in the Waters Synapt HDMS system which uses a traveling wave to accomplish ion mobility separation prior to time‐of‐flight (Tof) m/z analysis. The results indicated a similar loss of deuterium with or without use of mobility in the Synapt and a level of deuterium loss comparable with a non‐mobility Q‐Tof instrument. The drift time of this small protein and its peptic peptides did not noticeably change due to solution‐based deuterium incorporation. Importantly, ion mobility separations provided an orthogonal dimension of separation in addition to the reversed‐phase high‐performance liquid chromatography (RP‐HPLC). The additional dimension of separation allowed for the deconvolution of overlapping isotopic patterns for co‐eluting peptides and extraction of valuable deuterium incorporation data for those peptides. Taken together, these results indicate that including ion mobility separation in HX MS analyses further improves the mass spectrometry portion of such experiments. Copyright © 2008 John Wiley & Sons, Ltd.
Effect of age and food intake on dietary carbon turnover recorded in sheep wool
Authors: Zazzo Antoine , Moloney Aidan P. , Monahan Frank J. , Scrimgeour Charlie M. , Schmidt Olaf
Published: August 2008

We present the results of a series of controlled feeding experiments with sheep, designed to investigate the effects of age and level of food intake on the kinetics of incorporation of the dietary carbon signal into wool. Four different groups of three sheep each, ranging in age from 6 to 78 months, were fed a C3 diet and switched to a C4 diet for up to 250 days. Different quantities of the same C4 diet were provided to each group, in order to achieve different growth rates (high, low, and no growth). Wool was repeatedly shorn from each animal and processed for δ13C analyses. Results show that newly grown wool does not start recording the isotope composition of the new diet immediately after the diet‐switch. The time‐lag varies according to the age of the animal, from 6 ± 1 days in lambs to up to 15 ± 4 days in the older ewes. Wool from fast‐growing lambs approached equilibrium faster than that from slow‐growing lambs and young ewes, with old ewes being the slowest. However, 3 weeks after the diet‐switch, the differences in wool δ13C values between the four different groups of animals were relatively small and represented less than 15% of the isotopic difference between the two diets. These results suggest that a single equation can be used to reconstruct previous diets for animals of different age, provided that the diet is similar and all individuals are in positive protein balance. Copyright © 2008 John Wiley & Sons, Ltd.
Effects of acidification on carbon and nitrogen stable isotopes of benthic macrofauna from a tropical coral reef
Authors: Kolasinski Joanna , Rogers Karyne , Frouin Patrick
Published: August 2008

Stable isotope analyses are widely used to determine trophic levels in ecological studies. We have investigated the effects of carbonate removal via acidification on the stable carbon and nitrogen isotopic composition of 33 species of tropical benthic macrofauna, and we report guidelines for standardizing this procedure for higher taxa in tropical coral reef ecosystems. Many tropical benthic invertebrates are small in size, and therefore body tissue isolation (separating organic carbon from inorganic structures) is difficult and time‐consuming. Literature reviews of invertebrate studies show a lack of consistent procedures and guidelines for preparation techniques, especially for carbonate removal via acidification of whole individuals. We find that acidification decreases the δ13C values of samples containing carbonate, with shifts ranging from 0.21 to 3.20‰, which can be related to CaCO3 content (assessed by a carbonate proxy), justifying acid pre‐treatment. Carbonate‐containing taxa benefiting from acidification included Amphinomida, Terebellida (Annelida), Anomura, Brachyura, Caridea, Amphipoda, Tanaidacea (Arthropoda) and Edwardsiida (Cnidaria). The δ13C shifts of samples containing no carbonate varied up to 0.02 ± 0.20‰. As this induced δ13C shift was lower than the range of an average trophic level shift (0.5 to 1‰), we conclude that acid pre‐treatment is unnecessary. Carbonate‐free taxa consisted of Eunicida, Phyllodocida (Annelida) and Mollusca. We note minimal impact of acidification on δ15N values except for Brachyura, which showed a shift of 0.83 ± 0.46‰, which is still lower than a single trophic level shift (2.9–3.8‰). We conclude that for trophic level studies, both the δ13C and the δ15N of carbonate‐rich macrofauna can be determined from the same acidified sample. Copyright © 2008 John Wiley & Sons, Ltd.
Robotic choledochojejunostomy with intracorporeal Roux limb construction
Authors: Kohn Geoffrey P. , Overby D. Wayne , Martinie John B.
Published: August 2008

Background

Biliary surgery can often be very complex, with difficult access issues, small structures to be manipulated and sutured and proximity to major vessels. Additionally, biliary surgery is often reoperative. All of these issues have the potential to be aided by the use of technology which provides three‐dimensional (3D) vision, excellent illumination and access, with steady instrument control under maximal magnification. The robot is such a technology which is currently available.

Methods

The Da Vinci® robot was used to perform a robotic choledochojejunostomy, using five ports and a totally intracorporeal technique.

Results

Two patients were studied. There were no conversions to open operation. There was no mortality. One patient experienced a postoperative bile leak, which was successfully managed endoscopically.

Conclusions

Robotic choledochojejunostomy with intracorporeal Roux‐en‐Y anastomosis is a feasible operation with a definite learning curve. It has potential benefits to the patient. Copyright © 2008 John Wiley & Sons, Ltd.
Robotic‐assisted radical cystectomy
Authors: Khan Mohammad Shamim , Shah Shahzad Saleem , Hemel Ashok , Rimington Peter , Dasgupta Prokar
Published: August 2008

Objective

To evaluate the emerging role of robotic‐assisted radical cystectomy (RARC) in the management of bladder cancer.

Methods

Review of the published literature on robotic‐assisted radical cystectomy, including data from our cystectomy series of 30 patients.

Results

Nearly 150 procedures have been performed worldwide. The benefits of robotic‐assisted operations are similar to those of laparoscopically‐performed procedures. RARC appears to be technically safe, oncologically and functionally equivalent to open (ORC) and laparoscopic radical cystectomy (LRC). However, RARC offers superior ergonomics and better vision. These benefits come at extra initial capital expenditure and subsequent higher maintenance costs.

Conclusion

With the rapid spread of robotics, it is likely that RARC will become the standard of care in units with access to the technology. Copyright © 2008 John Wiley & Sons, Ltd.
An efficient soft tissue characterization algorithm from in vivo indentation experiments for medical simulation
Authors: Kim Jung , Ahn Bummo , De Suvranu , Srinivasan Mandayam A.
Published: August 2008

Background

Realistic virtual reality surgical training simulators require an accurate biomechanical model of in vivo soft tissue behaviour. One of the challenges in modelling is to characterize soft tissue properties incorporating the experimental measurements of organ behaviour.

Method

Organ measurements were collected from intra‐abdominal organs of pigs, using a robotic indenter and a force transducer. The constitutive model was fitted to the in vivo data using the Levenberg–Marquardt optimization algorithm, combined with a three‐dimensional non‐linear finite element (FE) simulation.

Results

This paper presents an integrated framework for measuring, modelling and calibrating organs' material properties and provides parameters for modelling pigs' intra‐abdominal organs.

Conclusion

The calibrated mechanical models are suitable for computing accurate reaction forces on surgical instruments and for computing the deformations of organs. They also provide a useful benchmark for measuring the realism of real‐time tissue models used in virtual reality‐based surgical trainers. Copyright © 2008 John Wiley & Sons, Ltd.
Periphyton contribution to nitrogen dynamics in the discharge from a wastewater treatment plant
Authors: Ogura Asami , Takeda Kazuhiko , Nakatsubo Takayuki
Published: August 2008

To evaluate the importance of periphyton to nitrogen dynamics in the discharge from wastewater treatment plants (WWTPs), we examined changes in total and inorganic nitrogen content downstream from a WWTP on the Kurose River in Hiroshima Prefecture, Japan. At 0.7 km downstream of the WWTP (point A), NH4+−N was the dominant form of inorganic nitrogen, but concentrations decreased rapidly to 5 km downstream (point B). In contrast, no significant change in the [NO2−+ + NO3−]−N concentration was observed between the two points. Total nitrogen (TN) load decreased significantly between the two points, suggesting that sorption and/or denitrification occurred in the river channel. Potential rates of nitrogen sorption and transformation by periphyton were determined in a loboratory experiment in which changes in the nitrogen content of river water were examined in an acrylic chamber with periphyton. Nitrification and nitrogen removal occurred mainly in the periphyton. The contributions of periphyton activity to TN and NH4+−N decrease in the field, as estimated from the results of the laboratory experiments, were 6–18% and 23–72%, respectively. These results suggest that periphyton plays an important role in decreasing NH4+−N concentration in the discharge from wastewater treatment plants.
Teachers' use of curriculum to support students in writing scientific arguments to explain phenomena
Authors: McNeill Katherine L.
Published: August 2008

The role of the teacher is essential for students' successful engagement in scientific inquiry practices. This study focuses on teachers' use of an 8‐week chemistry curriculum that explicitly supports students in one particular inquiry practice, the construction of scientific arguments to explain phenomena in which students justify their claims using evidence and reasoning. Participants included 6 teachers and 568 students. Videotapes, teacher questionnaires, and student pre‐ and posttests were analyzed to develop case studies that characterized the support the teachers provided their students for scientific argumentation and subsequent student learning. Patterns from the case studies suggest that one particular instructional practice, the way teachers defined scientific argumentation, characterized teachers' support and influenced the other practices they used in their classrooms. In some cases, the teachers' definitions of scientific argumentation did not align with the intended learning goal in the curriculum materials. These teachers' greater simplification of this complex inquiry practice resulted in decreased learning gains in terms of students' ability to write scientific arguments to explain phenomena using appropriate evidence and reasoning. Educative curriculum materials can have a positive impact on teachers' classroom support for scientific argumentation, but how the teachers use these materials influences student learning. © 2008 Wiley Periodicals, Inc. Sci Ed 93: 233–268, 2009
Conversion‐coating treatment applied to in situ TiB2p reinforced AlSi‐alloy composite for corrosion protection
Authors: Sun H. H. , Wang H. W. , Chen D. , Ma N. H. , Li X. F.
Published: August 2008

In this work, continuous conversion coatings on the surface of in situ TiB2 particulate reinforced A356 composite were formed successfully by cerium surface treatment for the first time. Scanning electron microscope (SEM) analysis showed that the conversion coatings were inhomogeneous and could be divided into two types of regions, namely, fine crack region and noncrack region. Many cerium‐rich nano‐nodules were uniformly distributed in the whole coatings. Energy dispersive spectroscopy (EDS) analysis testified that the crack coatings mainly covered the interdendritic sites occupied by TiB2 particulates and Si phases. X‐ray photoelectron spectroscopy (XPS) analysis indicated that the conversion coatings were composed of CeO2, Ce2O3, Ce(OH)4, Ce(OH)3, and a little amount of Al2O3. The electrochemical polarization tests showed that the cerium‐conversion treatment markedly improved the corrosion resistance of in situ TiB2p/A356 composite in chloride environment, and the protection degree of the coatings was superior to that of conventional chromate‐conversion coating. According to these results, the formation mechanism of cerium‐conversion coatings was discussed. Copyright © 2008 John Wiley & Sons, Ltd.
Adsorption of trisilylamine on the Si(100) surface
Authors: Bush B. W. , Marquis A. H. , Egwu O. , Craig J. H.
Published: August 2008

Adsorption of trisilylamine (TSA) on the Si(100) surface has been studied using temperature programmed desorption (TPD) and time‐of‐flight electron stimulated desorption (TOFESD). TPD spectra exhibit the presence of three desorption states denoted by β1, β2, and β3 associated with the presence of a mono‐, di‐, and tri‐hydride state respectively. This behavior is identical with previously observed desorption studies resulting from atomic hydrogen adsorption, indicating that the nitrogen species in the adsorbate has minimal impact on the surface structure of the hydride. Preliminary electron irradiation studies are reported and indicate that the formation of a thin silicon nitride layer is induced as a result of the irradiation. Copyright © 2008 John Wiley & Sons, Ltd.
Changes of surface chemical structure and composition of phenolphthalein poly(ether sulfone) in different radiations
Authors: Pei Xianqiang , Sun Xiaojun , Wang Qihua
Published: August 2008

To understand the different action mechanisms of space irradiation on polymers, phenolphthalein poly(ether sulfone) (PES‐C) blocks were irradiated by electrons and atomic oxygen. The changes in surface chemical structure and composition of PES‐C in different radiations were studied by attenuated total‐reflection FTIR (FTIR‐ATR) and XPS. It was found that PES‐C was prone to be influenced by space irradiation. Electron and atomic oxygen irradiation can destroy the molecular chain of PES‐C and result in changes of surface chemical composition of the polymer. But due to the different nature of the radiation sources, electron irradiation induced the carbonization of the polymer surface, while atomic oxygen irradiation resulted in the oxidation of the polymer surface. Besides this, the sulfone structure was reduced or oxidized depending on the nature of the radiation sources. So, different radiation sources might influence the surface chemical structure and composition of polymers differently. Copyright © 2008 John Wiley & Sons, Ltd.
Risk‐aversion in water allocation policies in semi‐arid regions
Authors: Ford David N. , Andersen Jennifer M.
Published: August 2008

The critical role of water infrastructure systems in sustainable development and the limitations of supply management have increased the importance of demand management in meeting water needs. As an integral part of demand management in water‐stressed regions, water allocation policies address the competition among user groups for scarce water resources. This paper presents a dynamic simulation model of a water system in semi‐arid regions and analyses the effectiveness of allocation policies in meeting two objectives: satisfy current demands and preserve adequate supply for future use. Field data identified risk aversion in managers, as reflected in their allocation policies, as a potentially important influence on policy effectiveness. The model was tested with data and policies from the island of Cyprus. Sensitivity analyses reveal the important role of managerial expectations and responses to supply and demand in determining system performance. Analysis of water allocation policies revealed that the level of risk in policies shifts performance between satisfying current demands and protecting against future drought conditions. Potential changes by managers for improved performance and research needs are discussed. Copyright © 2008 John Wiley & Sons, Ltd.
Photoactivatable GFP tagging cassettes for protein‐tracking studies in the budding yeast Saccharomyces cerevisiae
Authors: Vorvis Christina , Markus Steven M. , Lee Wei‐Lih
Published: August 2008

Yeast cell biologists use a variety of fluorescent protein tags for determining protein localization and for measuring protein dynamics using fluorescence recovery after photobleaching (FRAP). Although many modern fluorescent proteins, such as those with photoactivatable and photoconvertible characteristics, have been developed, none has been exploited for studies in budding yeast. We describe here the construction of yeast‐tagging vectors containing photoactivatable green fluorescent protein (PA–GFP) for analysis of protein behaviour. We tagged two yeast proteins, Erg6p and Num1p, with PA–GFP and demonstrated specific photoactivation of the fusion proteins in live cells. Fluorescence intensity measurements showed that a short 5 s exposure to 413 nm light is sufficient to produce the maximum level of activated GFP fluorescence. Local photoactivation of cortical Num1p‐PA–GFP showed movement of the marked proteins, providing new insights into the behaviour of Num1p at the cell cortex. Since photoactivation can be achieved using standard mercury arc illumination, the PA–GFP tag represents a convenient and economical way to determine protein dynamics in the cell. Thus, the tagging modules should facilitate protein‐tracking studies in a wide variety of cell biological processes in yeast. Published in 2008 by John Wiley & Sons, Ltd.
Exometabolic and transcriptional response in relation to phenotype and gene copy number in respiration‐related deletion mutants of S. cerevisiae
Authors: Pir Pınar , Kırdar Betül , Hayes Andrew , Önsan Z. İlsen , Ülgen Kutlu Ö. , Oliver Stephen G.
Published: August 2008

The transcriptional and metabolic impact of deleting one or both copies of a respiration‐related gene has been studied in glucose‐limited chemostats. Integration of literature information on phenotype with our exometabolome and transcriptome data enabled the identification of novel relationships between gene copy number, transcriptional regulation and phenotype. We found that the effect of complete respiratory deficiency on transcription was limited to downregulation of genes involved in oxidoreductase activity and iron assimilation. Partial respiratory deficiency had no significant impact on gene transcription. Changes in the copy number of two transcription‐factor genes, HAP4 and MIG1, had a major impact on genes involved in mitochondrial function. Regulation of respiratory chain components encoded in the nucleus and mitochondria appears to be divided between Hap4p and Oxa1p, respectively. Similarly, repression of respiration may be imposed by the action of Mig1p and Mba1p on nuclear and mitochondrial gene expression, respectively. However, it is not clear whether Oxa1p and Mba1p regulate mitochondrial gene expression via their interaction with mitochondrial ribosomes or by some indirect means. The phenotype of nuclear petite mutants may not simply be due to the absence of respiration; e.g. Oxa1p or Bcs1p may play a role in the regulation of ribosome assembly in the nucleolus. Integration between respiration and cell growth may also result from the action of a single transcription factor. Thus, Hap4p targets genes that are required for respiration and for fitness in nutrient‐limited conditions. This suggests that Hap4p may enable cells to adapt to nutrient limitation as well as diauxy. Copyright © 2008 John Wiley & Sons, Ltd.
Global gene expression profile of Saccharomyces cerevisiae induced by dictamnine
Authors: Guo Na , Yu Lu , Meng Rizeng , Fan Junwen , Wang Dacheng , Sun Guang , Deng Xuming
Published: August 2008

Dictamnine, a natural plant product, has been reported to have antimicrobial activity against bacteria and fungi; however, the dictamnine response mechanisms of microorganisms are still poorly understood. We have shown that dictamnine has antimicrobial activities against the model fungus Saccharomyces cerevisiae, with a minimum inhibitory concentration (MIC) value of 64 µg/ml. Commercial oligonucleotide microarrays were used to determine the global transcriptional response of S. cerevisiae triggered by treatment with dictamnine. We interpreted our microarray data using the hierarchical clustering tool, T‐profiler. Several major transcriptional responses were induced by dictamnine. The first was the induced environmental stress response, mainly under the control of the Msn2p and Msn4p transcription factors, and the repressed environmental stress response in genes containing the PAC (RNA polymerase A and C box) and rRPE (ribosomal RNA processing element) motifs. The second was the Upc2p‐mediated response involved in lipid biosynthesis. The third comprised the PDR3‐ and RPN4‐mediated responses involved in multidrug resistance (MDR). Finally, the TBP‐mediated response was induced with dictamnine treatment. TBP is an essential general transcription factor involved in directing the transcription of genes. Quantitative real‐time RT–PCR was performed on selected genes to verify the microarray results. Furthermore, morphological transitions during dictamnine exposure to S. cerevisiae L1190 (MATa/α) were examined, using confocal laser microscopy. Copyright © 2008 John Wiley & Sons, Ltd.
History, epidemiology and regional diversities of urolithiasis
Authors: López Michelle , Hoppe Bernd
Published: August 2008

Archeological findings give profound evidence that humans have suffered from kidney and bladder stones for centuries. Bladder stones were more prevalent during older ages, but kidney stones became more prevalent during the past 100 years, at least in the more developed countries. Also, treatment options and conservative measures, as well as ‘surgical’ interventions have also been known for a long time. Our current preventive measures are definitively comparable to those of our predecessors. Stone removal, first lithotomy for bladder stones, followed by transurethral methods, was definitively painful and had severe side effects. Then, as now, the incidence of urolithiasis in a given population was dependent on the geographic area, racial distribution, socio-economic status and dietary habits. Changes in the latter factors during the past decades have affected the incidence and also the site and chemical composition of calculi, with calcium oxalate stones being now the most prevalent. Major differences in frequency of other constituents, particularly uric acid and struvite, reflect eating habits and infection risk factors specific to certain populations. Extensive epidemiological observations have emphasized the importance of nutritional factors in the pathogenesis of urolithiasis, and specific dietary advice is, nowadays, often the most appropriate for prevention and treatment of urolithiasis.
Psycho‐social Counselling in Predictive Genetic Testing for Cancer: The Association Between Number of Supportive Sessions and Client Characteristics as Assessed by Psycho‐social Workers
Authors: Mollema E. D. , Smets E. M. A. , Richard M. E. , Schiphorst A. M. , Leschot N. J.
Published: August 2008

Given the increased demand on genetic services, it is important to identify clients who may require relatively more extensive psychosocial support. This paper describes which client characteristics, as assessed in the first psycho‐social counselling session, were associated with requiring relatively more psycho‐social support (≥3 sessions) in the process of predictive testing for cancer. The study population consisted of 244 counselees for hereditary cancer. Data were derived from an electronic data‐base, used by psycho‐social workers for the systematic registration of relevant details of each counselling session. Data were analysed for two respective groups: (A) patients who had a known mutation in the family and (B) patients with an as yet unknown mutation in the family. Results show that two or more psychosocial sessions were given if the information derived from the first session indicated the client to have childhood experiences with cancer (in group A), to experience the family role and/or the psychological impact as burdensome (in both groups) or to experience the social impact as burdensome (in group B). We conclude that the first assessment by a psychosocial worker already provides valuable information on the psychological support needs of patients. These findings provide insight into possible problem areas for clients dealing with predictive genetic testing.
Women and Smokers Have Elevated Urinary F2‐Isoprostane Metabolites: A Novel Extraction and LC–MS Methodology
Authors: Taylor Alan W. , Bruno Richard S. , Traber Maret G.
Published: August 2008

F2‐Isoprostanes (F2‐IsoPs), regio‐ and stereoisomers of prostaglandin F2α (PGF2α), and urinary F2‐IsoP metabolites including 2,3‐dinor‐5,6‐dihydro‐8‐iso‐PGF2α [2,3‐dinor‐8‐iso‐PGF1α (2,3‐dinor‐F1)] and 2,3 dinor‐8‐iso‐PGF2α (2,3‐dinor‐F2), have all been used as biomarkers of oxidative stress. A novel method was developed to measure these biomarkers using a single solid phase extraction (SPE) cartridge, separation by HPLC, and detection by negative mode selected reaction monitoring (SRM) mass spectrometry (MS), using authentic standards of PGF2α; 8‐iso‐PGF2α; 2,3‐dinor‐F1 and 2,3‐dinor‐F2 to identify specific chromatographic peaks. The method was validated in a population of healthy, college‐aged nonsmokers (n = 6 M/8F) and smokers (n = 6 M/5F). Urinary F2‐IsoP concentrations were ~0.2–1.5 μg/g creatinine, 2,3‐dinor‐F1 was ~1–3 μg/g and 2,3‐dinor‐F2 was ~3–5 μg/g. Additional F2‐IsoPs metabolites were identified using SRM. The sum of all urinary F2‐IsoP metabolites was 50–100 μg/g creatinine indicating their greater abundance than F2‐IsoPs. Women had higher F2‐IsoP metabolite concentrations than did men (MANOVA, main effect P = 0.003); cigarette smokers had higher concentrations than did nonsmokers (main effect P = 0.036). For men or women, respectively, smokers had higher metabolite concentrations than did nonsmokers (P < 0.05). Thus, our method simultaneously allows measurement of urinary F2‐IsoPs and their metabolites for the determination of oxidative stress.
The near pressure field of co-axial subsonic jets
Authors: TINNEY C. E. , JORDAN P.
Published: August 2008

Results are presented from pressure measurements performed in the irrotational near field of unbounded co-axial jets. Measurements were made for a variety of velocity and temperature ratios, and configurations both with and without serrations on the secondary nozzle lip. The principal objective of the study is to better understand the near pressure field of the jet, what it can tell us regarding the underlying turbulence structure, and in particular how it can be related to the source mechanisms of the flow.

A preliminary analysis of the axial, temporal and azimuthal structure of the pressure field shows it to be highly organized, with axial spatial modes (obtained by proper orthogonal decomposition) which resemble Fourier modes. The effects of serrations on the pressure fluctuations comprise a global reduction in level, a change in the axial energy distribution, and a modification of the evolution of the characteristic time scales.

A further analysis in frequency–wavenumber space is then performed, and a filtering operation is used to separate the convective and propagative footprints of the pressure field. This operation reveals two distinct signatures in the propagating component of the field: a low-frequency component which radiates at small angles to the flow axis and is characterized by extensive axial coherence, and a less-coherent high-frequency component which primarily radiates in sideline directions. The serrations are found to reduce the energy of the axially coherent propagating component, but its structure remains fundamentally unchanged; the high-frequency component is found to be enhanced. A further effect of the serrations involves a relative increase of the mean-square pressure level of the acoustic component – integrated over the measurement domain – with respect to the hydrodynamic component. The effect of increasing the velocity and temperature of the primary jet involves a relative increase in the acoustic component of the near field, while the hydrodynamic component remains relatively unchanged: this shows that the additional acoustic energy is generated by the mixing region which is produced by the interaction of the inner and the outer shear layers, whereas the hydrodynamic component of the near field is primarily driven by the outer shear layer.
Gravity currents with residual trapping
Authors: HESSE M. A. , ORR F. M. , TCHELEPI H. A.
Published: August 2008

Motivated by geological carbon dioxide (CO2) storage, we present a vertical-equilibrium sharp-interface model for the migration of immiscible gravity currents with constant residual trapping in a two-dimensional confined aquifer. The residual acts as a loss term that reduces the current volume continuously. In the limit of a horizontal aquifer, the interface shape is self-similar at early and at late times. The spreading of the current and the decay of its volume are governed by power-laws. At early times the exponent of the scaling law is independent of the residual, but at late times it decreases with increasing loss. Owing to the self-similar nature of the current the volume does not become zero, and the current continues to spread. In the hyperbolic limit, the leading edge of the current is given by a rarefaction and the trailing edge by a shock. In the presence of residual trapping, the current volume is reduced to zero in finite time. Expressions for the up-dip migration distance and the final migration time are obtained. Comparison with numerical results shows that the hyperbolic limit is a good approximation for currents with large mobility ratios even far from the hyperbolic limit. In gently sloping aquifers, the current evolution is divided into an initial near-parabolic stage, with power-law decrease of volume, and a later near-hyperbolic stage, characterized by a rapid decay of the plume volume. Our results suggest that the efficient residual trapping in dipping aquifers may allow CO2 storage in aquifers lacking structural closure, if CO2 is injected far enough from the outcrop of the aquifer.
Experimental and numerical investigation of the kinematic theory of unsteady separation
Authors: WELDON M. , PEACOCK T. , JACOBS G. B. , HELU M. , HALLER G.
Published: August 2008

We present the results of a combined experimental and numerical study of flow separation in the unsteady two-dimensional rotor-oscillator flow. Experimentally detected material spikes are directly compared to separation profiles predicted from numerical shear-stress and pressure data, using a recent kinematic theory of unsteady separation. For steady, periodic, quasi-periodic and random forcing, fixed separation is observed, and experimental observations and theoretical predictions are in close agreement. The transition from fixed to moving separation is also reported.
Interharmonics in internal gravity waves generated by tide-topography interaction
Authors: KOROBOV ALEXANDER S. , LAMB KEVIN G.
Published: August 2008

The dynamics and spectrum of internal gravity waves generated in a linearly stratified fluid by tidal flow over a flat-topped ridge are investigated at five different latitudes using an inviscid two-dimensional numerical model. The resulting wave field includes progressive freely propagating waves which satisfy the dispersion relation, and forced waves which are trapped non-propagating oscillations with frequencies outside the internal wave band. The flow is largely stable with respect to shear instabilities, and, throughout the runs, there is a negligibly small amount of overturning which is confined to the highly nonlinear regions along the sloping topography and where tidal beams reflect from the boundaries. The wave spectrum exhibits a self-similar structure with prominent peaks at tidal harmonics and interharmonics, whose magnitudes decay exponentially with frequency. Two strong subharmonics are generated by an instability of tidal beams which is particularly strong for near-critical latitudes where the Coriolis frequency is half the tidal frequency. When both subharmonics are within the free internal wave range (as in cases 0°–20° N), they form a resonant triad with the tidal harmonic. When at least one of the two subharmonics is outside of the range (as in cases 30°–40° N) the observed instability is no longer a resonant triad interaction. We argue that the two subharmonics are generated by parametric subharmonic instability that can produce both progressive and forced waves. Other interharmonics are produced through wave–wave interactions and are not an artefact of Doppler shifting as assumed by previous authors. As the two subharmonics are, in general, not proper fractions of the tidal frequency, the wave–wave interactions are capable of transferring energy to a continuum of frequencies.
Visualizing the geometry of state space in plane Couette flow
Authors: GIBSON J. F. , HALCROW J. , CVITANOVIĆ P.
Published: August 2008

Motivated by recent experimental and numerical studies of coherent structures in wall-bounded shear flows, we initiate a systematic exploration of the hierarchy of unstable invariant solutions of the Navier–Stokes equations. We construct a dynamical 105-dimensional state-space representation of plane Couette flow at Reynolds number Re = 400 in a small periodic cell and offer a new method of visualizing invariant manifolds embedded in such high dimensions. We compute a new equilibrium solution of plane Couette flow and the leading eigenvalues and eigenfunctions of known equilibria at this Re and cell size. What emerges from global continuations of their unstable manifolds is a surprisingly elegant dynamical-systems visualization of moderate-Re turbulence. The invariant manifolds partially tessellate the region of state space explored by transiently turbulent dynamics with a rigid web of symmetry-induced heteroclinic connections.
An experimental investigation of mixing mechanisms in shock-accelerated flow
Authors: TOMKINS C. , KUMAR S. , ORLICZ G. , PRESTRIDGE K.
Published: August 2008

An experimental investigation of mixing mechanisms in a shock-induced instability flow is described. We obtain quantitative two-dimensional maps of the heavy-gas (SF6) concentration using planar laser-induced fluorescence for the case of a shock-accelerated cylinder of heavy gas in air. The instantaneous scalar dissipation rate, or mixing rate, χ, is estimated experimentally for the first time in this type of flow, and used to identify the regions of most intense post-shock mixing and examine the underlying mechanisms. We observe instability growth in certain regions of the flow beginning at intermediate times. The mixing rate results show that while these unstable regions play a significant role in the mixing process, a large amount of mixing also occurs by mechanisms directly associated with the primary instability, including gradient intensification via the large-scale strain field in a particular non-turbulent region of the flow.
Turbulent fluctuations above the buffer layer of wall-bounded flows
Authors: JIMÉNEZ JAVIER , HOYAS SERGIO
Published: August 2008

The behaviour of the velocity and pressure fluctuations in the logarithmic and outer layers of turbulent flows is analysed using spectral information and probability density functions from channel simulations at Reτ≤2000. Comparisons are made with experimental data at higher Reynolds numbers. It is found, in agreement with previous investigations, that the intensity profiles of the streamwise and spanwise velocity components have logarithmic ranges that are traced to the widening spectral range of scales as the wall is approached. The same is true for the pressure, both theoretically and observationally, but not for the normal velocity or for the tangential stress cospectrum, although even those two quantities have structures with lengths of the order of several hundred times the wall distance. Because the logarithmic range grows longer as the Reynolds number increases, variables which are ‘attached’ in this sense scale in the buffer layer in mixed units. These results give strong support to the attached-eddy scenario proposed by Townsend (1976), but they are not linked to any particular eddy model. The scaling of the outer modes is also examined. The intensity of the streamwise velocity at fixed y/h increases with the Reynolds number. This is traced to the large-scale modes, and to an increased intensity of the ejections but not of the sweeps. Several differences are found between the outer structures of different flows. The outer modes of the spanwise and wall-normal velocities in boundary layers are stronger than in internal flows, and their streamwise velocities penetrate closer to the wall. As a consequence, their logarithmic layers are thinner, and some of their logarithmic slopes are different. The channel statistics are available electronically at http://torroja.dmt.upm.es/ftp/channels/.
Finite-amplitude river dunes
Authors: COLOMBINI M. , STOCCHINO A.
Published: August 2008

The linear and weakly nonlinear stability of a uniform flow in an infinitely wide open channel with erodible bottom is studied. Under suitable conditions the flow is found to be unstable, leading to the formation of dunes and antidunes. At a linear level, the corresponding regions of existence are presented and compared with experimental data. A weakly nonlinear analysis is then performed in a neighbourhood of the critical conditions for dune and antidune formation. The analysis shows that, for values of the ratio of the shear velocity to the depth-averaged velocity of practical interest, dune bifurcation is supercritical, whereas antidune bifurcation is subcritical. The latter result suggests a possible interpretation of the plane–antidune transition, where plane bed and antidune configurations are observed to coexist for the same values of the flow and the sediment parameters. The supercritical behaviour of the dune bifurcation allows for the prediction of an equilibrium amplitude that successfully compares with the amplitudes measured in laboratory experiments.
Global stability of swept flow around a parabolic body: connecting attachment-line and crossflow modes
Authors: MACK CHRISTOPH J. , SCHMID PETER J. , SESTERHENN JÖRN L.
Published: August 2008

The global linear stability of a three-dimensional compressible flow around a yawed parabolic body of infinite span is investigated using an iterative eigenvalue method in conjunction with direct numerical simulations. The computed global spectrum shows an unstable branch consisting of three-dimensional boundary layer modes whose amplitude distributions exhibit typical characteristics of both attachment-line and crossflow modes. In particular, global eigenfunctions with smaller phase velocities display a more pronounced structure near the stagnation line, reminiscent of attachment-line modes while still featuring strong crossflow vortices further downstream. This analysis establishes a link between the two prevailing instability mechanisms on a swept parabolic body which, so far, have only been studied separately and locally. A parameter study shows maximum modal growth for a spanwise wavenumber of β = 0.213, suggesting a preferred disturbance length scale in the sweep direction.
Very viscous horizontal convection
Authors: CHIU-WEBSTER S. , HINCH E. J. , LISTER J. R.
Published: August 2008

‘Horizontal convection’ arises when a temperature variation is imposed along a horizontal boundary of a finite fluid volume. Here we study the infinite-Prandtl-number limit relevant to very viscous fluids, motivated by the study of convection in glass furnaces. We consider a rectangular domain with insulating conditions on the sides and bottom, and a linear temperature gradient on the top. We describe steady states for a large range of aspect ratio A and Rayleigh number Ra, and find universal scalings for the transition from small to large Rayleigh numbers. At large Rayleigh number, the top boundary-layer thickness scales as Ra−1/5, with the circulation and heat flux scaling as Ra1/5. These scalings hold for both rigid and shear-free boundary conditions on the top or on the other boundaries, which is initially surprising, but is because the return flow is dominated by a horizontal intrusion immediately beneath the top boundary layer. A downwelling plume also forms on one side, but because of strong stratification in the interior, the volume flux it carries is much smaller than that of the horizontal intrusion, decaying as the inverse of the depth below the top boundary. The fluid in the plume detrains into the interior and then returns to the top boundary, thus forming a ‘filling box’. We find analytic solutions for the interior temperature and streamfunction and match them to a similarity solution for the plume. At depths comparable to the length of the top boundary the streamfunction has O(1) values and the temperature variations scale as 1/Ra. Transient calculations with a large, but finite, Prandtl number, show how the steady state is reached from hot and cold initial conditions.
Fine-scale statistics of temperature and its derivatives in convective turbulence
Authors: EMRAN M. S. , SCHUMACHER J.
Published: August 2008

We study the fine-scale statistics of temperature and its derivatives in turbulent Rayleigh–Bénard convection. Direct numerical simulations are carried out in a cylindrical cell with unit aspect ratio filled with a fluid with Prandtl number equal to 0.7 for Rayleigh numbers between 107 and 109. The probability density function of the temperature or its fluctuations is found to be always non-Gaussian. The asymmetry and strength of deviations from the Gaussian distribution are quantified as a function of the cell height. The deviations of the temperature fluctuations from the local isotropy, as measured by the skewness of the vertical derivative of the temperature fluctuations, decrease in the bulk, but increase in the thermal boundary layer for growing Rayleigh number, respectively. Similarly to the passive scalar mixing, the probability density function of the thermal dissipation rate deviates significantly from a log-normal distribution. The distribution is fitted well by a stretched exponential form. The tails become more extended with increasing Rayleigh number which displays an increasing degree of small-scale intermittency of the thermal dissipation field for both the bulk and the thermal boundary layer. We find that the thermal dissipation rate due to the temperature fluctuations is not only dominant in the bulk of the convection cell, but also yields a significant contribution to the total thermal dissipation in the thermal boundary layer. This is in contrast to the ansatz used in scaling theories and can explain the differences in the scaling of the total thermal dissipation rate with respect to the Rayleigh number.
Evolution of nonlinear processes in a hypersonic boundary layer on a sharp cone
Authors: BOUNTIN D. , SHIPLYUK A. , MASLOV A.
Published: August 2008

Nonlinear processes in a hypersonic boundary layer on a sharp cone are considered using the bicoherence method. The experiments are performed for a Mach number M∞ = 5.95 with introduction of artificial wave packets at the frequency of the second mode. It is shown that the basic mechanism of nonlinear interaction at the location of the maximum r.m.s. voltage fluctuation is the subharmonic resonance; all nonlinear interactions in the maximum r.m.s. voltage fluctuation layer are related to the second mode of disturbances; nonlinear processes above and below that layer are much more intense than those in it. The effect of artificial disturbances on nonlinear interactions in the boundary layer is shown to be insignificant.