bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational study of shock‐wave interaction with solid obstacles using immersed boundary methods
Authors: Chaudhuri A. , Hadjadj A. , Sadot O. , Glazer E. 
Published: September 2011

SUMMARYIn this study, an immersed boundary (IB) method based on a direct forcing is coupled with a high‐order weighted‐essentially non‐oscillatory (WENO) scheme to simulate fluid–solid interaction (FSI) problems with complex geometries. The IB is a general simulation method for FSI, whereas the WENO is an efficient scheme for fluid flow simulations and shock waves, and both of them work on regular cartesian grids. The effectiveness and the accuracy of the coupled scheme are first analyzed on well‐documented supersonic test problems for a wide range of Mach numbers. The results are in good agreement with both analytical and experimental data. A comprehensive analysis of the interaction of the moving shock through an array of cylinder matrix is then conducted by varying the number of cylinders in the matrix block while keeping the same opening passage. The relaxation length between two adjacent columns of cylinders is kept identical to study uniquely the effect of surface‐to‐volume ratio of the obstacle matrix. It is shown that the configuration with higher surface‐to‐volume ratio produces more post‐shock flow instabilities downstream of the matrix block. The complex shock/shock and shock/vortex interactions are well resolved by the present computation. It is being observed that after the passage of the shock through the cylinder matrix, eddies of different length scales are generated, but the later stage of shock/vortex and shocklet/vortexlet interactions are different for the two cases. The analysis of the PSD of the total kinetic energy globally conforms to Richardson's inviscid cascade. An intermittent peaked PDF of downstream instantaneous vorticity field is obtained in the limit of Re →  ∞ . The baroclinic production of vorticity is found to be feeble as previously founded by Sun and Takayama (J. Fluid Mech. 2003; 478:237–256). Copyright © 2011 John Wiley & Sons, Ltd.
Free fetal DNA levels in patients at risk of preterm labour
Authors: Illanes S. , Gomez R. , Fornes R. , Figueroa‐Diesel H. , Schepeler M. , Searovic P. , Serra R. , Perez A. , Nien J. K. 
Published: September 2011

ObjectivesOur main goals were to evaluate the capability of ffDNA to increase the accuracy in prediction of preterm labour by cervical length and to explore potential mechanisms of disease associated with this pathology.MethodsFifty‐six women, with male fetus, with cervical length assessment at between 22 and 24 weeks were included in the study and divided in 1) Short cervix (<15 mm) delivered at term (T = 20); 2) Short cervix delivered before 37 weeks (PT = 14); and 3) Patients who delivered at term with normal cervical length (N = 22). Maternal plasma samples were collected between 22 and 24 weeks of gestational age. PCR using primers against DYS14 gene were used to quantified ffDNA in plasma samples. Statistical analysis was done using ANOVA test and spearman´s correlation.ResultsThe median gestational age at delivery for short cervix groups was 26 + 1 for PT and 39 + 3 for T. The control group delivered at a median gestational age of 39 + 6 weeks. ffDNA was detectable in all cases. There was no significant difference between the 3 groups. Similarly, no significant correlation was observed between ffDNA and gestational age at delivery (r = −0.23; p = 0.07).ConclusionsffDNA does not increase the accuracy of short cervix at between 22 and 24 weeks for the prediction of preterm labour. Copyright © 2011 John Wiley & Sons, Ltd.
Autonomic healing and welding by interdiffusion of dangling chains in a weak gel
Authors: Yamaguchi Masayuki , Maeda Rika , Kobayashi Ryota , Wada Tadashi , Ono Susumu , Nobukawa Shogo 
Published: September 2011

AbstractEntanglement couplings of dangling chains in a weak gel are found to be applicable to the design of a self‐repairing polymer. It is confirmed that a cleavage applied using a razor blade is healed at room temperature without any manual intervention. Further, the healing efficiency is improved when the molecular weight of a prepolymer, which affects the length of dangling chains, is high. Because the healing occurs by interdiffusion of dangling chains, the relation between ambient temperature and glass transition temperature determines the time required for healing. In other words, a soft rubbery material whose glass transition temperature is lower than room temperature shows immediate healing. A weak gel whose tensile modulus is 100 MPa at room temperature, i.e. a leather‐like material, shows healing even at room temperature in a relatively short time (ca 2 h). Finally, when a weak gel shows crystallinity, healing occurs at a temperature above the melting point. Because the material has a permanent network structure, it will not show macroscopic flow even after exposure to high temperature. Copyright © 2011 Society of Chemical Industry
Identification of novel secreted proteases during extracellular proteolysis by dermatophytes at acidic pH
Authors: Sriranganadane Dev , Waridel Patrice , Salamin Karine , Feuermann Marc , Mignon Bernard , Staib Peter , Neuhaus Jean‐Marc , Quadroni Manfredo , Monod Michel 
Published: September 2011

AbstractThe dermatophytes are a group of closely related fungi which are responsible for the great majority of superficial mycoses in humans and animals. Among various potential virulence factors, their secreted proteolytic activity attracts a lot of attention. Most dermatophyte‐secreted proteases which have so far been isolated in vitro are neutral or alkaline enzymes. However, inspection of the recently decoded dermatophyte genomes revealed many other hypothetical secreted proteases, in particular acidic proteases similar to those characterized in Aspergillus spp. The validation of such genome predictions instigated the present study on two dermatophyte species, Microsporum canis and Arthroderma benhamiae. Both fungi were found to grow well in a protein medium at acidic pH, accompanied by extracellular proteolysis. Shotgun MS analysis of secreted protein revealed fundamentally different protease profiles during fungal growth in acidic versus neutral pH conditions. Most notably, novel dermatophyte‐secreted proteases were identified at acidic pH such as pepsins, sedolisins and acidic carboxypeptidases. Therefore, our results not only support genome predictions, but demonstrate for the first time the secretion of acidic proteases by dermatophytes. Our findings also suggest the existence of different pathways of protein degradation into amino acids and short peptides in these highly specialized pathogenic fungi.
Identifying psychological morbidity among people with cancer using the Hospital Anxiety and Depression Scale: time to revisit first principles?
Authors: Carey Mariko , Noble Natasha , Sanson‐Fisher Robert , Mackenzie Lisa 
Published: September 2011

AbstractBackgroundThe aim of this review was to describe the findings and methodological quality of studies, which sought to validate the Hospital Anxiety and Depression Scale (HADS) against the Structured Clinical Interview for DSM in cancer populations. We also sought to compare the cut points recommended by these validation studies with the way in which the HADS is currently used to determine prevalence of psychological morbidity in cancer populations.MethodsAn electronic database search was conducted of Medline from 1983 to October 2010 for validation studies of the HADS in cancer populations. Reference lists of HADS reviews were hand searched. To examine which cut points are commonly used in cancer specific literature to identify the prevalence of psychological disorders, studies published in 2009 were identified via an electronic database search of Medline.ResultsTen studies, which validated the HADS against the Structured Clinical Interview for DSM in cancer patient populations, were found and examined in detail. None met all methodological criteria associated with the selection of a screening instrument. Recommendations for optimal HADS thresholds varied substantially across these studies. The most commonly used threshold for determining caseness in the 2009 literature on prevalence of psychological distress among patients with cancer was a subscale score of ≥ 8. This threshold was poorly supported by the results of the 10 cancer HADS validation studies examined.ConclusionsCaution is warranted in interpreting the results of prevalence studies using the HADS. There is a need to develop evidence about the optimal thresholds for defining caseness using the HADS. Copyright © 2011 John Wiley & Sons, Ltd.
Inhibition of Granzyme B by PI‐9 protects prostate cancer cells from apoptosis
Authors: Ray Manisha , Hostetter Daniel R. , Loeb Carly R.K. , Simko Jeffry , Craik Charles S. 
Published: September 2011

AbstractBACKGROUNDIn order for tumors to grow and proliferate, they must avoid recognition by immune cells and subsequent death by apoptosis. Granzyme B (GrB), a protease located in natural killer cells, initiates apoptosis in target cells. Inhibition of GrB by PI‐9, its natural inhibitor, can prevent apoptosis. Here we investigate whether PI‐9 protects prostate cancer cells from apoptosis.METHODSThe expression of PI‐9 was quantified by qPCR in several prostate cancer cell lines, and GrB activity was tested in each cell line. PI‐9 was overexpressed in LNCaP cells, which lack endogenous PI‐9. Apoptosis was induced by natural killer cells in LNCaP cells that either contained or lacked PI‐9, and the percent cell death was quantified. Lastly, PI‐9 levels were examined by qPCR and immunohistochemistry in prostate tumor tissue.RESULTSProstate cancer cell lines that expressed PI‐9 could inhibit GrB. Overexpression of PI‐9 protected LNCaP cells from natural killer cell‐mediated apoptosis. Examination of the levels of PI‐9 in tissue from prostate tumors showed that PI‐9 could be upregulated in low grade tumors and stochastically dysregulated in high grade tumors. Additionally, PI‐9 was found consistently in high grade prostatic intraepithelial neoplasia and atrophic lesions.CONCLUSIONSThese results indicate that overexpression of PI‐9 can protect prostate cancer cells from apoptosis, and this effect may occur in human prostate tumors. These findings imply that early prostatic inflammation may trigger this increase in PI‐9. This suggests that PI‐9 upregulation is needed early in tumor progression, before additional protective mechanisms are in place. Prostate 72:846–855, 2012. © 2011 Wiley Periodicals, Inc.
Integrative genomic, transcriptomic, and RNAi analysis indicates a potential oncogenic role for FAM110B in castration‐resistant prostate cancer
Authors: Vainio Paula , Wolf Maija , Edgren Henrik , He Tao , Kohonen Pekka , Mpindi John‐Patrick , Smit Frank , Verhaegh Gerald , Schalken Jack , Perälä Merja , Iljin Kristiina , Kallioniemi Olli 
Published: September 2011

AbstractBACKGROUNDCastration‐resistant prostate cancer (CRPC) represents a therapeutic challenge for current medications.METHODSIn order to explore the molecular mechanisms involved in CRPC progression and to identify new therapeutic targets, we analyzed a unique sample set of 11 CRPCs and 7 advanced tumors by array‐CGH and gene expression microarrays. The genome‐wide DNA and RNA data were integrated to identify genes whose overexpression was driven by their amplification. To assess the functional role of these genes, their expression was analyzed in a transcriptional data set of 329 clinical prostate cancers and the corresponding gene products were silenced using RNA interference in prostate cancer cells.RESULTSSix recurrent genetic targets were identified in the CRPCs; ATP1B1, AR, FAM110B, LAS1L, MYC, and YIPF6. In addition to AR and MYC, FAM110B emerged as a potential key gene involved in CRPC progression in a subset of the tumors. FAM110B was able to regulate AR signaling in prostate cancer cells and FAM110B itself was regulated by androgens. FAM110B siRNA inhibited the growth of prostate cancer cells in vitro, and this effect was substantially enhanced in androgen deficient conditions. Ectopic FAM110B expression in non‐cancerous epithelial prostate cells induced aneuploidy and impaired antigen presentation.CONCLUSIONSThe DNA/RNA gene outlier detection combined with siRNA cell proliferation assay identified FAM110B as a potential growth promoting key gene for CRPC. FAM110B appears to have a key role in the androgen signaling and progression of CRPC impacting multiple cancer hallmarks and therefore highlighting a potential therapeutic target. Prostate 72:789–802, 2012. © 2011 Wiley Periodicals, Inc.
Structural requirements essential for elastin coacervation: favorable spatial arrangements of valine ridges on the three‐dimensional structure of elastin‐derived polypeptide (VPGVG)n
Authors: Maeda Iori , Fukumoto Yoshiteru , Nose Takeru , Shimohigashi Yasuyuki , Nezu Takashi , Terada Yoshihiro , Kodama Hiroaki , Kaibara Kozue , Okamoto Kouji 
Published: September 2011

AbstractThe elastin precursor tropoelastin possesses a number of polymeric peptides with repeating 3–9 mer sequences. One of these is the pentapeptide Val‐Pro‐Gly‐Val‐Gly (VPGVG) present in almost all animal species, and its polymer (VPGVG)n coacervates just as does tropoelastin. In the present study, in order to explore the structural requirements essential for coacervation, (VPGVG)n and its shortened repeat analogs (VPGV)n, (VPG)n, and (PGVG)n were synthesized and their structural properties were investigated. In our turbidity measurements, (VPGVG)n demonstrated complete reversible coacervation in agreement with previous findings. The Gly5‐deleted polymer (VPGV)n also achieved self‐association, though the onset of self‐association occurred at a lower temperature. However, the dissociation of (VPGV)n upon temperature lowering was found to occur in a three‐step process; the Vali4‐Vali+11 structure arising in the VPGV polypeptide appeared to perturb the dissociation. No self‐association was observed for (VPG)n or (PGVG)n repeats. Spectroscopic measurements by CD, FT‐IR, and 1H‐NMR showed that the (VPGV)n and (VPG)n both assumed ordered structures similar to that of (VPGVG)n. These results demonstrated that VPGVG is a structural element essential to achieving the β‐spiral structure required for self‐association followed by coacervation, probably due to the ideal spatial arrangement of the hydrophobic Val residues. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.
Biochemical and mass spectrometry recognition of phospholipid–peptide complexes in wheat sprouts extract
Authors: Perni Stefano , Calzuola Isabella , Gianfranceschi Gian Luigi , Giavarini Flavio , Lucci Paolo , Pacetti Deborah , Frega Natale Giuseppe , Marsili Valeria 
Published: September 2011

AbstractTotal hydroalcoholic extract of wheat sprouts was treated with 90% cold acetone as a preliminary step directed to separate antioxidant peptides from antioxidant polyphenols. Surprisingly, the addition of acetone causes the formation of a yellow buoyant gelatinous drop that prevailingly contains peptides and phospholipids. In this context, evidences have been presented that support the hypothesis that peptides (and perhaps other active molecules) are complexed with phospholipids. In fact, the MS/MS analysis of some main ions, present in RP HPLC fractions of wheat sprout extract, generates several ions that correspond to molecular weight of phospholipids or phospholipid fragments. Moreover, several ions were detected that correspond to lysophosphatidylcholine or phosphatidylcholine–peptide complexes. The possibility that phospholipids can be complexed with peptides has been discussed in the light of potential involvement in the peptide bioavailability. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.
Assessing implicit large eddy simulation for two‐dimensional flow
Authors: Kent James , Thuburn John , Wood Nigel 
Published: September 2011

AbstractNumerical models of the atmosphere cannot resolve all relevant scales; the effects of unresolved scales on resolved scales must be represented by a subgrid model or parametrization. When the unresolved scales are similar in character to the resolved scales (as in three‐dimensional or layerwise two‐dimensional turbulence) the problem is essentially one of large eddy simulation. In this situation, one approach to subgrid modelling is implicit large eddy simulation (ILES), where the truncation errors of the numerical model attempt to act as the subgrid model. ILES has been shown to have some success for three‐dimensional turbulence, but the validity of the approach has not previously been examined for two‐dimensional or layerwise two‐dimensional flow, which is the regime relevant to weather and climate modelling. Two‐dimensional turbulence differs qualitatively from three‐dimensional turbulence in several ways, most notably in having upscale energy and downscale enstrophy transfers. The question is of practical importance since many atmospheric models in effect use the ILES approach, for example through the use of a semi‐Lagrangian advection scheme. In this paper a number of candidate numerical schemes are tested to determine whether their truncation errors can approximate the subgrid terms of the barotropic vorticity equation. Results show that some schemes can implicitly model the effects of the subgrid term associated with the stretching and thinning of vorticity filaments to unresolvable scales; the subgrid term is then diffusive and is associated with the downscale enstrophy transfer. Conservation of vorticity, by using a flux form scheme rather than advective form for advection of vorticity, was found to improve performance of a candidate ILES scheme. Some effects of the subgrid terms could not be captured by any of the schemes tested, whether using an implicit or a simple explicit subgrid model: none of the schemes tested is able to capture the upscale transfer of energy from unresolved to resolved scales. Copyright © 2011 Royal Meteorological Society and British Crown Copyright, the Met Office
THE IPOS FRAMEWORK: LINKING FISH SWIMMING PERFORMANCE IN ALTERED FLOWS FROM LABORATORY EXPERIMENTS TO RIVERS
Authors: Lacey R. W. Jay , Neary Vincent S. , Liao James C. , Enders Eva C. , Tritico Hans M. 
Published: September 2011

ABSTRACTThe current understanding of the effects of turbulence on the swimming performance of fish is primarily derived from laboratory experiments under pressurised flow swim tunnels and open‐channel flow facilities. These studies have produced valuable information on the swimming mechanics and behaviour of fish in turbulent flow. However, laboratory studies have limited representation of the flows fish experience in nature. The flow structure in rivers is imparted primarily by the highly heterogeneous nonuniform bed, and the flow is generally much more complex than in laboratory experiments. The goal of the current work is to direct future laboratory and field studies to adopt a common framework that will shape the integration of both approaches. This article outlines four characteristics of turbulent flow, which we suggest should be evaluated when generalising results from fish turbulent studies in both the laboratory and the field. The framework is based on four turbulence characteristics that are summarised under the acronym IPOS: intensity, periodicity, orientation and scale. Copyright © 2011 John Wiley & Sons, Ltd.
Improving representational competence using molecular simulations embedded in inquiry activities
Authors: Stieff Mike 
Published: September 2011

AbstractThe present article discusses the design and impact of computer‐based visualization tools for supporting student learning and representational competence in science. Specifically, learning outcomes and student representation use are compared between eight secondary classrooms utilizing The Connected Chemistry Curriculum and eight secondary chemistry using lecture‐based methods. Results from the quasi‐experimental intervention indicate that the curriculum and accompanying visualization tool yield only small to modest gains in student achievement on summative assessments. Analysis of student representation use on pre‐ and post‐assessments, however, indicate the students in Connected Chemistry classrooms are significantly more likely to use submicroscopic representations of chemical systems that are consistent with teacher and expert representation use. The affordances of visualization tools in inquiry activities to improve students' representational competence and conceptual understanding of content in the science classroom are discussed. © 2011 Wiley Periodicals, Inc. J Res Sci Teach 48: 1137–1158, 2011
A series of pregnancies in women with inherited metabolic disease
Authors: Langendonk Janneke G , Roos Jonathan CP , Angus Lindsay , Williams Monique , Karstens François PJ , de Klerk Johannes BC , Maritz Charlé , Ben‐Omran Tawfeg , Williamson Catherine , Lachmann Robin H , Murphy Elaine 
Published: September 2011

AbstractIn this case series we report 12 pregnancies, in women treated at four centres, illustrating some of the issues that may be encountered during pregnancy by women with inherited metabolic disease. We discuss how specific pregnancy, labour and delivery issues for mothers with methylmalonic acidemia, homocystinuria, propionic acidemia, glutaric acidemia type 1, ornithine transcarbamylase (OTC) deficiency and 3‐hydroxy‐3‐methylglutaric(HMG)‐CoA lyase deficiency were managed and the outcome for the mother and child in each case. Eight of the 12 pregnancies resulted in the successful delivery of a liveborn infant. Several women experienced decompensation of their condition during pregnancy or the post‐partum period. There was one maternal death in a women with 3‐hydroxy‐3‐methylglutaric(HMG)‐CoA lyase deficiency. Pre‐pregnancy counselling and co‐management of high risk medical patients by obstetricians and specialist physicians with an understanding of the relationship between pregnancy and inherited metabolic disease is essential.
Bifidobacterium adolescentis supplementation ameliorates visceral fat accumulation and insulin sensitivity in an experimental model of the metabolic syndrome
Authors: Chen Jinjin , Wang Ren , Li Xiao-Fang , Wang Rui-Liang 
Published: September 2011

The aim of the present study was to investigate the effects of Bifidobacterium adolescentis (Bif) supplementation on visceral fat accumulation and insulin sensitivity of the metabolic syndrome in HF-diet-fed rats. Adult male Wistar rats (n 10 per group) were fed four different experimental diets for 12 weeks as follows: standard diet; high-fat (HF) diet; a mix of HF diet and Bif; a mix of standard diet and Bif. Liver, mesenteric fat, epididymal fat, retroperitoneal fat, and inguinal fat, pancreas and triceps surae in all four groups of the rats were weighed, while liver steatosis and insulin sensitivity were evaluated at the end point of the study. As the number of intestinal Bifidobacterium species decreased obviously, fat pad weight and body weight increased significantly in the HF group compared with in the other three groups (P <0·05). Addition of Bif led to a reduction in body weight and fat pad weight (P <0·05). With an increase in liver weight, more severe steatosis of hepatocytes was observed in the HF group compared with in the other three groups. A significant decrease of the glucose infusion rate and pancreas weight was found in the HF group (P <0·05). This deleterious effect was alleviated when Bif was added to the diets. Bifidobacterium supplementation ameliorated visceral fat accumulation and insulin sensitivity of the metabolic syndrome in HF-diet-fed rats.