bluuebunny/crossref_metadata_2025_split huggingface dataset:
Morphological effects of different channel‐forming discharges in a gravel‐bed river
Authors: Surian Nicola , Mao Luca , Giacomin Matteo , Ziliani Luca 
Published: March 2009

AbstractThe study analyses the morphological response of a gravel‐bed river to discharges of different magnitude (from moderate events that occur several times a year to a 12‐year flood) and so defines the range of formative discharges for single morphological units (channels, bars, islands) and a range of magnitude of morphological activity from the threshold discharges for gravel transport and minor bar modification up to flows causing major morphological changes.The study was conducted on the Tagliamento River, a large gravel‐bed river in north‐eastern Italy, using two different methods, analysis of aerial photographs and field observation of painted gravel particles. The available photographs (five flights from August 1997 to November 2002) and the two commissioned flights (June 2006 and April 2007) do not define periods with a single flood event, but the intervals are short enough (11 to 22 months) to have a limited number of flood events in each case. The fieldwork, which involved cross‐section survey, grain‐size analysis and observation of painted sediments, complemented the aerial surveys by allowing analysis of channel response to single flood events.Substantial morphological changes (e.g. bank erosion of several tens of metres up to more than 100 m) associated with flood events with a recurrence interval between 1·1 year and 12 years have been documented. Multiple forming discharges were defined based on the activity of different morphological units. Discharges equal to 20–50% of the bankfull discharge are formative for the channels, whereas the bankfull discharge (1·1 year flood in this case of the Tagliamento River) is formative for low bars. Larger floods, but still relatively frequent (with a recurrence interval less than five years), are required for full gravel transport on high bars and significant morphological changes of islands. Copyright © 2009 John Wiley & Sons, Ltd.
Shortcomings of discontinuous‐pressure finite element methods on a class of transient problems
Authors: Jog C. S. , Kumar Rakesh 
Published: March 2009

AbstractPast studies that have compared LBB stable discontinuous‐ and continuous‐pressure finite element formulations on a variety of problems have concluded that both methods yield solutions of comparable accuracy, and that the choice of interpolation is dictated by which of the two is more efficient. In this work, we show that using discontinuous‐pressure interpolations can yield inaccurate solutions at large times on a class of transient problems, while the continuous‐pressure formulation yields solutions that are in good agreement with the analytical solution. Copyright © 2009 John Wiley & Sons, Ltd.
Tuning of the visual word processing system: Distinct developmental ERP and fMRI effects
Authors: Brem Silvia , Halder Pascal , Bucher Kerstin , Summers Paul , Martin Ernst , Brandeis Daniel 
Published: March 2009

AbstractVisual tuning for words vs. symbol strings yields complementary increases of fast occipito‐temporal activity (N1 or N170) in the event‐related potential (ERP), and posterior–anterior gradients of increasing word‐specific activity with functional magnetic resonance imaging (fMRI) in the visual word form system (VWFS). However, correlation of these coarse ERP and fMRI tuning responses seems limited to the most anterior part of the VWFS in adult and adolescent readers (Brem et al. [ 2006]: Neuroimage 29:822–837). We thus focused on fMRI tuning gradients of young readers with their more pronounced ERP print tuning, and compared developmental aspects of ERP and fMRI response tuning in the VWFS. Children (10.3 y, n = 19), adolescents (16.2 y, n = 13) and adults (25.2 y, n = 18) were tested with the same implicit reading paradigm using counterbalanced ERP and fMRI imaging. The word‐specific occipito‐temporal N1 specialization, its corresponding source activity, as well as the integrated source activity (0–700 ms) were most prominent in children and showed a marked decrease with age. The posterior–anterior fMRI gradient of word‐specific activity instead which was fully established in children did not develop further, but exhibited a dependence on reading skills independent of age. To conclude, prominent developmental dissociation of the ERP and fMRI tuning patterns emerged despite convergent VWFS localization. The ERP response may selectively reflect fast visual aspects of print specialization, which become less important with age, while the fMRI response seems dominated by integrated task‐ and reading‐related activations in the same regions. Hum Brain Mapp, 2009. © 2009 Wiley‐Liss, Inc.
Effect of plasmonic nanostructures and nanofilms on fluorescence resonance energy transfer
Authors: Szmacinski Henryk , Ray Krishanu , Lakowicz Joseph R. 
Published: March 2009

AbstractWe investigate the effect of silver nanostructures and nanofilms on fluorescence resonance energy transfer (FRET). Thin layers of poly (vinyl alcohol) of 10 or 20 nm with homogenously distributed donor (Cy3) and acceptor (Cy5) molecules were coated on silver islands and continuous silver films. Several geometrical configurations were studied with multiple donor‐acceptor (D‐A) samples with various acceptor concentrations. The acceptor concentrations were adjusted to yield FRET efficiencies from about 10 to 92% on bare glass surfaces. Time‐resolved fluorescence spectroscopy was used to determine the energy transfer efficiency and the relative transfer rate. It was found that the relative transfer rate increased 2‐fold in the presence of continuous silver films and about 25‐fold in presence of silver island films. The largest enhancements in the energy transfer efficiency, up to 90%, were observed for low acceptor concentrations (large donor‐acceptor separations). To a first approximation, observed changes in FRET efficiencies were explained by an increase of the quantum yield of the donor molecules in the presence of silver islands. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Label free optical sensor for Avidin based on single gold nanoparticles functionalized with aptamers
Authors: Hernandez Frank Jeyson , Dondapati Srujan Kumar , Ozalp V. Cengiz , Pinto Alessandro , O'Sullivan Ciara K. , Klar Thomas A. , Katakis Ioannis 
Published: March 2009

AbstractOptical spectroscopy of a single gold nanoparticle, functionalized with an aptamer, is used to sense the specific binding of avidin. Herewith, the field of single noble metal nanoparticle biosensors is extended to the important field of aptamer based assays. The sensitivity of this initial, but not yet optimized apta‐nano‐sensor is in the range of 20 nM. Due to its nanoscopic size, this single nanoparticle based apta‐sensor may be used in nanoscopic volumes such as in array type assays or even inside cells. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A novel hydrophilic poly(lactide‐co‐glycolide)/lecithin hybrid microspheres sintered scaffold for bone repair
Authors: Shi Xuetao , Wang Yingjun , Ren Li , Lai Chen , Gong Yihong , Wang Dong‐An 
Published: March 2009

AbstractNovel 3‐D porous scaffolds made of sintered poly(lacide‐co‐glycolide) (PLGA)/lecithin hybrid microspheres (PLGA/Lec‐SMS) were developed and investigated. The addition of lecithin in PLGA bulk successfully managed the desired hydrophilic modification without sacrificing bulk properties. The outcomes were verified with infrared (ATR‐FTIR) spectroscopy, X‐ray photoelectron spectroscopy (XPS), and contact angle analyses. Specifically, this model of scaffold gained significant improvement in mechanical (mainly compressive) strength upon an optimization of lecithin fractions aligning with sintering conditions. Given a perspective of bone tissue engineering use, human fetal osteoblasts were seeded into a series of these PLGA/Lec‐SMS scaffolds upon which key parameters of cytocompatibility and osteoconductivity (including cell viability, alkaline phosphatase activity, calcium secretion, and osteogenic genes expression) were assessed. Osteoblasts seeded on PLGA scaffolds with 5 wt % lecithin demonstrated high cell viability and alkaline phosphatase activity. Moreover, elevated lecithin also enhanced the expression of type I collagen. Taken together, these results suggest PLGA/Lec‐SMS are promising scaffolds for bone repair. © 2009 Wiley Periodicals, Inc. J Biomed Mater Res, 2010
Preparation and evaluation of thiolated chitosan scaffolds for tissue engineering
Authors: Li Zhe , Cen Lian , Zhao Li , Cui Lei , Liu Wei , Cao Yilin 
Published: March 2009

AbstractThiolated chitosan (TCS) was proposed as a promising candidate as scaffold material for tissue engineering. However, a continuous exploration of such material as a three‐dimensional (3D) scaffold with controllable design of microstructure as well as mechanical strength was necessitated. The current study was thus carried out to substantiate such potential of TCS. Thioglycolic acid (TGA) was first introduced on the side chain of chitosan (CS) via the amide bond formation between COOH groups of TGA and NH2 groups of CS. Composite TCS/CS scaffolds with different ratios were prepared via freeze‐drying under different temperatures to optimize the structural properties. The microstructure of the scaffolds was observed by scanning electron microscopy (SEM), and tensile strength of scaffolds was measured. Both the TCS/CS proportion and freezing temperature affected the microstructure and mechanical property of scaffolds, which in turn rendered effects on the growth of cultured fibroblasts. Scaffolds obtained from the TCS/CS proportion of 7:3 and a freezing temperature of −20°C had the maximum tensile strength with a pore distribution ranging from a few to several hundred micrometers. The preferential growth of fibroblasts on this scaffold was also demonstrated. Hence, results in this study would offer valuable information on the preparation of suitable TCS scaffolds for tissue engineering. © 2009 Wiley Periodicals, Inc. J Biomed Mater Res, 2010
Docking to heme proteins
Authors: Röhrig Ute F. , Grosdidier Aurélien , Zoete Vincent , Michielin Olivier 
Published: March 2009

AbstractIn silico screening has become a valuable tool in drug design, but some drug targets represent real challenges for docking algorithms. This is especially true for metalloproteins, whose interactions with ligands are difficult to parametrize. Our docking algorithm, EADock, is based on the CHARMM force field, which assures a physically sound scoring function and a good transferability to a wide range of systems, but also exhibits difficulties in case of some metalloproteins. Here, we consider the therapeutically important case of heme proteins featuring an iron core at the active site. Using a standard docking protocol, where the iron–ligand interaction is underestimated, we obtained a success rate of 28% for a test set of 50 heme‐containing complexes with iron‐ligand contact. By introducing Morse‐like metal binding potentials (MMBP), which are fitted to reproduce density functional theory calculations, we are able to increase the success rate to 62%. The remaining failures are mainly due to specific ligand–water interactions in the X‐ray structures. Testing of the MMBP on a second data set of non iron binders (14 cases) demonstrates that they do not introduce a spurious bias towards metal binding, which suggests that they may reliably be used also for cross‐docking studies. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009
Diagnostic assay of chromium (VI) in the ex vivo fluid of the urine of a smoker using a fluorine‐doped handmade sensor
Authors: Ly Suw Young , Kim Min Joon 
Published: March 2009

AbstractA voltammetric diagnosis of a chromium (VI) ion was investigated using a fluorine‐doped graphite pencil electrode. Square wave (SW) stripping working conditions were attained at a high range of 0.051–0.45 mg L−1 and a microrange of 0.05–0.4 µg L−1 in a 0.1 M NH4H2PO4 electrolyte solution, at a relative standard deviation of 1.68% (RSD, n=15), using 10.0 µg L−1 Cr(VI). A fast experimental time was used only for the 120 sec SW accumulation time. An analytical detection‐limit (DL) of 0.008 µg L−1 was attained. DL appeared to be more sensitive than common voltammetric and spectrophotometric assays. The developed sensor was applied to tap water and the urine of a smoker. It was found that the methods can be applicable for in vivo fluid or medicinal diagnosis. J. Clin. Lab. Anal. 23:82–87, 2009. © 2009 Wiley‐Liss, Inc.
Evaluation of metalloproteinases 2 and 9 and their inhibitors in physiologic and pre‐eclamptic pregnancy
Authors: Montagnana Martina , Lippi Giuseppe , Albiero Alessandro , Scevarolli Silvia , Salvagno Gian Luca , Franchi Massimo , Guidi Gian Cesare 
Published: March 2009

AbstractMatrix metalloproteinases (MMPs) are a family of zinc and calcium‐dependent endopeptidases involved in remodeling and physiological homeostasis of extracellular matrix (ECM). The metalloproteinases activity is predominantly modulated by specific tissue inhibitors of matrix metalloproteinases (TIMPs). The balance between MMPs and TIMPs is likely to play an important role in remodeling uterine arteries in pregnancy, and it may represent means by which vasodilatation is maintained in later pregnancy. Moreover, increased levels of MMPs and in particular MMP‐2 play a role in the vascular alterations induced by hypertension. The aim of this study was the evaluation of MMP‐2 and ‐9, along with their inhibitors TIMP‐1 and ‐2, in pre‐eclamptic women compared with normotensive pregnancy and non‐pregnant women. Fourteen pre‐eclamptic women were compared with 37 normotensive women in different gestational age and 21 non‐pregnant women. Multiplexed sandwich enzyme‐linked immunosorbent assay was used to measure MMPs and TIMPs simultaneously. MMP‐2 levels were significantly higher in pre‐eclamptic women vs. both non‐pregnant and physiologic pregnant women. MMP‐9 concentrations were significantly higher in physiologic pregnant vs. non‐pregnant women. The serum levels of TIMP‐1 were significantly higher in pre‐eclamptic vs. both non‐pregnant and physiologic pregnant women. TIMP‐2 values were higher in physiologic pregnant women and pre‐eclamptic women vs. non‐pregnant women. A positive correlation between MMP‐9 values and gestational age was observed in normal pregnant women. Results of the present investigation confirm that MMP‐2 and TIMP‐1 values are significantly higher in preeclampsia. We confirm that the modification of the fine balance between MMPs and their inhibitors plays a greater role in the structural and functional vascular changes of women with complicated pregnancies. J. Clin. Lab. Anal. 23:88–92, 2009. © 2009 Wiley‐Liss, Inc.
Lipid peroxidation and antioxidant enzyme activities in infertile men: correlation with semen parameter
Authors: Ben Abdallah Fatma , Dammak Ines , Attia Hamadi , Hentati Basma , Ammar‐Keskes Leila 
Published: March 2009

AbstractThe aim of this study was to investigate the oxidative stress status and antioxidant enzyme activities in infertile men's semen and to determine their relationship with spermatozoa characteristics. Four groups of infertile men, normozoospermic (n=9), azoospermic (n=13), oligoasthenozoospermic (n=38), and asthenozoospermic (n=42), were tested for malonaldialdehyde (MDA) concentration and catalase (CAT) and superoxide dismutase (SOD) activities in semen using spectrophotometric methods. We found that MDA levels in semen and SOD activity in seminal plasma (SP) were significantly higher in oligoasthenozoospermic and asthenozoospermic groups compared with normozoospermic group. In contrast, the mean values of CAT activity were not significantly different in all groups. We found positive correlations between semen MDA concentration and SOD activity (P<0.01). MDA levels in sperm pellet and in SP were also positively correlated with mobility grade b (P<0.01), acrosome anomalies (P<0.01), and residual cytoplasmic droplets (P<0.05). In contrast, SOD activity in SP was negatively correlated with sperm concentration and normal morphology (P<0.05). Similarly, CAT activity in SP was negatively correlated with sperm and leukocyte concentrations (P<0.05). In conclusion, our results suggest that the evaluation of oxidative status and antioxidant defenses may be taken as an important tool for diagnosis and treatment of male infertility. J. Clin. Lab. Anal. 23:99–104, 2009. © 2009 Wiley‐Liss, Inc.
Detection of C1236T, G2677T/A, and C3435T polymorphism ofMDR1by amplification refractory mutation system PCR
Authors: Chen Bing , Fang Jie , Zhang Weixia , Jin Zhao , Yu Zichen , Cai Weimin 
Published: March 2009

AbstractC1236T, G2677T/A, and C3435T polymorphism of the multidrug resistance (MDR1) gene have substantial impact on expression or activity of P‐glycoprotein (P‐gp). We developed new methods based on amplification refractory mutation system (ARMS) to detect these polymorphisms. Tetra‐primers amplification in a single tube was established to detect C1236T and C3435T polymorphism. For G2677T/A polymorphism, a two‐step allele‐specific amplification method was used.MDR1genotypes of 177 Chinese subjects were determined by the methods we established. The methods we established were verified with gene sequencing. Gene frequencies of 1236C and 1236T were 37.8 and 62.2%, respectively; gene frequencies of 2677G, 2677T and 2677A were 44.1, 38.4 and 17.5%, respectively; the gene frequencies of 3435C and 3435T were 65.0 and 35.0%, respectively. The results were similar with other studies on Oriental subjects. The methods we established are simple, accurate, and economical, and can provide reliable approaches for determiningMDR1polymorphism. J. Clin. Lab. Anal. 23:110–116, 2009. © 2009 Wiley‐Liss, Inc.
Associations of IgG N‐linked oligosaccharide chains and proteases in sera of prostate cancer patients with and without α2‐macroglobulin deficiency
Authors: Kanoh Yuhsaku , Egawa Shin , Baba Shiro , Akahoshi Tohru 
Published: March 2009

AbstractWe previously reported on a number of cases of metastatic prostate cancer (PCa) in which serum α2‐macroglobulin (α2M) levels were markedly decreased to less than 20 mg/dl (α2M deficiency). All PCa patients with α2M deficiency had multiple bone metastases. Proteases in ten PCa patients with and without α2M deficiency were studied and compared against ten healthy controls in order to elucidate the relationships between changes in sugar chain structure and neoplasia. We assessed the relationship between ratios of Fr4 to Fr1 and Fr2 (Fr4/Fr1+Fr2 ratios) of oligosaccharide chains, and ratios of free prostate‐specific antigen (PSA) to total PSA (F/T ratios), and serum levels of matrix‐metalloproteinase‐2 (MMP‐2) in PCa progression. Measurement of serum α2M concentration was performed by laser nephelometry. Serum PSA and MMP‐2 levels were determined by enzyme immunoassay and free PSA by radioimmunoassay. N‐linked oligosaccharides of human serum immunoglobulin G were analyzed using fluorophore‐associated carbohydrate electrophoresis. In those PCa patients with α2M deficiency: (a) serum α2M and F/T ratios were lower (P<0.05) and (b) Fr4/Fr1+Fr2 ratios and serum MMP‐2 levels were higher when compared with those PCa patients without α2M deficiency. There was a significant correlation between Fr4/Fr1+Fr2 ratios and F/T ratios or serum MMP‐2 levels in PCa with α2M deficiency (P<0.05). Therefore, these markers may serve as an auxiliary serum tumor marker for monitoring of the bone metastases or progression of disease in PCa. J. Clin. Lab. Anal. 23:125–131, 2009. © 2009 Wiley‐Liss, Inc.
Serum prolidase activity and oxidative status in patients with bronchial asthma
Authors: Cakmak Alpay , Zeyrek Dost , Atas Ali , Celik Hakim , Aksoy Nurten , Erel Ozcan 
Published: March 2009

AbstractAsthma is a disease where there is an accumulation of collagen in the reticular basal membrane of the airway leading to chronic inflammation. The enzyme prolidase plays an important role in the breakdown of collagen and the breakdown of intracellular protein especially in the final stage when peptides and dipeptides contain a high level of proline. To evaluate the relationship between prolidase activity and oxidative status in asthma patients. Comparison was made between 42 patients diagnosed with bronchial asthma and 32 healthy children of similar age and gender. Serum prolidase activity was measured spectrophotometrically. Oxidative status was determined using total antioxidant capacity (TAC) and total oxidant status (TOS) measurement. The prolidase activity of the asthma patient group was statistically significant compared with the control group (P≤0.001). TAC and TOS levels in the asthma patient group were higher than the control group (P≤0.001, P≤0.002, respectively). No correlation was found between the prolidase and oxidative levels of the two groups. A positive correlation was determined between the prolidase activity and TAC in the asthma patient group (P≤0.001, r=0.501). The prolidase enzyme activity, which plays a role in the collagen turnover, was low in the asthma patients; therefore, their collagen metabolism had undergone a change and this indicates that there may be an effect on the accumulation of collagen in the reticular basal membrane. Moreover, the high level of TOS indicates that these patients were exposed to severe oxidative stress with an increased TAC response. J. Clin. Lab. Anal. 23:132–138, 2009. © 2009 Wiley‐Liss, Inc.
Detection of Paracoccidioides brasiliensis gp43 Gene in Sputa by Loop‐Mediated Isothermal Amplification Method
Authors: Tatibana B. T. , Sano A. , Uno J. , Kamei K. , Igarashi T. , Mikami Y. , Miyaji M. , Nishimura K. , Itano E. N. 
Published: March 2009

AbstractThe fungus Paracoccidioides brasiliensis is the pathogen of paracoccidioidomycosis (PCM), a systemic mycosis prevalent in Latin America. The loop‐mediated isothermal amplification method (LAMP) was used in this study to detect the presence of P. brasiliensis in sputa samples from patients with chronic PCM, suspected PCM, and a negative control. The target P. brasiliensis gp43 gene was amplified in less than 4 hr in 11 of 18 sputa samples tested. The LAMPmethod had the advantage of speed and simplicity compared with the classic diagnostic methods such as the histopathological test or biological material culture and did not require sophisticated technical apparatus. It would be an important aid in cases where immediate treatment would mean patient survival, especially in immune‐suppressed patients. J. Clin. Lab. Anal. 23:139–143 2009. © 2009 Wiley‐Liss, Inc.