bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Highly Active Single‐Mutation Variant of P450BM3 (CYP102A1)
Authors: Whitehouse Christopher J. C. , Bell Stephen G. , Yang Wen , Yorke Jake A. , Blanford Christopher F. , Strong Anthony J. F. , Morse Edward J. , Bartlam Mark , Rao Zihe , Wong Luet‐Lok 
Published: June 2009

AbstractThe power of proline: Bold amino acid substitutions in sensitive protein regions are frequently unproductive, while more subtle mutations can be sufficient to bring about dramatic changes. But introducing proline at the residue next to the sulfur ligand in P450BM3 (CYP102A1) has the unexpected and desirable effect of enhancing the activity of this fatty acid hydroxylase with a broad range of non‐natural substrates, as illustrated by the figure.magnified image
Photocatalytic Redox Reactions for In‐Source Peptide Fragmentation
Authors: Qiao Liang , Bi Hongyan , Busnel Jean‐Marc , Waser Jerome , Yang Pengyuan , Girault Hubert H. , Liu Baohong 
Published: June 2009

AbstractIn‐source oxidation: In‐source photocatalytic redox reactions for inducing peptide fragmentation are achieved on a TiO2‐derived target plate during laser desorption ionization mass spectrometry in the presence of samples and glucose acting as both an electron donor and a hole conductor (see scheme).magnified imageIn‐source photocatalytic redox reactions based on a photosensitive target plate have been developed to realize peptide fragmentation during laser desorption ionization. Sample peptides and glucose are simply deposited on a spot of sintered TiO2nanoparticles. With the irradiation of UV laser on TiO2, electrons are excited from the valence to the conduction band, leaving oxidative holes and reductive electrons to drive various in‐source redox reactions. Glucose, working here as a hole scavenger and conductor, can favor both on‐surface reduction and long distance in‐plume oxidation, therefore inducing peptide fragmentation. CαC backbone cleavage was observed to generatea,xfragment decay, while the NCαbond cleavage was also sometimes obtained to inducec,zfragmentation, but was rather weaker. The former dissociation is believed to originate from oxidative routes induced by the valence band holes, based on the oxidation of nitrogen atom at the peptide backbone, including hydrogen‐radical abstraction and electron transfer. In contrast, the latter dissociation is supposed to be the result of reductive processes by the conduction band electrons, which are then rather similar to electron capture dissociation in tandem mass spectrometry.
In vivo visualization of transplanted pancreatic islets by MRI: comparison between in vivo, histological and electron microscopy findings
Authors: Marzola Pasquina , Longoni Biancamaria , Szilagyi Erzsebet , Merigo Flavia , Nicolato Elena , Fiorini Silvia , Paoli Giacomo T. , Benati Donatella , Mosca Franco , Sbarbati Andrea 
Published: June 2009

AbstractThe aim of the work was to compare in vivo MRI visualization of pancreatic islets labeled with clinical‐grade superparamagnetic iron oxide (SPIOs) contrast agents with ex vivo examination of liver tissue in an experimental model of marginal mass transplantation in rats. Seven hundred IEq (Islet Equivalent) from Wistar rats, labeled by incubation with Endorem® or Resovist®, were transplanted into Sprague–Dawley rats through the portal vein. Liver MR images of recipient rats were acquired at different time points (3–42 days) after transplantation. Animals were sacrificed during this period and their livers were excised and prepared for histology and electron microscopy. Hypointense spots originating from iron particles were observed in MR images. The number of separate spots was counted. Three days after transplantation one spot for every three or four transplanted islets was observed. Seven days after transplantation, histological sections showed the presence of iron within pancreatic islets. The time course of MR images showed a decrease in the number of spots, at 42 days, amounting to 65 and 22% of the initial value, for Resovist® and Endorem® respectively, while no immunopositive endocrine cells were detected in histological slices. The present work shows that pancreatic islets can be labeled using clinically approved SPIO contrast agents and visualized using in vivo MRI with high sensitivity, consistently with findings in the literature. Differently from reports in the literature, our findings indicate that iron particles could last in the liver for long periods, independently of the presence of intact pancreatic islets. Copyright © 2009 John Wiley & Sons, Ltd.
Topography and Recognition Imaging of Protein‐Patterned Surfaces Generated by AFM Nanolithography
Authors: Zhu Rong , Ebner Andreas , Kastner Markus , Preiner Johannes , Howorka Stefan , Hinterdorfer Peter 
Published: June 2009

AbstractNative‐protein nanolithography is combined with topography and recognition imaging to synergistically use AFM tips to write and image nanoscale protein patterns on a surface (see picture). The approach is validated with different feedback modes, using surface‐bound biotinylated bovine serum albumin (BSA) protein and AFM tips carrying streptavidin.magnified image
A Substrate‐Independent Approach for the Surface Immobilization of Oligonucleotides using Aldehyde Functionalized Surfaces
Authors: McGettrick James D. , Schofield Wayne C. E. , Garrod Richard P. , Badyal Jas Pal S. 
Published: June 2009

AbstractA highly efficient approach for the covalent immobilization of single‐strand DNA onto solid surfaces and their subsequent hybridization to complementary strands is described. This entails pulsed plasma deposition of poly(3‐vinylbenzaldehyde) followed by the Schiff‐base reaction. A range of substrates, including glass slides, silicon wafers, polystyrene microspheres, and single‐walled carbon nanotubes (SWNTs), are functionalized employing this methodology.
Growth of Polypyrrole‐like Films on Self‐Assembly Nanostructured Silicon Surfaces by PECVD
Authors: Yagüe Jose Luis , Agulló Núria , Borrós Salvador 
Published: June 2009

AbstractThe development of conducting polymers has become the aim of many research groups. This paper describes attempts to carry out a plasma polymerization of polypyrrole (PPy) on a nanostructured surface by attaching a 11‐(pyrrol‐1‐yl‐undecyl)dimethylchlorosilane molecule onto a silicon wafer surface in order to form a self‐assembled monolayer (SAM). The effect of the SAM in the polymerization process is also studied. Important differences in the polymer deposition are found whether or not the surface has been modified with a SAM. Atomic force microscopy (AFM) and time‐of‐flight secondary ion mass spectrometry (TOF‐SIMS) analyses are performed to study the morphology, deposition, and growth of polypyrrole.
Bridging Experiments and Simulations in Oblique Angle Polymerization
Authors: Cetinkaya Murat , Demirel Melik C. 
Published: June 2009

AbstractIn this paper, we report the growth of nanostructured poly(p‐xylylene) (PPX) films by oblique angle polymerization at various deposition angles. Additionally, a two‐dimensional computational (Monte Carlo) model is implemented to study the nanostructured growth process. The morphology of the nanostructured polymer films are characterized by atomic force microscopy and scanning electron microscopy. Based on the experimental results, a competitive growth model is proposed and quantified in terms of column geometry (i.e., diameter and height), column spacing (i.e., periodicity), and column packing (i.e., number of columns per unit area). We show that the nanostructured polymer growth obeys a universal power‐law scaling mechanism at various deposition angles. The computational model predicts similar nanostructured morphologies to the oblique angle polymerization obtained experimentally. Nanostructured polymer films may provide great advances in sensing and biomedical applications.
Partially Fluorinated Poly‐p‐xylylenes Synthesized by CVD Polymerization
Authors: Elkasabi Yaseen , Nandivada Himabindu , Chen Hsien‐Yeh , Bhaskar Srijanani , D'Arcy John , Bondarenko Lidija , Lahann Joerg 
Published: June 2009

AbstractThis paper describes partially fluorinated poly‐p‐xylylenes prepared by CVD polymerization. The synthesis, characterization, and surface modification of two partially fluorinated polymer coatings, namely poly(4,12‐dibromo‐1,1,9,9‐tetrafluoro‐p‐xylylene) (2) and poly(4‐heptadecafluorononanoyl‐p‐xylylene‐co‐p‐xylylene) (4), is described. Polymer 2 is synthesized from 4,12‐dibromo‐1,1,9,9‐tetrafluoro[2.2]paracyclophane (1), which is fluorinated at the aliphatic bridge, while 4‐heptadecafluorononanoyl[2.2]paracyclophane (3), which contains a perfluorinated keto group at the aromatic ring, is used to synthesize polymer 4. Furthermore, the keto‐functionalized polymer 4 introduces both extreme hydrophobicity and surface reactivity towards hydrazide‐containing ligands.
A review of family intervention guidelines for pediatric acquired brain injuries
Authors: Cole Wesley R. , Paulos Stephanie K. , Cole Carolyn A.S. , Tankard Carol 
Published: June 2009

AbstractPediatric acquired brain injury (BI) not only affects the child with the injury, but also greatly impacts their family. Studies suggest there are higher rates of caregiver and sibling psychological distress after a child in the family has sustained a BI. Also, family functioning after BI impacts the child's recovery. In reviewing the literature, we identified seven theoretical clinical guidelines for working with families of children and adolescents with BI. These clinical guidelines are as follows: (1) select developmentally appropriate interventions, (2) match the intervention to the family, (3) provide advocacy, (4) provide injury education, (5) focus on family realignment, (6) appropriately adjust the child's environment, and (7) provide skills training to the family and child. The existing research on family interventions for BI is reviewed within the context of these theoretical guidelines, and the empirical support for each guideline is subsequently evaluated using specific criteria for empirically supported treatments. Unfortunately, very few randomized controlled studies exist, and continued research is needed to classify all clinical guidelines as “efficacious.” In addition, continued research will aid in informing professionals of specific approaches to utilize when working with a family of a child with BI. Currently, clinicians and researchers can turn to the existing clinical guidelines to help address the numerous barriers posed by implementing and studying family interventions for pediatric BI. © 2009 Wiley‐Liss, Inc. Dev Disabil Res Rev 2009;15:159–166.
Behavior management for children and adolescents with acquired brain injury
Authors: Slifer Keith J. , Amari Adrianna 
Published: June 2009

AbstractBehavioral problems such as disinhibition, irritability, restlessness, distractibility, and aggression are common after acquired brain injury (ABI). The persistence and severity of these problems impair the brain‐injured individual's reintegration into family, school, and community life. Since the early 1980s, behavior analysis and therapy have been used to address the behavioral sequelae of ABI. These interventions are based on principles of learning and behavior that have been robustly successful when applied across a broad range of other clinical populations. Most of the research on behavioral treatment after ABI has involved clinical case studies or studies employing single‐subject experimental designs across a series of cases. The literature supports the effectiveness of these interventions across ages, injury severities, and stages of recovery after ABI. Recommended guidelines for behavior management include: direct behavioral observations, systematic assessment of environmental and within‐patient variables associated with aberrant behavior, antecedent management to minimize the probability of aberrant behavior, provision of functionally equivalent alternative means of controlling the environment, and differential reinforcement to shape positive behavior and coping strategies while not inadvertently shaping emergent, disruptive sequelae. This package of interventions requires direction by a highly skilled behavioral psychologist or therapist who systematically monitors target behavior to evaluate progress and guide treatment decisions. A coordinated multisite effort is needed to design intervention protocols that can be studied prospectively in randomized controlled trials. However, there will continue to be an important role for single subject experimental design for studying the results of individualized interventions and obtaining pilot data to guide subsequent randomized controlled trails. © 2009 Wiley‐Liss, Inc. Dev Disabil Res Rev 2009;15:144–151.
How soil conservation affects the catchment sediment budget – a comprehensive study in the north Ethiopian highlands
Authors: Nyssen Jan , Clymans Wim , Poesen Jean , Vandecasteele Ine , De Baets Sarah , Haregeweyn Nigussie , Naudts Jozef , Hadera Amanuel , Moeyersons Jan , Haile Mitiku , Deckers Jozef 
Published: June 2009

AbstractAn overall approach to assess the effectiveness of soil conservation measures at catchment scale is the comparison of sediment budgets before and after implementation of a catchment management programme. In the May Zeg‐zeg catchment (187 ha) in Tigray, north Ethiopia, integrated catchment management has been implemented since 2004: stone bunds were built in the whole catchment, vegetation was allowed to re‐grow on steep slopes and other marginal land, stubble grazing abandoned, and check dams built in gullies. Land use and management were mapped and analysed for 2000 and 2006, whereby particular attention was given to the quantification of changes in soil loss due to the abandonment of stubble grazing. Sediment yield was also measured at the catchment's outlet. A combination of decreased soil loss (from 14·3 t ha–1 y–1 in 2000 to 9·0 t ha–1 y–1 in 2006) and increased sediment deposition (from 5·8 to 7·1 t ha–1 y–1) has led to strongly decreased sediment yield (from 8·5 to 1·9 t ha–1 y–1) and sediment delivery ratio (from 0·6 to 0·21). This diachronic comparison of sediment budgets revealed that integrated catchment management is most effective and efficient and is the advisable and desirable way to combat land degradation in Tigray and other tropical mountains. Copyright © 2009 John Wiley & Sons, Ltd.
Remote sensing of volumetric storage changes in lakes
Authors: Smith Laurence C. , Pavelsky Tamlin M. 
Published: June 2009

AbstractThree‐dimensional remote sensing promises a giant leap forward for surface‐water hydrology in much the same way that radar altimetry transformed physical oceanography. However, the complex geometries of small terrestrial water bodies introduce difficulties, particularly with respect to trade‐offs between changing water depth and inundation area. We use in situ measurements of water‐surface stage (ΔH/dt) and remotely‐sensed area (A) to compute time varying storage changes (ΔS) in nine lakes of the Peace‐Athabasca Delta, Canada. Despite their identical geomorphic setting, regression slopes between ΔH and A vary significantly between lakes, primarily from a predictable ‘area‐effect’ but also small bathymetric variations between basins. On average, lateral contraction/expansion (versus stage adjustment) contributes as little as 7% (versus 93%) to as much as 76% (versus 24%) of overall storage change ΔS. We conclude that both surface‐area and ΔH/dt, rather than just either alone, must be measured to confidently estimate ΔS from space. Copyright © 2009 John Wiley & Sons, Ltd.
Pseudostress–velocity formulation for incompressible Navier–Stokes equations
Authors: Cai Zhiqiang , Wang Yanqiu 
Published: June 2009

AbstractThis paper presents a numerical algorithm using the pseudostress–velocity formulation to solve incompressible Newtonian flows. The pseudostress–velocity formulation is a variation of the stress–velocity formulation, which does not require symmetric tensor spaces in the finite element discretization. Hence its discretization is greatly simplified. The discrete system is further decoupled into an H(div) problem for the pseudostress and a post‐process resolving the velocity. This can be done conveniently by using the penalty method for steady‐state flows or by using the time discretization for nonsteady‐state flows. We apply this formulation to the 2D lid‐driven cavity problem and study its grid convergence rate. Also, computational results of the time‐dependent‐driven cavity problem and the flow past rectangular problem are reported. Copyright © 2009 John Wiley & Sons, Ltd.
A high‐fidelity low‐cost aerodynamic model using proper orthogonal decomposition
Authors: Mifsud M. J. , Shaw S. T. , MacManus D. G. 
Published: June 2009

AbstractIn this paper a high‐fidelity aerodynamic model is presented for use in parametric studies of weapon aerodynamics. The method employs a reduced‐order model obtained from the proper orthogonal decomposition (POD) of an ensemble of computational fluid dynamics (CFD) solutions with varying parameters. This decomposition produces an optimal linear set of orthogonal basis functions that best describe the ensemble of numerical solutions. These solutions are then projected onto this set of basis functions to provide a finite set of scalar coefficients that represent the solutions. A pseudo‐continuous representation of these projection coefficients is constructed, which allows predictions to be made of parameter combinations not in the original set of observations. The paper explores the performance of a few design‐of‐experiment approaches for the generation of the initial ensemble of computational experiments. Response surface construction methods based on parametric and non‐parametric models for the pseudo‐continuous representation of the projection coefficients are also evaluated. The model has been applied to two‐flow problems related to high‐speed weapon aerodynamics, inviscid flow around a flare‐stabilized hypersonic projectile and supersonic turbulent flow around a fin‐stabilized projectile with drooping nose control. Comparisons of model predictions with high‐fidelity CFD simulations suggest that the POD provides a reliable and robust approach to the construction of reduced‐order models. The practicality of the model is shown to be sensitive to the technique used to generate the ensemble of observations from which the model is constructed, while the accuracy of the approach depends on the pseudo‐continuous representation of the projection coefficients. Copyright © 2009 John Wiley & Sons, Ltd.
Big diameter tunnelling beneath low rock cover
Authors: Meyer Dieter , Brodbeck Frank , McKenzie Nick 
Published: June 2009

AbstractThe Clem Jones Tunnel (former North‐South Bypass Tunnel) is the first project to get underway as part of Brisbane's transport plan which aims to improve the urban road network. The total length to be excavated is 6.8 km which includes 4.8 km of driven tunnel and associated road connections. Construction commenced in August 2006 with project completion targeted well before the contractual completion date of October 2010. Due to the local geology, in particular the hard Brisbane tuff and Neranleigh‐Fernvale formation a combination of tunnel excavation methods are used. The majority of the tunnel is excavated by two tunnel boring machines in rock having a compressive strength of between 80 and 150 MPa. Ten roadheaders are excavating the remaining tunnels such as ramps, access tunnels, cross passages and merges.A major challenge arose during the planning of the initial mainline excavation underneath the Royal National Association Showground in Bowen Hills. This section contains low rock cover and historical maps indicate that the Showground is located within a former topographic depression (alluvial valley) where a creek once flowed through. Due to traffic merge design requirements, both TBM and roadheader excavation methods were required to be used in this challenging geological profile. The answer was to stabilise the alluvium above both TBM section tunnels from the surface prior to excavation and to operate the TBM in single shield mode with immediate grouting of annular void from the tail shield. In addition, the roadheader section of tunnel required additional support by spiles and canopy tubes installed from the tunnel face.
The influence of grout and bentonite slurry on the process of TBM tunnelling
Authors: Bezuijen Adam 
Published: June 2009

AbstractThe bentonite and grout flow around a TBM is elaborated, as well as grout flow along the lining. The calculated grout flow along the lining is compared with the results of measurements. Measurement data for the flow around the TBM are not available. Both the bentonite and the grout are modelled as a Bingham liquid and it will be shown that, due to the relatively low flow velocities, the yield stress is the governing parameter. The results of the calculations show that both the flow around the TBM and the flow around the lining may significantly influence loading on the TBM, the soil, and the lining. The bentonite and grout flow around the TBM may result in a lower volume loss than calculated when assuming that the soil follows the tapered TBM. The grout flow and especially grout consolidation lead to lower pressures around the lining if the tunnel is constructed in sandy soil.
TRAIL receptor upregulation and the implication of KRAS/BRAF mutations in human colon cancer tumors
Authors: Oikonomou Eftychia , Kosmidou Vivian , Katseli Anastasia , Kothonidis Konstantinos , Mourtzoukou Despina , Kontogeorgos George , Andera Ladislav , Zografos Georgios , Pintzas Alexander 
Published: June 2009

AbstractTRAIL raises hopes as a promising anti‐tumor agent due to its selectivity toward cancer cells. Higher expression of its pro‐death receptors TRAIL‐R1 (DR4) and TRAIL‐R2 (DR5) attenuates higher sensitivity to TRAIL‐induced apoptosis, and represents a marker for better cancer prognosis and treatment. Since receptor availability can be analogous to ligand efficacy, we performed RT‐PCR analysis of DR4 and DR5 in 51 colon cancer biopsy specimens and respective normal mucosa, while 11 of these tumors were determined immunohistochemically for protein expression. Transcriptional analysis showed that DR4 and DR5 were significantly upregulated in 37 and 47% of the tumor samples respectively, while both DR4 and DR5 were coinstantaneously upregulated in 31% of the samples analyzed. Positive transcriptional regulation of DRs was recorded as early as Dukes' A stage. Furthermore, protein expression analysis yielded results comparable to DR4 and DR5 increased mRNA levels. Possible contributing events to DR upregulation involve presence of frequent oncogenic mutations in the MAPK pathway, and was investigated by direct sequencing in all 51 tumors. Samples (6/8) hosting either a KRASG12Vor BRAFV600Emutation, significantly amplified the upregulated expression of DR4 and DR5, showing strong inter‐relation between overexpression and presence of oncogenic KRAS/ BRAF mutations. In the light of recent data concerning TRAIL receptor distribution, we contribute further by presenting DR5 as the most frequently upregulated DR in colon cancer. Furthermore, oncogenic mutations may directly or indirectly enhance DR expression, potentially sensitizing these tumors to TRAIL‐based therapies. © 2009 UICC