bluuebunny/crossref_metadata_2025_split huggingface dataset:
Controlled preparation of poly(ethylene glycol) and poly(L‐lactide) block copolymers in the presence of a monomer activator
Authors: Hyo Lee Sang , Oh Jae Min , Son Jin Soo , Lee Jung Won , Kim Byung Soo , Khang Gilson , Han Dong Keun , Kim Jae Ho , Lee Hai Bang , Kim Moon Suk 
Published: September 2009

AbstractPolymerization of L‐lactide (LA) was performed in the presence of trifluoromethanesulfonic acid (CF3SO3H) via an activated monomer mechanism to synthesize various block copolymers composed of polyethyleneglycol (PEG) and poly(L‐lactide) (PLLA). The PLLAs obtained had molecular weights close to theoretical values calculated from LA/PEG molar ratios and exhibited monomodal GPC curves. A 1H NMR spectroscopic study showed that the LA carbonyl carbon signal exhibited a change in chemical shift to lower field, caused by electron delocalization of the carbonyl carbon by CF3SO3H. We successfully prepared PEG and PLLA block copolymers using this activated monomer mechanism. We concluded that synthesis proceeded by LA ring‐opening polymerization caused by PEG in the presence of CF3SO3H to yield PEG and PLLA block copolymers. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 5917–5922, 2009
Evaluation of a Range of Surface Modifications for the Enhancement of Lateral Flow Assays on Cyclic Polyolefin Micropillar Devices
Authors: Dudek Magdalena M. , Gandhiraman R. P. , Volcke C. , Daniels Stephen , Killard Anthony J. 
Published: September 2009

AbstractWe report the evaluation of a range of surface modifications for the formation of a stable, uniform, hydrophilic surface on cyclic polyolefin‐based microfluidic devices. The surface modifications employed were oxygen plasma treatment alone, or in combination with polyelectrolyte (PE) modifications or chemical vapour deposition (CVD) of silicon dioxide as well as dextran modification. The surface modifications were characterised by atomic force microscopy (AFM), contact angle (CA) measurements and both quantitative and qualitative lateral flow measurements. It was demonstrated that the silicon dioxide and PE treatments produced the lowest CAs and therefore most hydrophilic surfaces, which was reflected in the improved lateral flow rates on this normally hydrophobic polymer. However, the non‐uniformity of the PE coating as well as its reduced reproducibility and stability over time in comparison to the silicon dioxide coating meant that the silicon dioxide was the favoured surface modification.magnified image
Symmetry‐restrained molecular dynamics simulations improve homology models of potassium channels
Authors: Anishkin Andriy , Milac Adina L. , Guy H. Robert 
Published: September 2009

AbstractMost crystallized homo‐oligomeric ion channels are highly symmetric, which dramatically decreases conformational space and facilitates building homology models (HMs). However, in molecular dynamics (MD) simulations channels deviate from ideal symmetry and accumulate thermal defects, which complicate the refinement of HMs using MD. In this work we evaluate the ability of symmetry constrained MD simulations to improve HMs accuracy, using an approach conceptually similar to Critical Assessment of techniques for protein Structure Prediction (CASP) competition: build HMs of channels with known structure and evaluate the efficiency of proposed methods in improving HMs accuracy (measured as deviation from experimental structure). Results indicate that unrestrained MD does not improve the accuracy of HMs, instantaneous symmetrization improves accuracy but not stability of HMs during subsequent unrestrained MD, while gradually imposing symmetry constraints improves both accuracy (by 5–50%) and stability of HMs. Moreover, accuracy and stability are strongly correlated, making stability a reliable criterion in predicting the accuracy of new HMs. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Unraveling the molecular basis for ligand binding in truncated hemoglobins: The trHbO Bacillus subtilis case
Authors: Boechi Leonardo , Mañez Pau Arroyo , Luque F. Javier , Marti Marcelo A. , Estrin Dario A. 
Published: September 2009

AbstractTruncated hemoglobins (trHbs) are heme proteins present in bacteria, unicellular eukaryotes, and higher plants. Their tertiary structure consists in a 2‐over‐2 helical sandwich, which display typically an inner tunnel/cavity system for ligand migration and/or storage. The microorganism Bacillus subtilis contains a peculiar trHb, which does not show an evident tunnel/cavity system connecting the protein active site with the solvent, and exhibits anyway a very high oxygen association rate. Moreover, resonant Raman results of CO bound protein, showed that a complex hydrogen bond network exists in the distal cavity, making it difficult to assign unambiguously the residues involved in the stabilization of the bound ligand. To understand these experimental results with atomistic detail, we performed classical molecular dynamics simulations of the oxy, carboxy, and deoxy proteins. The free energy profiles for ligand migration suggest that there is a key residue, GlnE11, that presents an alternate conformation, in which a wide ligand migration tunnel is formed, consistently with the kinetic data. This tunnel is topologically related to the one found in group I trHbs. On the other hand, the results for the CO and O2 bound protein show that GlnE11 is directly involved in the stabilization of the cordinated ligand, playing a similar role as TyrB10 and TrpG8 in other trHbs. Our results not only reconcile the structural data with the kinetic information, but also provide additional insight into the general behaviour of trHbs. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Improving the analysis of NMR spectra tracking pH‐induced conformational changes: Removing artefacts of the electric field on the NMR chemical shift
Authors: Kukić Predrag , Farrell Damien , Søndergaard Chresten R. , Bjarnadottir Una , Bradley John , Pollastri Gianluca , Nielsen Jens Erik 
Published: September 2009

AbstractpH‐induced chemical shift perturbations (CSPs) can be used to study pH‐dependent conformational transitions in proteins. Recently, an elegant principal component analysis (PCA) algorithm was developed and used to study the pH‐dependent structural transitions in bovine β‐lactoglobulin (βLG) by analyzing its NMR pH‐titration spectra. Here, we augment this analysis method by filtering out changes in the NMR chemical shift that stem from effects that are electrostatic in nature. Specifically, we examine how many CSPs can be explained by purely electrostatic effects arising from titrational events in βLG. The results show that around 20% of the amide nuclei CSPs in βLG originate exclusively from “through‐space” electric field effects. A PCA of NMR data where electric field artefacts have been removed gives a different picture of the pH‐dependent structural transitions in βLG. The method implemented here is well suited to be applied on a whole range of proteins, which experience at least one pH‐dependent conformational change. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Multi‐scale characterization of the energy landscape of proteins with application to the C3D/Efb‐C complex
Authors: Haspel Nurit , Geisbrecht Brian V. , Lambris John , Kavraki Lydia 
Published: September 2009

AbstractWe present a novel multi‐level methodology to explore and characterize the low energy landscape and the thermodynamics of proteins. Traditional conformational search methods typically explore only a small portion of the conformational space of proteins and are hard to apply to large proteins due to the large amount of calculations required. In our multi‐scale approach, we first provide an initial characterization of the equilibrium state ensemble of a protein using an efficient computational conformational sampling method. We then enrich the obtained ensemble by performing short Molecular Dynamics (MD) simulations on selected conformations from the ensembles as starting points. To facilitate the analysis of the results, we project the resulting conformations on a low‐dimensional landscape to efficiently focus on important interactions and examine low energy regions. This methodology provides a more extensive sampling of the low energy landscape than an MD simulation starting from a single crystal structure as it explores multiple trajectories of the protein. This enables us to obtain a broader view of the dynamics of proteins and it can help in understanding complex binding, improving docking results and more. In this work, we apply the methodology to provide an extensive characterization of the bound complexes of the C3d fragment of human Complement component C3 and one of its powerful bacterial inhibitors, the inhibitory domain of Staphylococcus aureus extra‐cellular fibrinogen‐binding domain (Efb‐C) and two of its mutants. We characterize several important interactions along the binding interface and define low free energy regions in the three complexes. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Neuroprotective effects of Brazilian green propolis and its main constituents against oxygen‐glucose deprivation Stress, with a gene‐expression analysis
Authors: Nakajima Yoshimi , Shimazawa Masamitsu , Mishima Satoshi , Hara Hideaki 
Published: September 2009

AbstractOur purpose was to investigate the neuroprotective effects (and the underlying mechanism) exerted by water extract of Brazilian green propolis (WEP) and its main constituents against the neuronal damage induced by oxygen‐glucose deprivation (OGD)/reoxygenation in retinal ganglion cells (RGC‐5, a rat ganglion cell‐line transformed using E1A virus). Cell damage was induced by OGD 4 h plus reoxygenation 18 h exposure. In RGC‐5, and also in PC12 (rat pheochromocytoma, neuronal cells), WEP and some of its main constituents attenuated the cell damage. At the end of the period of OGD/reoxygenation, RNA was extracted and DNA microarray analysis was performed to examine the gene‐expression profile in RGC‐5. Expression of casein kinase 2 (CK2) was down‐regulated and that of Bcl‐2‐related ovarian killer protein (Bok) was up‐regulated following OGD stress, results that were confirmed by quantitative reverse transcriptase‐PCR (qRT‐PCR). These effects were normalized by WEP. Our findings indicate that WEP has neuroprotective effects against OGD/reoxygenation‐induced cell damage and that certain constituents of WEP (caffeoylquinic acid derivatives, artepillin C, and p‐coumaric acid) may be partly responsible for its neuroprotective effects. Furthermore, the protective mechanism may involve normalization of the expressions of antioxidant‐ and apoptosis‐related genes (such as CK2 and Bok, respectively). Copyright © 2009 John Wiley & Sons, Ltd.
The effect of latent cooling processes in tropical cyclone simulations
Authors: Frisius Thomas , Hasselbeck Thomas 
Published: September 2009

AbstractIn order to estimate the role of latent cooling processes for tropical cyclones, we have performed sensitivity simulations with both the axisymmetric cloud‐resolving model HURMOD and the fully three‐dimensional COSMO model of the German Weather Service. As an idealised initial state, a convectively unstable vortex with superimposed entropy anomalies has been assumed. While growth rate and maximum wind speeds become unnaturally large in simulations without latent cooling processes, the presence of these processes proves to be necessary to maintain convection outside the eyewall and turns out to be responsible for a delayed development of the tropical cyclone. The latter result is in accordance with the findings of Gray, based on observations. Furthermore, intensity fluctuations of the mature tropical cyclone only occur in HURMOD when latent cooling processes are simulated.An analysis of CAPE, CIN and DCAPE reveals that convection outside the eyewall explains these intensity fluctuations by mixing low‐entropy air into the boundary layer, while without latent cooling processes significant convective inhibition due to drying by absence of evaporation and cyclone‐scale subsidence suppresses vertical mixing. HURMOD does not exhibit a threshold amplitude but a sea‐surface temperature threshold for tropical cyclogenesis, while the latter only occurs with latent cooling processes. However, a threshold depending on the initial vortex amplitude, together with a stronger response to latent cooling processes, is found in the COSMO model simulations. This seems to be caused by non‐axisymmetric disturbances which may circumvent cyclogenesis for a small initial vortex amplitude. Copyright © 2009 Royal Meteorological Society
Theoretical studies on ionization potential of aluminum clusters
Authors: Phung Thi Viet Bac , Hashimoto Taihei , Nishikawa Kyoshi , Nagao Hidemi 
Published: September 2009

AbstractThe ionization potentials (IPs) of aluminum Al (clustersN) are investigated using density functional calculations based on the plane‐wave basis set and the projector‐augmented wave method. We discuss the size dependence of the IP in relation to the electron affinity, the chemical hardness of both the small‐sized and large cuboctahedral AlN containing up to 923 atoms and compare the computational results with other models of Wood and Perdew based on the jellium model. We show that the IP and electron affinity of large clusters in this size region can be extrapolated to the value of the work function for the bulk aluminum. Expressions of the higher‐order IP of metallic clusters are derived by the extension of the Perdew model. We discuss the IP of a collective system of metallic clusters as a simple model of clusters on a thin film in the framework of the Perdew model. The critical size of superconductivity of aluminium cluster is discussed by using the present results of the average energy‐level spacing. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Molecular simulation of the water meniscus in dip‐pen nanolithography
Authors: Kim Hyojeong , Saha Leton C. , Saha Joyanta K. , Jang Joonkyung 
Published: September 2009

AbstractWe report a molecular dynamics simulation of the nanometer water meniscus formed in dip‐pen nanolithography (DPN). When an atomic force microscope tip is in contact with a surface, the meniscus is significantly asymmetric around the tip axis. The meniscus as a whole can move away from the tip axis due to surface diffusion. The structure of the meniscus fluctuates and its periphery has a finite thickness as large as 25% of its width. We simulated the transport of nonpolar hydrophobic molecules through a water meniscus. Molecules move on the surface of, not dissolving into the interior of, the meniscus. As a result, an annular pattern forms in DPN. Even if the meniscus is cylindrically symmetric, the molecular flow from the tip and the subsequent pattern growth on the surface are anisotropic at the nanosecond timescale. SCANNING 32: 2–8, 2010. © 2009 Wiley Periodicals, Inc.
Toward the Development of “Nano‐QSARs”: Advances and Challenges
Authors: Puzyn Tomasz , Leszczynska Danuta , Leszczynski Jerzy 
Published: September 2009

AbstractThe most significant achievements and challenges relating to an application of quantitative structure–activity relationship (QSAR) approach in the risk assessment of nanometer‐sized materials are highlighted. Recent advances are discussed in the context of “classical” QSAR methodology. The possible ways for the structural characterization of compounds existing at the nanoscale (at least one dimension of 100 nm or less) are briefly reviewed. The applicability of the existing toxicological data for developing QSAR models is evaluated. Finally, the existing models are presented. The need to develop new interpretative descriptors for the nanosystems is also highlighted. It is suggested that, due to high variability in the molecular structures and different mechanisms of toxicity, individual classes of nanoparticles should be modeled separately.magnified image
Microfabricated Devices for Enhanced Bioadhesive Drug Delivery: Attachment to and Small‐Molecule Release Through a Cell Monolayer Under Flow
Authors: Ainslie Kristy M. , Lowe Rachel D. , Beaudette Tristan T. , Petty Lamar , Bachelder Eric M. , Desai Tejal A. 
Published: September 2009

AbstractThe development of a novel microfabricated device for oral drug delivery that overcomes many of the common barriers present in the gastrointestinal tract is reported. Specifically, the attachment of targeting ligands, subsequent device binding, and small molecule release from the microdevices in flow are investigated. A diffusion chamber that permits the simultaneous study of particle binding and small‐molecule release under physiologically relevant shear conditions is developed. It is observed that once the particles bind to the cell surface, they remain attached. A small fraction of the devices detach in flow; however, most of these devices readily reattach to the cell layer in a new location. This steady‐state density of microdevices is most likely the result of larger order microdevice clusters releasing their loose interactions with nearby microdevices, shifting slightly downstream, and subsequently reattaching to the cell monolayer. The release of a model small molecule from microdevices over time is roughly linear and approximately ten times greater than that observed with the small molecule alone. Overall, the preparation and characterization of an oral drug‐delivery microdevice system capable of both targeting and asymmetric release in flow is reported.
Nanomolding of PEG‐Based Hydrogels with Sub‐10‐nm Resolution
Authors: Diez Mar , Mela Petra , Seshan Venkatash , Möller Martin , Lensen Marga C. 
Published: September 2009

AbstractA simple, soft nanolithographic method is used to fabricate sub‐10‐nm structures on star polyethylene glycol‐based hydrogels and perfluoropolyether‐based materials. Very small features, for example, gold nanoparticles of size ≈8 nm with an interparticle distance of ≈100 nm, are successfully reproduced from a hard silicon master into both elastomers. Scanning force microscopy is used to investigate the replicas, and the original hexagonal pattern of the nanoparticles is clearly recognized. In addition, both replicas are usable as secondary, soft molds yielding positive copies of the primary, hard master. The results presented here show similar replication capabilities for both elastomers despite the markedly different properties of the precursors. Moreover, the hydrogel material can be easily peeled off from both soft and silicon masters without the need for surface treatment. The procedure allows nanopatterning of a biocompatible material over large areas, which is a useful tool to investigate cellular responses to defined nanotopography.
Droplet‐Based Microfluidic Synthesis of Anisotropic Metal Nanocrystals
Authors: Duraiswamy Suhanya , Khan Saif A. 
Published: September 2009

AbstractA droplet‐based microfluidic method for the preparation of anisotropic gold nanocrystal dispersions is presented. Gold nanoparticle seeds and growth reagents are dispensed into monodisperse picoliter droplets within a microchannel. Confinement within small droplets prevents contact between the growing nanocrystals and the microchannel walls. The critical factors in translating macroscale flask‐based methods to a flow‐based microfluidic method are highlighted and approaches are demonstrated to flexibly fine tune nanoparticle shapes into three broad classes: spheres/spheroids, rods, and extended sharp‐edged structures, thus varying the optical resonances in the visible–near‐infrared (NIR) spectral range.
Structural Trends in Coordination Polymers Containing Perfluorinated Dicarboxylates and 4,4′‐Bipyridine
Authors: Hulvey Zeric , Ayala Elizabeth , Cheetham Anthony K. 
Published: September 2009

AbstractA new family of coordination polymers has been synthesized using cobalt or zinc, 4,4′‐bipyridine (4,4′‐bpy), and the perfluorinated dicarboxylates tetrafluoroterephthalate (tftpa), tetrafluorophthalate (tfpha), tetrafluoroisophthalate (tfipa), and tetrafluorosuccinate (tfsuc). These materials form under similar conditions and all display similar octahedral metal coordination environments despite significant differences in their structures. The compounds M(4,4′‐bpy)(tftpa)(H2O)2 (M = Co, Zn) (1) and M(4,4′‐bpy)(tfpha)(H2O)2 (M = Co, Zn) (2) are two‐dimensional layered structures, whereas Co(4,4′‐bpy)(tfsuc)(H2O)2 (3) and M(4,4′‐bpy)(tfipa)(H2O)2 (M = Co, Zn) (4) display three‐dimensional connectivity built up from two types of interconnected chains.
Ultrasound and pain in children: A review
Authors: Mossetti Valeria , Ivani Giorgio 
Published: September 2009

AbstractUltrasound guidance has been demonstrated to improve block characteristics in children including shorter block performance time, higher success rates, shorter onset time, longer block duration, less volume of local anesthetic agents and visibility of neuraxial structures.Clinical studies in children suggest that ultrasound guidance has some advantages over more traditional nerve stimulation‐based techniques for regional block. However, the advantage of ultrasound guidance on safety over traditional has not been adequately demonstrated in children except ilio‐inguinal blocks.There are only a limited number of randomized control trails in children comparing ultrasound guided peripheral nerve block with other techniques. Available evidence in children demonstrates that ultrasound guided peripheral nerve blocks improve the quality, onset, duration and success rate of nerve blocks and help to lower the local anesthetic volume needed to perform blocks.
Cesarean delivery outcomes from the WHO global survey on maternal and perinatal health in Africa
Authors: Shah Archana , Fawole Bukola , M'Imunya James Machoki , Amokrane Faouzi , Nafiou Idi , Wolomby Jean‐José , Mugerwa Kidza , Neves Isilda , Nguti Rosemary , Kublickas Marius , Mathai Matthews 
Published: September 2009

AbstractObjectiveTo assess the association between cesarean delivery rates and pregnancy outcomes in African health facilities.MethodsData were obtained from all births over 2–3 months in 131 facilities. Outcomes included maternal deaths, severe maternal morbidity, fresh stillbirths, and neonatal deaths and morbidity.ResultsMedian cesarean delivery rate was 8.8% among 83 439 births. Cesarean deliveries were performed in only 95 (73%) facilities. Facility‐specific cesarean delivery rates were influenced by previous cesarean, pre‐eclampsia, induced labor, referral status, and higher health facility classification scores. Pre‐eclampsia increased the risks of maternal death, fresh stillbirths, and severe neonatal morbidity. Adjusted emergency cesarean delivery rate was associated with more fresh stillbirths, neonatal deaths, and severe neonatal morbidity—probably related to prolonged labor, asphyxia, and sepsis. Adjusted elective cesarean delivery rate was associated with fewer perinatal deaths.ConclusionUse of cesarean delivery is limited in the African health facilities surveyed. Emergency cesareans, when performed, are often too late to reduce perinatal deaths.