bluuebunny/crossref_metadata_2025_split huggingface dataset:
u‐TA: A ubiquitous teaching assistant using knowledge retrieval and adaptive learning techniques
Authors: Huang Lu‐Hui , Dow Chyi‐Ren , Li Yi‐Hsung , Hsuan Pa 
Published: July 2010

AbstractUsing mobile agents to assist students in virtual learning environments has become increasingly common for hands‐on experiments. Although virtual learning environments provide mobile agents as a platform for services to learners, one type of mobile agent only serves in one course, bringing possible benefits to users. This study was conducted to use agent techniques to construct a ubiquitous teaching assistant (u‐TA) for assisting students solve problems in laboratory courses. We gave the u‐TA enhanced social skills so that it can reduce the burden on teachers. The proposed u‐TA system consists of both Web‐based and instant messenger‐based (IM‐based) interfaces, and the u‐TA can learn from other agents by analyzing their dialogues. Experiments were conducted to evaluate the effectiveness of the u‐TA and the results show that the u‐TA can assist students and share the TA's workload in courses. The experimental results also demonstrated that the u‐TA has good communications ability; its two user interfaces can increase interactions with students. © 2010 Wiley Periodicals, Inc. Comput Appl Eng Educ 21: 245–255, 2013
PlanetLab@UOC: A real lab over the Internet to experiment with distributed systems
Authors: Marquès Joan Manuel , Lazaro Daniel , Juan Angel A. , Vilajosana Xavier , Domingo Marc , Jorba Josep 
Published: July 2010

AbstractThis paper presents an innovative academic experience regarding the use of PlanetLab—an open large‐scale platform over the Internet—in engineering courses on distributed systems. By integrating a live‐deployment environment such as PlanetLab into distributed‐systems courses, software implementations developed by students can interact with instructors' implementations in a real Internet‐distributed scenario. To the best of our knowledge, this is the first experience regarding the use of the PlanetLab nodes available over Internet to teach distributed computing concepts to engineering students, since most of the existing literature on distributed‐systems courses describes only learning experiences in lab‐simulated or lab‐emulated scenarios. As discussed in this paper, experimenting with a real laboratory over the Internet adds some complexity to students' practical activities, but it also facilitates a deeper and more intensive learning experience. A survey among students shows some clear benefits of this approach over the use of simulation labs, as well as some pitfalls that must be avoided whenever possible. The paper ends with a set of recommendations for instructors that might want to design similar courses as well as with an overview of future work to be performed in this field. © 2010 Wiley Periodicals, Inc. Comput Appl Eng Educ 21: 265–275, 2013
A Single Molecular Beacon Probe Is Sufficient for the Analysis of Multiple Nucleic Acid Sequences
Authors: Gerasimova Yulia V. , Hayson Aaron , Ballantyne Jack , Kolpashchikov Dmitry M. 
Published: July 2010

AbstractMolecular beacon (MB) probes are dual‐labeled hairpin‐shaped oligodeoxyribonucleotides that are extensively used for real‐time detection of specific RNA/DNA analytes. In the MB probe, the loop fragment is complementary to the analyte: therefore, a unique probe is required for the analysis of each new analyte sequence. The conjugation of an oligonucleotide with two dyes and subsequent purification procedures add to the cost of MB probes, thus reducing their application in multiplex formats. Here we demonstrate how one MB probe can be used for the analysis of an arbitrary nucleic acid. The approach takes advantage of two oligonucleotide adaptor strands, each of which contains a fragment complementary to the analyte and a fragment complementary to an MB probe. The presence of the analyte leads to association of MB probe and the two DNA strands in quadripartite complex. The MB probe fluorescently reports the formation of this complex. In this design, the MB does not bind the analyte directly; therefore, the MB sequence is independent of the analyte. In this study one universal MB probe was used to genotype three human polymorphic sites. This approach promises to reduce the cost of multiplex real‐time assays and improve the accuracy of single‐nucleotide polymorphism genotyping.
Molecular Recognition of Peloruside A by Microtubules. The C24 Primary Alcohol is Essential for Biological Activity
Authors: Pera Benet , Razzak Mina , Trigili Chiara , Pineda Oriol , Canales Angeles , Buey Rubén M. , Jiménez‐Barbero Jesús , Northcote Peter T. , Paterson Ian , Barasoain Isabel , Díaz José Fernando 
Published: July 2010

AbstractPeloruside is a microtubule‐stabilizing agent that targets the same site as laulimalide. It binds to microtubules with a 1:1 stoichiometry and with a binding affinity in the low‐μM range; thereby reducing the number of microtubular protofilaments in the same way as paclitaxel. Although the binding affinity of the compound is comparable to that of the low‐affinity stabilizing agent sarcodictyin, peloruside is more active in inducing microtubule assembly and is more cytotoxic to tumor cells; this suggests that the peloruside site is a more effective site for stabilizing microtubules. Acetylation of the C24 hydroxyl group results in inactive compounds. According to molecular modeling, this substitution at the C24 hydroxyl group presumably disrupts the interaction of the side chain with Arg320 in the putative binding site on α‐tubulin. The binding epitope of peloruside on microtubules has been studied by using NMR spectroscopic techniques, and is compatible with the same binding site.
Cu Nanoparticles in PEG: A New Recyclable Catalytic System for N‐Arylation of Amines with Aryl Halides
Authors: Kidwai Mazaahir , Mishra Neeraj Kumar , Bhardwaj Saurav , Jahan Anwar , Kumar Ajeet , Mozumdar Subho 
Published: July 2010

AbstractA new protocol for the N‐arylation of aryl halides with anilines using Cu nanoparticles in polyethylene glycol (PEG) as an efficient and reusable catalytic system has been developed. The reaction did not require any cocatalyst. Various solvents were screened, and PEG400 provided the best results. The studies showed that the mechanism of catalytic action is dependent on the size of the nanoparticles. The Cu nanoparticles and PEG were recyclable and retained their activity. This newly developed protocol was also found to be suitable for the cross coupling of NH heterocycles with iodobenzene. The present methodology offers several advantages, such as excellent yields, short reaction times, and milder reaction conditions.
Biocatalytic Production of Coenzyme A Analogues
Authors: Strauss Erick , de Villiers Marianne , Rootman Ilse 
Published: July 2010

AbstractCoenzyme A (CoA) analogues are widely used as tools in chemical biology. Their applications include being used as inhibitors and mechanistic probes of CoA‐dependent enzymes, and in the labeling of especially carrier proteins active in polyketide and nonribosomal peptide synthesis with fluorescent probes or affinity tags, or with chemically reactive cross‐linking moieties. The preparation of CoA analogues has been simplified tremendously since the discovery of the CoA biosynthetic enzymes. Consequently a large number of such analogues have been prepared in recent years by the biotransformation of pantothenamide precursors (a bottom‐up approach) or by aminolysis of activated pre‐CoA thioesters (a top‐down approach). This Minireview provides an analysis of the biosynthetic enzymes used in the biocatalytic production of CoA analogues, an overview of the different ways in which they are currently applied and a description of the types of CoA analogues that are currently easily accessed by such methods.
Asymmetric Retro‐Henry Reaction Catalyzed by Hydroxynitrile Lyase from Hevea brasiliensis
Authors: Yuryev Ruslan , Briechle Sebastian , Gruber‐Khadjawi Mandana , Griengl Herfried , Liese Andreas 
Published: July 2010

AbstractHydroxynitrile lyase from Hevea brasiliensis (HbHNL) is a promiscuous biocatalyst that, besides the native cyanohydrin reaction, also catalyzes the asymmetric Henry reaction yielding (S)‐β‐nitroalcohols with high enantiomeric excess. Since the Henry reaction is reversible, the enzyme can be also utilized for the production (R)‐enantiomers by means of resolution of racemic β‐nitroalcohols. Herein the biocatalytic retro‐Henry reaction is studied using the cleavage of 2‐nitro‐1‐phenylethanol as a model system. The main problem that prevents high levels of conversion or high ee values during the cleavage of the β‐nitroalcohol is the formation of benzaldehyde, which is known to be a strong enzyme inhibitor. The product inhibition is overcome by performing the biocatalytic retro‐Henry reaction in the presence of HCN, which reacts in situ with benzaldehyde and converts it to the less‐inhibitive mandelonitrile. By using such a reaction cascade, it was possible to conduct the resolution practically to completion (95 % ee, 49 % conversion). Furthermore, the catalyst productivity achieved during the resolution was ten times higher than that in the HbHNL‐catalyzed synthesis of (S)‐2‐nitro‐1‐phenylethanol by condensation of benzaldehyde and nitromethane.
Filtering of Clay Colloids in Bentonite Detritus Material
Authors: Richards T. , Neretnieks I. 
Published: July 2010

AbstractBentonite clay consists of two types of materials, small nanoscale smectite particles and larger accessory material particles. When used as a barrier, it is important that as little material as possible is lost. This loss may occur if water with low salinity passes by the bentonite clay. First, the clay will swell and then the smectite particles can solubilize. This study investigates under which circumstances the material can form a filter cake of the accessory material and slow down or stop the penetration of smectite through the filter cake. It has been shown that it is possible to form such a filter cake and that the filter cake can be further improved by adding other particles.
Parallel factor analysis of EEM of the fluorescence of carbon dots nanoparticles
Authors: Leitão João M. M. , Gonçalves Helena , da Silva Joaquim C. G. Esteves 
Published: July 2010

AbstractThe effect of experimental factors [pH and Hg(II)] on the fluorescence excitation emission matrices (EEMs) of nanosensor carbon dots (CDs) was analyzed by multiway decomposition methods based on parallel factor (PARAFAC) analysis. PARAFAC analysis of the EEM structures identifies three components corresponding to two different‐sized CDs with the Hg(II) and pH profiles highly correlated plus a background. Parallel profiles with Linear Dependences (PARALIND) model with three components in the excitation–emission spectral modes and two components in the Hg(II) or pH mode gave similar results as PARAFAC, but is more useful from a theoretical point of view because PARALIND shows that the two different‐sized CDs have similar chemical reactivity toward Hg(II) and pH. PARAFAC2 was used as a trilinear confirmatory test of the data structures under analysis. Copyright © 2010 John Wiley & Sons, Ltd.
Structure–Activity Relationship Analysis of Pd–PEPPSI Complexes in Cross‐Couplings: A Close Inspection of the Catalytic Cycle and the Precatalyst Activation Model
Authors: Nasielski Joanna , Hadei Nilofaur , Achonduh George , Kantchev Eric Assen B. , O'Brien Christopher J. , Lough Alan , Organ Michael G. 
Published: July 2010

AbstractA series of Pd–N‐heterocyclic carbene (Pd–NHC) complexes with various NHC, halide and pyridine ligands (PEPPSI (pyridine, enhanced, precatalyst, preparation, stabilisation and initiation) precatalysts) were prepared, and the effects of these ligands on catalyst activation and performance were studied in the Kumada–Tamao–Corriu (KTC), Negishi, and Suzuki–Miyaura cross‐coupling reactions. The lowered reactivity of more hindered 2,6‐dimethylpyridyl complex 4 in the Negishi and KTC reactions is consistent with slow reductive dimerisation of the organometallic reaction partner during precatalyst activation. Comparative rate studies of complexes 1, 4 and 5 in the KTC and Suzuki–Miyaura reactions verify that 4 activated more slowly than the others. A potential on/off mechanism of pyridine coordination to NHC–Pd0 is also plausible, in which the more basic pyridine stays bound for longer.
Promoted H2 Generation from NH3BH3 Thermal Dehydrogenation Catalyzed by Metal–Organic Framework Based Catalysts
Authors: Li Yaoqi , Song Ping , Zheng Jie , Li Xingguo 
Published: July 2010

AbstractThe application of ammonium borane (AB) as a hydrogen storage material is limited by the sluggish kinetics of H2 release. Two catalysts based on metal–organic frameworks (MOFs) have been prepared either by applying MOF as precursors or by the in situ reduction method. In the release of H2 from AB, the high H2 content of the whole system, the remarkably lower reaction onset temperature, the significantly increased H2 release rates at ≤90 °C, and the decreased reaction exothermicity have all been achieved with only 1.0 mol % MOF‐based catalyst. Moreover, the clear catalytic diversity of three catalysts has been observed and discussed. The in situ synthesized Ni0 sites and the MOF supports in the catalysts were proven to show significant and different effects to promote the catalytic activities. With MOF‐based catalysts, both the enhanced kinetics and the high H2 capacity of the AB system present great advantages for future use.
Characterization, Direct Electrochemistry, and Amperometric Biosensing of Graphene by Noncovalent Functionalization with Picket‐Fence Porphyrin
Authors: Tu Wenwen , Lei Jianping , Zhang Siyuan , Ju Huangxian 
Published: July 2010

AbstractReduced graphene oxide (RGO) was prepared and functionalized with picket‐fence porphyrin, 5,10,15,20‐tetrakis [αααα‐2‐trismethylammoniomethylphenyl] porphyrin iron(III) pentachloride (FeTMAPP), through π–π interactions. The resulting nanocomposite was characterized by atomic force microscopy (AFM); transmission electron microscopy (TEM); contact angle measurements; and fluorescence, Raman, and UV/Vis absorption spectroscopy. On account of the introduction of positively charged FeTMAPP, the functionalized RGO showed good dispersion in aqueous solution. The RGO could greatly accelerate the electron transfer of FeTMAPP to produce a well‐defined redox couple of FeIII/FeII at −0.291 and −0.314 V. Due to the synergic effect between RGO and the porphyrin, the nanocomposite showed excellent electrocatalytic activity toward the reduction of chlorite, thus leading to highly sensitive amperometric biosensing at low applied potential. The biosensor for chlorite showed a linear range from 5.0×10−8 to 1.2×10−4 mol L−1 with a detection limit of 2.4×10−8 mol L−1 at a signal‐to‐noise ratio of 3. The picket‐fence porphyrin could serve as an efficient species to functionalize graphene for electronic and optical applications.
On the Design of Fluorescent Ratiometric Nanosensors
Authors: Doussineau Tristan , Schulz Anja , Lapresta‐Fernandez Alejandro , Moro Artur , Körsten Susanne , Trupp Sabine , Mohr Gerhard J. 
Published: July 2010

AbstractAdvances in nanoparticle technology have recently offered new tools to the bioanalytical field of research. In particular, new nanoparticle‐based sensors have appeared able to give quantitative information about different species (ions, metabolites, biomolecules) in biosamples through ratiometric measurements. This article describes the methodologies developed so far in the design of such nanosensors. In particular, the different approaches to immobilize fluorescent chemosensor dyes to nanoparticles are presented. Concept designs of ratiometric nanosensors in terms of composition and architecture are also described and illustrated with examples taken from the literature.
Unifying Metal and Brønsted Acid Catalysis—Concepts, Mechanisms, and Classifications
Authors: Rueping Magnus , Koenigs Rene M. , Atodiresei Iuliana 
Published: July 2010

AbstractAsymmetric catalysis is a key feature of modern synthetic organic chemistry. Traditionally, different combinations of ligands and metals are used to perform highly enantioselective reactions. Since the renaissance of organocatalysis in the early 2000s, tremendous improvement in the field of metal‐free catalysis has been achieved. Recently, the combination of transition metals and organocatalysts has allowed the development of new protocols enabling transformations that could not previously be realized. This article aims to present the latest contributions in the field of combined chiral Brønsted acid and metal catalyzed reactions, highlighting the advantages of these catalytic systems as well as describing the uncertainties regarding the molecular structure of the catalytically active species and the reaction mechanisms.
Enzymatic Synthesis of Enantiomerically Pure β‐Amino Ketones, β‐Amino Esters, and β‐Amino Alcohols with Baeyer–Villiger Monooxygenases
Authors: Rehdorf Jessica , Mihovilovic Marko D. , Fraaije Marco W. , Bornscheuer Uwe T. 
Published: July 2010

AbstractThe enzymatic kinetic resolution of a broad set of β‐amino ketones was investigated by using a collection of 16 Baeyer–Villiger monooxygenases from different bacterial origins, which display various substrate specificities. Within this platform of enzymes excellent enantioselectivities (E>200) were found towards aliphatic and aromatic 4‐amino‐2‐ketones, and some enzymes even showed opposite enantioselectivity. The intermediate β‐aminoalkyl acetates underwent autohydrolysis yielding optically pure β‐amino alcohols, which are key intermediates in the synthesis of natural products and bioactive compounds of high interest for the pharmaceutical industry. Furthermore, in some cases the abnormal esters were formed.
Background migration of USPIO/MLs is a major drawback for in situ labeling of endogenous neural progenitor cells
Authors: Vreys Ruth , Soenen Stefaan J. H. , De Cuyper Marcel , Van der Linden Annemie 
Published: July 2010

AbstractMR‐labeling of endogenous neural progenitor cells (NPCs) to follow up cellular migration with in vivo magnetic resonance imaging (MRI) is a very promising tool in the rapidly growing field of cellular imaging. To date, most of the in situ labeling work has been performed using micron‐sized iron oxide particles. In this work magnetoliposomes (MLs), i.e. ultrasmall superparamagnetic iron oxide cores (USPIOs), each individually coated by a phospholipid bilayer, were used as the MR contrast agent. One of the main advantages of MLs is that the phospholipid bilayer allows easy modification of the surface, which creates the opportunity to construct a wide range of MLs optimized for specific biomedical applications. We have investigated the ability of MLs to label endogenous NPCs after direct injection into the adult mouse brain. Whereas MRI revealed contrast relocation towards the olfactory bulb, our data strongly imply that this relocation is independent of the migration of endogenous NPCs but represents background migration of MLs along a white matter tract. Our findings suggest that the small size of USPIOs/MLs intrinsically limits their potential for in situ labeling of NPCs. Copyright © 2010 John Wiley & Sons, Ltd.
Surrogate MR markers of response to chemo‐ or radiotherapy in association with co‐treatments: a retrospective analysis of multi‐modal studies
Authors: Jordan Bénédicte F. , Gallez Bernard 
Published: July 2010

AbstractThe study of magnetic resonance (MR) markers over the past decade has provided evidence that the tumor microenvironnement and hemodynamics play a major role in determining tumor response to therapy. The aim of the present work is to predict and monitor the efficacy of co‐treatments to radio‐ and chemotherapy by noninvasive MR imaging. Ten different co‐treatments were involved in this retrospective analysis of our previously published data, including NO‐mediated co‐treatments (insulin and isosorbide dinitrate), anti‐inflammatory drugs (hydrocortisone, NS‐398), anti‐angiogenic agents (thalidomide, SU5416 and ZD6474), a vasoactive agent (xanthinol nicotinate), botulinum toxin and carbogen breathing. Dynamic contrast enhanced (DCE) MRI, intrinsic susceptibility‐weighted (BOLD) MRI and electronic paramagnetic resonance (EPR) oximetry all reflect tumor microenvironment hemodynamic variables that are known to influence tumor response. Eight MR‐derived parameters (markers) were tested for their ability to predict therapeutic outcome (factor of increase in regrowth delay) in experimental tumor models (TLT and FSaII) after radiation therapy and/or chemotherapy with cyclophosphamide, namely tumor pO2 and O2 consumption rate (using EPR oximetry); tumor blood flow and permeability, i.e. V p, K trans, K ep and percentage of perfused vessels (using DCE‐MRI); and BOLD signal intensity and R 2* (using functional MRI). This multi‐modal comparison of co‐treatment efficacy points out the limitations of each MR marker and identifies in vivo pO2 as a relevant endpoint for radiation therapy. DCE parameters (V p and K ep) were identified as a relevant endpoints for cyclophosphamide chemotherapy in our tumor models. This study helps qualify relevant imaging endpoints in the preclinical setting of cancer therapy. Copyright © 2010 John Wiley & Sons, Ltd.
Quantitative 1H MRI, 19F MRI, and 19F MRS of cell‐internalized perfluorocarbon paramagnetic nanoparticles
Authors: Kok Maarten B. , de Vries Anke , Abdurrachim Desiree , Prompers Jeanine J. , Grüll Holger , Nicolay Klaas , Strijkers Gustav J. 
Published: July 2010

AbstractIn vivo molecular imaging with targeted MRI contrast agents will require sensitive methods to quantify local concentrations of contrast agent, enabling not only imaging‐based recognition of pathological biomarkers but also detection of changes in expression levels as a consequence of disease development, therapeutic interventions or recurrence of disease. In recent years, targeted paramagnetic perfluorocarbon emulsions have been frequently applied in this context, permitting high–resolution 1H MRI combined with quantitative 19F MR imaging or spectroscopy, under the assumption that the fluorine signal is not altered by the local tissue and cellular environment. In this in vitro study we have investigated the 19F MR–based quantification potential of a paramagnetic perfluorocarbon emulsion conjugated with RGD–peptide to target the cell–internalizing ανβ3–integrin expressed on endothelial cells, using a combination of 1H MRI, 19F MRI and 19F MRS. The cells took up the targeted emulsion to a greater extent than nontargeted emulsion. The targeted emulsion was internalized into large 1–7 µm diameter vesicles in the perinuclear region, whereas nontargeted emulsion ended up in 1–4 µm diameter vesicles, which were more evenly distributed in the cytoplasm. Association of the targeted emulsion with the cells resulted in different proton longitudinal relaxivity values, r1, for targeted and control nanoparticles, prohibiting unambiguous quantification of local contrast agent concentration. Upon cellular association, the fluorine R1 was constant with concentration, while the fluorine R2 increased nonlinearly with concentration. Even though the fluorine relaxation rate was not constant, the 19F MRI and 19F MRS signals for both targeted nanoparticles and controls were linear and quantifiable as function of nanoparticle concentration. Copyright © 2010 John Wiley & Sons, Ltd.