bluuebunny/crossref_metadata_2025_split huggingface dataset:
An iterative knowledge‐based scoring function to predict protein–ligand interactions: II. Validation of the scoring function
Authors: Huang Sheng‐You , Zou Xiaoqin 
Published: September 2006

AbstractWe have developed an iterative knowledge‐based scoring function (ITScore) to describe protein–ligand interactions. Here, we assess ITScore through extensive tests on native structure identification, binding affinity prediction, and virtual database screening. Specifically, ITScore was first applied to a test set of 100 protein–ligand complexes constructed by Wang et al. (J Med Chem 2003, 46, 2287), and compared with 14 other scoring functions. The results show that ITScore yielded a high success rate of 82% on identifying native‐like binding modes under the criterion of rmsd ≤2 Å for each top‐ranked ligand conformation. The success rate increased to 98% if the top five conformations were considered for each ligand. In the case of binding affinity prediction, ITScore also obtained a good correlation for this test set (R = 0.65). Next, ITScore was used to predict binding affinities of a second diverse test set of 77 protein–ligand complexes prepared by Muegge and Martin (J Med Chem 1999, 42, 791), and compared with four other widely used knowledge‐based scoring functions. ITScore yielded a high correlation of R2 = 0.65 (or R = 0.81) in the affinity prediction. Finally, enrichment tests were performed with ITScore against four target proteins using the compound databases constructed by Jacobsson et al. (J Med Chem 2003, 46, 5781). The results were compared with those of eight other scoring functions. ITScore yielded high enrichments in all four database screening tests. ITScore can be easily combined with the existing docking programs for the use of structure‐based drug design. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006
Control of delocalization and structural changes by means of an electric field
Authors: Karafiloglou Padeleimon 
Published: September 2006

AbstractThe strength and, mainly, the direction of a static electric field can be used to control delocalization effects occurring in a non‐polar π‐system. The delocalization energy, the weights, and the probabilities of some local electronic structures, the behavior of electron pairs, and the electronic fluctuations are considered and examined in cis‐butadiene, used as model system. The effects of the electric field are detected and evaluated in the basis of natural orbital spaces appropriate to investigate the behavior of one‐ and poly‐electron distributions. The consequences of modifying the delocalization effects on structural changes are also investigated. Full geometry optimizations in both Hartree–Fock and MP2 levels show that the changes in bond lengths, guided by the changes of the behavior of the electronic assembly, can be controlled by means of the electric field. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006
QM/QM study of the coverage effects on the adsorption of amino‐cyclopentene at the Si(100) surface
Authors: Santos Hugo R. R. , Ujaque Gregori , Ramos Maria J. , Gomes José A. N. F. 
Published: September 2006

AbstractIn this work, we have tested 30 different adsorption situations in several coverage scenarios for the 1‐amino‐3‐cyclopentene (ACP) molecule on the Si(100) surface. We have used a five‐spot testing zone inserted in the high‐level part of a quantum‐mechanical/quantum‐mechanical study performed in a big cluster. By defining several different scenarios, each one with a typical adsorption energy, we were able to understand in detail the process of surface functionalization. We are able to justify why the functionalization of this silicon surface achieves only a coverage of ˜0.5ML (half monolayer) and why the completely covered surface should be thermodynamically impossible to obtain. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006
Analysis of the segmented contraction of basis functions using density matrix theory
Authors: Custodio Rogério , Gomes André Severo Pereira , Sensato Fabrício Ronil , Trevas Júlio Murilo dos Santos 
Published: September 2006

AbstractA particular formulation based on density matrix (DM) theory at the Hartree‐Fock level of theory and the description of the atomic orbitals as integral transforms is introduced. This formulation leads to a continuous representation of the density matrices as functions of a generator coordinate and to the possibility of plotting either the continuous or discrete density matrices as functions of the exponents of primitive Gaussian basis functions. The analysis of these diagrams provides useful information allowing: (a) the determination of the most important primitives for a given orbital, (b) the core‐valence separation, and (c) support for the development of contracted basis sets by the segmented method. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006
Spatial and acoustic pressure dependence of microbubble‐mediated gene delivery targeted using focused ultrasound
Authors: Rahim Ahad A. , Taylor Sarah L. , Bush Nigel L. , ter Haar Gail R. , Bamber Jeffrey C. , Porter Colin D. 
Published: September 2006

AbstractBackgroundUltrasound/microbubble‐mediated gene delivery has the potential to be targeted to tissue deep in the body by directing the ultrasound beam following vector administration. Application of this technology would be minimally invasive and benefit from the widespread clinical experience of using ultrasound and microbubble contrast agents. In this study we evaluate the targeting ability and spatial distribution of gene delivery using focused ultrasound.MethodsUsing a custom‐built exposure tank, Chinese hamster ovary cells in the presence of SonoVue® microbubbles and plasmid encoding β‐galactosidase were exposed to ultrasound in the focal plane of a 1 MHz transducer. Gene delivery and cell viability were subsequently assessed. Characterisation of the acoustic field and high‐resolution spatial analysis of transfection were used to examine the relationship between gene delivery efficiency and acoustic pressure.ResultsIn contrast to that seen in the homogeneous field close to the transducer face, gene delivery in the focal plane was concentrated on the ultrasound beam axis. Above a minimum peak‐to‐peak value of 0.1 MPa, transfection efficiency increased as acoustic pressure increased towards the focus, reaching a maximum above 1 MPa. Delivery was microbubble‐dependent and cell viability was maintained.ConclusionsGene delivery can be targeted using focused ultrasound and microbubbles. Since delivery is dependent on acoustic pressure, the degree of targeting can be determined by appropriate transducer design to modify the ultrasound field. In contrast to other physical gene delivery approaches, the non‐invasive targeting ability of ultrasound makes this technology an attractive option for clinical gene therapy. Copyright © 2006 John Wiley & Sons, Ltd.
A peptide‐based immunoassay for antibodies against botulinum neurotoxin A
Authors: Atassi M. Zouhair , Dolimbek Behzod Z. , Deitiker Philip , Jankovic Joseph , Aoki K. Roger 
Published: September 2006

AbstractCervical dystonia (CD) is due to neck‐muscle spasms that cause pain and involuntary contractions resulting in abnormal neck movements and posture. Symptoms can be relieved by injecting the affected muscle with a botulinum neurotoxin (BoNT, usually type A or type B). The therapeutic benefits are impermanent and toxin injections need to be repeated every 3–6 months. In a very small percentage of patients (less with BoNT/A than with BoNT/B) the treatment elicits blocking anti‐toxin antibodies (Abs), which reduce or terminate the patient's responsiveness to further treatment. We have recently mapped (Dolimbek et al., 2006) the CD sera Ab‐binding profile using a panel of 60, 19‐residue peptides that encompassed the entire H chain sequence 449–1296 and overlapped consecutively by 5 residues. Abs in CD sera bound to one or more of the peptides N25, C10, C15, C20, and C31. This suggested the possibility that binding to these peptides could be used for assay of Abs in CD sera. Data analysis reported here found that Ab binding to these regions showed very significant deviations from the control responses. Of these four peptides, C10 showed the most significant level of separation between patient and control groups (p = 5 × 10−7) and the theoretical resolution (i.e., ability to distinguish CD patients from control, see full definition under ‘Statistical analysis’ in Methods), 84%, was about 4% higher than the least resolved response, C31 (p = 6 × 10−6, resolution 80%). Since the amounts of Abs bound to a given peptide varied with the patient and not all the patients necessarily recognized all four peptides, there was the possibility that binding to combinations of two or more peptides might give a better discriminatory capability. Using two peptides, C10 plus C31, the resolution improved to 87% (p = 4 × 10−8). These two peptides appeared to compliment each other and negate the lower resolution of C31. Combination of three peptides gave resolutions that ranged from 85 (N25 + C15 + C31; p = 2 × 10−7) to 88% (C10 + C15 + C31; p = 1 × 10−8). Finally, using the data of all four peptides, N25 + C10 + C15 + C31, gave a resolution of 86% (p = 1 × 10−7). Although these levels of resolution are somewhat lower than that obtained with whole BoNT/A (resolution 97%; p = 6 × 10−12), it may be concluded that the two‐peptide combination C10 + C31, or the three‐peptide combination C10 + C15 + C31 (affording resolutions of 87 and 88%, respectively) provide a good diagnostic, toxin‐free procedure for assay of total specific anti‐toxin Abs in BoNT/A‐treated CD patients. Copyright © 2006 John Wiley & Sons, Ltd.
Quantitative analysis of EO9 (apaziquone) and its metabolite EO5a in human plasma by high‐performance liquid chromatography under basic conditions coupled to electrospray tandem mass spectrometry
Authors: Vainchtein Liia D. , Rosing Hilde , Mirejovsky Dorla , Huynh Van , Lenaz Luigi , Hillebrand Michel J. X. , Schellens Jan H. M. , Beijnen Jos H. 
Published: September 2006

AbstractA sensitive and specific LC‐MS/MS assay for the quantitative determination of EO9 and its metabolite EO5a is presented. A 200‐µl human plasma aliquot was spiked with a mixture of deuterated internal standards EO9‐d3 and EO5a‐d4 and extracted with 1.25 ml ethyl acetate. Dried extracts were reconstituted in 0.1 M ammonium acetate—methanol (7 : 3, v/v) and 25 µl‐volumes were injected into the HPLC system. Separation was achieved on a 150 × 2.1 mm C18 column using an alkaline eluent (1 mM ammonium hydroxide—methanol (gradient system)). Detection was performed by positive ion electrospray followed by tandem mass spectrometry. The assay quantifies a range from 5 to 2500 ng/ml for EO9 and from 10 to 2500 ng/ml EO5a using 200 µl of human plasma samples. Validation results demonstrate that EO9 and EO5a concentrations can be accurately and precisely quantified in human plasma. This assay will be used to support clinical pharmacologic studies with EO9. Copyright © 2006 John Wiley & Sons, Ltd.
Striatal specificity of gene expression dysregulation in Huntington's disease
Authors: Thomas Elizabeth A. 
Published: September 2006

AbstractHuntington's disease (HD) is a progressive neurodegenerative disorder caused by an expanded CAG repeat region in exon 1 of the HD gene. This mutation results in the presence of an abnormally long polyglutamine tract in the encoded protein, huntingtin (htt). A major question in this field is how the mutant htt protein, which is expressed ubiquitously throughout the brain and body, causes severe neuropathologic changes predominantly in the striatum. The mechanisms accounting for this specificity are unknown. The role of transcriptional dysregulation in the pathophysiology of HD has gained much attention in recent years, however, this theory has been unable to explain the specificity of dysfunction and degeneration in HD. Microarray studies have showed hundreds of gene expression changes in mouse models of HD and in post‐mortem brain samples from HD subjects. Among the genes whose expression levels are preferentially altered are those that exhibit enriched expression in the striatum, which we have argued are the most relevant to disease pathology. These “striatal‐enriched” genes are associated with several systems previously implicated in HD pathology, especially disturbances in transcriptional processes and calcium homeostasis. Large‐scale changes in striatal gene expression in this manner would likely have particularly devastating effects to normal striatal function and could explain the specificity of striatal dysfunction and ultimate neurodegeneration observed in HD. © 2006 Wiley‐Liss, Inc.
Phosphorylation of glutamate receptors: A potential mechanism for the regulation of receptor function and psychostimulant action
Authors: Wang John Q. , Liu Xianyu , Zhang Guochi , Parelkar Nikhil K. , Arora Anish , Haines Michelle , Fibuch Eugene E. , Mao Limin 
Published: September 2006

AbstractIonotropic glutamate receptors,N‐methyl‐d‐aspartate receptors (NMDARs) and α‐amino‐3‐hydroxy‐5‐methylisoxazole‐4‐propionic acid receptors (AMPARs), are densely distributed in the mammalian brain and actively regulate a variety of cellular activities. Expression and function of these receptors are also under a tight regulation by many molecular mechanisms. Protein phosphorylation represents one of the important mechanisms for the posttranslational modulation of these receptors. Constitutive and regulatory phosphorylation occurs at distinct sites (serine, threonine, or tyrosine) on the intracellular C‐terminal domain of almost all subunits capable of assembling a functional channel. Several key protein kinases, such as protein kinase A, protein kinase C, Ca2+/calmodulin‐dependent protein kinases, and tyrosine kinases are involved in the site‐specific catalyzation and regulation of NMDAR and AMPAR phosphorylation. Through the phosphorylation mechanism, these protein kinases as well as protein phosphatases control biochemi cal properties (biosynthesis, delivery, and subunit assembling), subcellular distribution, and interactions of these receptors with various synaptic proteins, which ultimately modify the efficacy and strength of excitatory synapses containing NMDARs and AMPARs and many forms of synaptic plasticity. Emerging evidence shows that psychostimulants (cocaine and amphetamine) are among effective agents that profoundly alter the phosphorylation status of both receptors in striatal neurons in vivo. Thus, psychostimulants may modulate NMDAR and AMPAR function through the phosphorylation mechanism to shape the excitatory synaptic plasticity related to additive properties of drugs of abuse. © 2006 Wiley‐Liss, Inc.
Brain‐derived neurotrophic factor regulation of N‐methyl‐D‐aspartate receptor‐mediated synaptic currents in suprachiasmatic nucleus neurons
Authors: Kim Y.I. , Choi H.‐J. , Colwell C.S. 
Published: September 2006

AbstractLight information reaches the suprachiasmatic nucleus (SCN) through a subpopulation of retinal ganglion cells. Previous work raises the possibility that brain‐derived neurotrophic factor (BDNF) and its high‐affinity receptor TrkB may be important as modulators of this excitatory input into the SCN. To test this possibility, we used whole‐cell patch‐clamp methods to measure excitatory currents in rat SCN neurons. These currents were evoked by electrical stimulation of the optic nerve. We found that the amplitude of the N‐methyl‐D‐aspartate (NMDA) component of the evoked excitatory postsynaptic currents (NMDA‐EPSC) was increased by application of BDNF. The neurotrophin also increased the magnitude of NMDA‐evoked currents in SCN neurons. The BDNF enhancement of the NMDA‐EPSC was blocked by treatment with the neurotrophin receptor antagonist K252a as well as treatment with the soluble form of the TrkB receptor engineered as an immunoadhesin (TrkB IgG). Finally, the BDNF enhancement was lost in brain slices treated with the NR2B antagonist ifenprodil. The results demonstrate that BDNF and TrkB receptors are important regulators of retinal glutamatergic synaptic transmission within the SCN. © 2006 Wiley‐Liss, Inc.
Effect of short‐term anaerobic conditions on the production of volatiles, activity of alcohol acetyltransferase and other quality traits of ripened bananas. Sumithra K Wendakoon. Yoshinori Ueda. Yoshihiro Imahori. Megumi Ishimaru. Journal of the Science of Food and Agriculture, 2006; 86: 1475–1480
Authors: Wendakoon Sumithra K , Ueda Yoshinori , Imahori Yoshihiro , Ishimaru Megumi 
Published: September 2006

AbstractThe original article to which this Erratum refers was published in Journal of the Science of Food and Agriculture, 2006; 86: 1475–1480.
A pilot investigation comparing low‐energy, double pass 1,450 nm laser treatment of acne to conventional single‐pass, high‐energy treatment
Authors: Bernstein Eric F. 
Published: September 2006

AbstractBackground and ObjectivesLaser treatment using a 1,450 nm diode laser has been shown to improve acne and acne scarring. Its widespread adoption in younger populations has been significantly limited by discomfort.Study Design/Materials and MethodsSix subjects with active papular acne were treated in a pilot study to determine parameters for a split‐face, double‐pass, low‐energy protocol of 1,450 nm laser treatment. Sides of the face were randomized to receive single‐pass, high‐energy treatment (13–14 J/cm2), or double‐pass, low energy treatment (8–11 J/cm2), for a total of four treatments delivered at monthly intervals. Acne counts and standardized, digital photograph were performed 2 months following the final treatment, and compared to pre‐treatment counts and photographs.ResultsImprovement was evaluated comparing pre‐ and post‐treatment photos and averaged 2.5 for the high‐energy, single‐pass side and 2.3 for the low‐energy, double‐pass side, using a 0 (worse) to 4 (max improvement) scale. Acne counts were reduced 78% on the high‐energy, single‐pass side and 67% on the low‐energy, double‐pass side. Pain ratings on a 1 (min) to 10 (max) scale averaged 5.6 (range 1–9) for the high‐energy, single‐pass side and 1.3 (range 1–2) for the low‐energy, double‐pass side.ConclusionsLow‐energy, double‐pass 1,450 nm laser treatment effectively reduces acne counts 2 months post‐treatment, and dramatically reduces the pain associated with treatment. The treatment parameters used in this study have eliminated the need for anesthetic cream in daily practice. Lasers Surg. Med. 39:193–198, 2007. © 2007 Wiley‐Liss, Inc.
Erosion Behavior of Ionically Crosslinked Polyampholyte Gels Under DC Electric Fields
Authors: Zhao Yanbing , Chen Wanyu , Xia Jianjun , Liu Wei , Yang Yajiang , Xu Huibi , Yang Xiangliang 
Published: September 2006

AbstractSummary: An ionic complex of anionic and cationic monomers was obtained when (N,N‐diethylamino)ethylmethacrylate (DEAEM) was protonated with acrylic acid (AAc). Through the free radical copolymerization of the ionic complex and acrylamide (AAm) in aqueous solution, a novel ionically crosslinked polyampholyte gel (poly(AAc‐DEAEM‐AAm), designated PADA) was prepared without chemical crosslinker. An investigation of swelling behavior indicated that PADA gels exhibited peculiar erosion phenomena under contact and non‐contact DC electric fields. Under contact DC electric fields, PADA gels of swollen equilibrium experienced a dual response to DC fields, i.e., swelling first and then erosion. This phenomenon has not been described elsewhere. In contrast to with the contact DC electric fields, PADA gels did not undergo a swelling process, but eroded completely within 20 min under non‐contact DC fields. The NaCl concentration in electrolyte solutions greatly influenced the swelling/eroding behavior of PADA gels because the ionic crosslinkages of PADA gels could be weakened and screened by salt ions. The combined effects of higher NaCl concentration and local pH change near the electrode under DC electric fields resulted in crosslinkages quickly dissociating into cationic and anionic groups. In this case, PADA gels did not experience the swelling process, but directly eroded. Moreover, the erosion rate of PADA gels was related to the voltage of the electric field. The swelling/eroding rate for the gels in contact with the cathode was faster than that for the gels in contact with the anode. This difference can be attributed to varying local pH near different electrodes.The erosion process of PADA gels under non‐contact DC fields.magnified imageThe erosion process of PADA gels under non‐contact DC fields.
(Co)polymerisation Behaviour of Supported Metallocene Catalysts: Carrier Effect
Authors: Białek Marzena , Czaja Krystyna 
Published: September 2006

AbstractSummary: The polymerisation and copolymerisation of ethylene with 1‐hexene over metallocene catalysts L2ZrCl2/MAO (L = Cp, n‐BuCp, t‐BuCp, i‐PrCp, Me5Cp) supported on different types of carriers (MgCl2(MeOH)6 or silica with CH3 surface groups obtained in the sol‐gel process) were studied. It was demonstrated that both the metallocene structure and the type of inorganic support affected catalyst activity and polymer properties such as melting point, molecular weight and molecular weight distribution. The metallocene structure also determined comonomer incorporation, both for homogeneous and supported catalytic systems. When a catalyst is anchored on a support, it becomes less effective at incorporating a comonomer into the polyethylene chain, and the type of the support material has no influence on that process. The type of carrier used does, however, have an influence on the molecular weight and molecular weight distribution of the product obtained. Most polymers and copolymers obtained with catalysts supported on an oxide carrier have higher molecular weights and broader molecular weight distributions than those produced by catalysts anchored on a magnesium compound.Melting curves (obtained using the SSA method) of ethylene/1‐hexene copolymers synthesised with Cp2ZrCl2/MAO (A) and with the same catalyst supported on various carriers (B,C,D).magnified imageMelting curves (obtained using the SSA method) of ethylene/1‐hexene copolymers synthesised with Cp2ZrCl2/MAO (A) and with the same catalyst supported on various carriers (B,C,D).
Fractionation and Characterisation of Propylene‐Ethylene Random Copolymers: Effect of the Comonomer on Crystallisation of Poly(propylene) in the γ‐Phase
Authors: Harding Gareth W. , van Reenen Albert J. 
Published: September 2006

AbstractSummary: Three propylene‐ethylene random copolymers, of varying ethylene content, were fractionated using preparative TREF. The TREF fractions were subsequently analysed offline by CRYSTAF, DSC, 13C NMR spectroscopy, HT‐GPC, and WAXD. The effect of the ethylene comonomer on the crystallisability of the propylene was investigated, along with the effect of the comonomer on the type of crystal phase formed during the crystallisation. The results show that the comonomer inhibits the crystallisation of the copolymer and that as the ethylene content increases, the crystallisation and melting points decrease. It was also shown that the higher the ethylene content, the more of the γ‐phase crystal type is formed. The inter‐molecular distribution of the ethylene comonomer and stereo errors vary between the samples analysed, and this accounts for the relative differences in crystallisation behaviour of the samples.13C NMR of propylene‐ethylene random copolymer.magnified image13C NMR of propylene‐ethylene random copolymer.