bluuebunny/crossref_metadata_2025_split huggingface dataset:
Block copolymers by chemoenzymatic cascade polymerization: A comparison of consecutive and simultaneous reactions
Authors: de Geus Matthijs , Schormans Linda , Palmans Anja R. A. , Koning Cor E. , Heise Andreas 
Published: June 2006

AbstractThe synthetic parameters for the chemoenzymatic cascade synthesis of block copolymers combining enzymatic ring‐opening polymerization (EROP) and atom transfer radical polymerization (ATRP) in one pot were investigated. A detailed analysis of the mutual interactions between the single reaction components revealed that the ATRP catalyst system could have a significant inhibiting effect on the enzyme activity. The inhibition of the enzyme was less pronounced in the presence of multivalent ligands such as dinonyl bipyridine, which thus could be used in this reaction as an ATRP catalyst. Moreover, the choice of the ATRP monomer was investigated. Methyl methacrylate interfered with EROP by transesterification, whereas t‐butyl methacrylate was inert. Block copolymers were successfully synthesized with this cascade approach by the activation of ATRP after EROP by the addition of the ATRP catalyst and, with lower block copolymer yields, by the mixing of all the components before the copolymerization. Adetailed kinetic analysis of the reactions and the structure of the block copolymers showed that the first procedure proceeded smoothly to high block copolymer yields, whereas in the latter a noteworthy amount of the poly(t‐butyl methacrylate) homopolymer was detected. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 4290–4297, 2006
New solvent for polyrotaxane. II. Dissolution behavior of polyrotaxane in ionic liquids and preparation of ionic liquid‐containing slide‐ring gels
Authors: Samitsu Sadaki , Araki Jun , Kataoka Toshiyuki , Ito Kohzo 
Published: June 2006

AbstractThe dissolution behavior of polyrotaxanes, consisting of α‐cyclodextrin and poly(ethylene glycol), with different molecular weights (2000 and 35,000) was investigated. Halogen‐containing ionic liquids, such as chlorides or bromides, were found to be good solvents for polyrotaxanes, regardless of their cations. Dissolution required a high temperature (above 90 °C), while intensive heating over 105 °C seemed to cause decomposition of the polyrotaxane. The discovery of new solvents for polyrotaxane was applied in the preparation of ionic liquid‐containing slide‐ring gels (SR gels), that is supramolecular networks of polyrotaxane swollen with ionic liquids, using a devised “non‐drying” technique accompanied by solvent exchange. Significant swelling of the SR gels with the ionic liquids was confirmed by dynamic mechanical measurements. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1985–1994, 2006
Structures of N‐acetylornithine transcarbamoylase from Xanthomonas campestris complexed with substrates and substrate analogs imply mechanisms for substrate binding and catalysis
Authors: Shi Dashuang , Yu Xiaolin , Roth Lauren , Morizono Hiroki , Tuchman Mendel , Allewell Norma M. 
Published: June 2006

AbstractN‐acetyl‐L‐ornithine transcarbamoylase (AOTCase) is a new member of the transcarbamoylase superfamily that is essential for arginine biosynthesis in several eubacteria. We report here crystal structures of the binary complexes of AOTCase with its substrates, carbamoyl phosphate (CP) or N‐acetyl‐L‐ornithine (AORN), and the ternary complex with CP and N‐acetyl‐L‐norvaline. Comparison of these structures demonstrates that the substrate‐binding mechanism of this novel transcarbamoylase is different from those of aspartate and ornithine transcarbamoylases, both of which show ordered substrate binding with large domain movements. CP and AORN bind to AOTCase independently, and the main conformational change upon substrate binding is ordering of the 80's loop, with a small domain closure around the active site and little movement of the 240's loop. The structures of the complexes provide insight into the mode of substrate binding and the mechanism of the transcarbamoylation reaction. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Prediction of protein subcellular localization
Authors: Yu Chin‐Sheng , Chen Yu‐Ching , Lu Chih‐Hao , Hwang Jenn‐Kang 
Published: June 2006

AbstractBecause the protein's function is usually related to its subcellular localization, the ability to predict subcellular localization directly from protein sequences will be useful for inferring protein functions. Recent years have seen a surging interest in the development of novel computational tools to predict subcellular localization. At present, these approaches, based on a wide range of algorithms, have achieved varying degrees of success for specific organisms and for certain localization categories. A number of authors have noticed that sequence similarity is useful in predicting subcellular localization. For example, Nair and Rost (Protein Sci 2002;11:2836–2847) have carried out extensive analysis of the relation between sequence similarity and identity in subcellular localization, and have found a close relationship between them above a certain similarity threshold. However, many existing benchmark data sets used for the prediction accuracy assessment contain highly homologous sequences—some data sets comprising sequences up to 80–90% sequence identity. Using these benchmark test data will surely lead to overestimation of the performance of the methods considered. Here, we develop an approach based on a two‐level support vector machine (SVM) system: the first level comprises a number of SVM classifiers, each based on a specific type of feature vectors derived from sequences; the second level SVM classifier functions as the jury machine to generate the probability distribution of decisions for possible localizations. We compare our approach with a global sequence alignment approach and other existing approaches for two benchmark data sets—one comprising prokaryotic sequences and the other eukaryotic sequences. Furthermore, we carried out all‐against‐all sequence alignment for several data sets to investigate the relationship between sequence homology and subcellular localization. Our results, which are consistent with previous studies, indicate that the homology search approach performs well down to 30% sequence identity, although its performance deteriorates considerably for sequences sharing lower sequence identity. A data set of high homology levels will undoubtedly lead to biased assessment of the performances of the predictive approaches—especially those relying on homology search or sequence annotations. Our two‐level classification system based on SVM does not rely on homology search; therefore, its performance remains relatively unaffected by sequence homology. When compared with other approaches, our approach performed significantly better. Furthermore, we also develop a practical hybrid method, which combines the two‐level SVM classifier and the homology search method, as a general tool for the sequence annotation of subcellular localization. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Tebufenozide resistance selected in Plutella xylostella and its cross‐resistance and fitness cost
Authors: Cao Guangchun , Han Zhaojun 
Published: June 2006

AbstractA susceptible strain of diamondback moth, Plutella xylostella (L.), was used to select for resistance to tebufenozide in the laboratory. After continuous selection with tebufenozide 17 times during 35 generations, a resistant strain was achieved with high resistance to tebufenozide (RR 93.8). Bioassay revealed that this strain showed high cross‐resistance to abamectin (RR 35.7), methoxyfenozide (29.1) and JS118 (16.5), and a little to deltamethrin (3.9), but no obvious cross‐resistance was found to cypermethrin (1.3), fipronil (1.3), trichlorfon (1.1), chlorfenapyr (1.0), phoxim (0.9) and acephate (0.8). The resistant and susceptible insects had similar development rates, but life table tests indicated that the resistant strain showed reproductive disadvantages, including decreased copulation rate, reproductivity and hatchability. When compared with the susceptible strain, the resistant insects had a relative fitness of only 0.3. This indicated that tebufenozide resistance selected under laboratory conditions had considerable fitness costs in this pest, and therefore rotational use of insecticides without cross‐resistance is recommended to delay development of resistance. Copyright © 2006 Society of Chemical Industry
Inhibition of protein tyrosine phosphatase 1B by lignans from Myristica fragrans
Authors: Yang Senugmi , Min Kyun Na , Jang Jun Pil , Kim Kyung Ah , Kim Bo Yeon , Sung Nak Ju , Oh Won Keun , Ahn Jong Seog 
Published: June 2006

AbstractInhibition of protein tyrosine phosphatase 1B (PTP1B) has been proposed as one of the drug targets for treating type 2 diabetes and obesity. Bioassay‐guided fractionation of a MeOH extract of the semen of Myristica fragrans Houtt. (Myristicaceae) afforded PTP1B inhibitory compounds, meso‐dihydroguaiaretic acid (1) and otobaphenol (2). Compounds 1 and 2 inhibited PTP1B with IC50 values of 19.6 ± 0.3 and 48.9 ± 0.5 µm, respectively, in the manner of non‐competitive inhibitors. Treatment with compound 1 on 32D cells overexpressing the insulin receptor (IR) resulted in a dose‐dependent increase in the tyrosine phosphorylation of IR. These results indicate that compound 1 can act as an enhancing agent in intracellular insulin signaling, possibly through the inhibition of PTP1B activity. Copyright © 2006 John Wiley & Sons, Ltd.
A new method to determine interstitial flow patterns in flume studies of sub‐aqueous gravel bedforms such as fish nests
Authors: Carling P. A. , Whitcombe L. , Benson I. A. , Hankin B. G. , Radecki‐Pawlik A. M. 
Published: June 2006

AbstractFlume studies often seek to measure and record the interstitial flow within plane‐bed sediment bodies and within sediment beds with wavy surfaces, such as those typified by salmonid fish spawning nests and river‐dunes. A simple, inexpensive method is described to record and map, at discrete points, the spatial variation in interstitial flow speeds in experimental fine gravel beds. The procedure uses activated carbon granules to capture a tracer: Rhodamine WT dye. Calibration of the uptake of dye by the carbon for known interstitial flow speeds allows mapping of point flow speed data initially in the nominal x‐dimension. Using interpolation procedures available in a range of commercial ‘mapping’ software packages, the point data can be used to produce quasi two‐dimensional ‘slices’ along sampling planes within the three‐dimensional gravel bed. Similarly, three‐dimensional representations can be produced within which lines of equal current speed (‘isovels’) are interpolated such that the flow vectors (in x, y and z coordinates) may be inferred. Copyright © 2006 John Wiley & Sons, Ltd.
Measurement of serotonin transporter binding with PET and [11C]MADAM: A test–retest reproducibility study
Authors: Lundberg Johan , Halldin Christer , Farde Lars 
Published: June 2006

Abstract[11C]MADAM, or [11C]N,N‐dimethyl‐2‐(2‐amino‐4‐methylphenyl thio)benzylamine, is a radioligand suitable for positron emission tomography (PET) studies of the serotonin transporter (5‐HTT) in man. The purpose of this study was to examine the test–retest reproducibility using a design tailored for future applied studies. Nine healthy male subjects were examined with PET and [11C]MADAM under baseline conditions at two occasions 4–8 weeks apart. The subjects participated in a Phase 1 trial to which the present study was an addendum. Eight regions of interest were studied, including frontal cortex, hippocampal complex, and the raphe nuclei. All regions, but the raphe nuclei, were defined on MR‐images to which the PET‐images were coregistered using SPM2. Binding potentials were calculated using the simplified reference tissue model, with cerebellum as reference region. Test–retest data were calculated from the binding potentials, and included binding potential (BP) quotient, BP difference, and the intraclass correlation coefficient. The quotient was about one in all regions, and the mean difference varied between 0 and 11%. The intraclass correlation coefficient varied between 0.96 and 0.51 in the raphe nuclei and averaged bilateral regions. [11C]MADAM was shown to have good to excellent reliability in measurements of 5‐HTT binding in brain regions of interest in research on psychiatric disorders. Synapse 60:256–263, 2006. © 2006 Wiley‐Liss, Inc.
Malleus–stapes assembly: experience with two prostheses
Authors: Al-Qudah M , Dawes P J D 
Published: June 2006

Tympanoplasty is often a necessary part of middle-ear surgery, the most common defect being that between an intact, mobile stapes and the malleus handle. The most readily available tissue is the patient's incus, reshaped to bridge the space between an intact stapes and the malleus. When the incus cannot be used, the hydroxyapatite Wehrs incus prosthesis® can be used as an alternative.Twenty-six patients had an autograft incus ossiculoplasty and 20 patients underwent modified Wehrs incus prosthesis ossiculoplasty. The average post-operative air–bone gaps (ABGs) were 16.2 dB hearing loss (dBHL) and 17.2 dBHL, respectively. Air–bone gap closure to within 15 dBHL was achieved for 48 per cent of incus autografts and for 57 per cent of Wehrs prostheses, and to within 20 dBHL for 77 per cent and 62 per cent, respectively. Over four years follow up, the reconstruction was stable for each group, the ABGs being 17.7 dBHL and 17.1 dBHL, respectively.
Bilateral medialization thyroplasty: an effective approach to severe, chronic aspiration
Authors: Thevasagayam M S , Willson K , Jennings C , Pracy P 
Published: June 2006

Aims: To demonstrate the efficacy of bilateral medialization thyroplasty as a treatment for severe, chronic aspiration. To review the literature on surgical options available in the treatment of severe aspiration.Materials and methods: Three cases that underwent bilateral medialization thyroplasty are described. The technique used was the standard medialization thyroplasty described by Isshiki as a unilateral procedure. The assessment and rehabilitation of these patients is discussed.Results: All patients stopped aspirating following surgery. One patient returned to a normal diet and one patient returned to a solid diet. All patients required a permanent tracheostomy.Conclusion: Bilateral medialization thyroplasty offers an effective surgical option in the treatment of severe, chronic aspiration. It maintains good voice, with a possible return to oral diet. The operation is easily reversible if the patient's condition alters.
Insight in first-episode psychosis
Authors: McEVOY JOSEPH P. , JOHNSON JACKIE , PERKINS DIANA , LIEBERMAN JEFFREY A. , HAMER ROBERT M. , KEEFE RICHARD S. E. , TOHEN MAURICIO , GLICK IRA D. , SHARMA TONMOY 
Published: June 2006

Background. We report here a study examining the relationships between insight and psychopathology, cognitive performance, brain volume and co-morbid depression in 251 patients experiencing a first episode of psychosis, who were then randomly assigned to 2 years of double-blind treatment with either olanzapine or haloperidol.Method. Repeated measures of insight were obtained at baseline and 12, 24, 52 and 104 weeks by the Insight and Treatment Attitudes Questionnaire (ITAQ).Results. Older age, female gender and white ethnicity were associated with more insight. Higher total, positive, negative and general psychopathology scores on the Positive and Negative Syndromes Scale (PANSS) were associated with less insight. Higher depression scores were associated with more insight. Better neurocognitive function and large brain volumes were associated with more insight. More insight throughout the study was associated with longer time to medication non-adherence. However, baseline insight was not significantly related to the probability of discontinuing the study before 2 years. Insight improved significantly over the course of the study, but the improvement in insight was not significantly different between the two antipsychotic treatment groups.Conclusions. Multiple factors contribute to insight. Patients experiencing a first episode of psychosis who have little insight are at increased risk of discontinuing their medication.
Are extended working days sustainable in radiotherapy?
Authors: Routsis D. , Thomas S. , Head J. 
Published: June 2006

A number of Radiotherapy Departments have extended the working day on linear accelerators, as a method of increasing treatment capacity. However, reports from the Royal College of Radiologists predict a rate of increase in requirements for radiotherapy, significantly in excess of the rate at which radiographers will become available to run the necessary equipment.Based on the premise that radiographers are the most difficult staff group to recruit, a number of different patterns of radiotherapy linear accelerator use has been investigated, with an aim of seeing which delivers the greatest return on radiographer time. The requirement for radiographers per linac-hour has been examined for a number of lengths of day and utilising various staffing assumptions.Given current patterns of work, the greatest manpower efficiency in use of trained radiographers is achieved if machines are run for a 7-h-day or for an 8-h-day if part-time radiographers are available. This working pattern relies on all ancillary tasks being removed from the treatment unit, many of which can be performed by other appropriately trained, non-radiographer, staff groups.With linac-hour demand projected to rise faster than the rate at which new trained radiographers become available, extended working days are not sustainable without significant change to current work patterns.
An evaluation of ultrasound localisation for verification of external beam radiotherapy to the prostate
Authors: Richards J. 
Published: June 2006

The recent advent of highly conformal three-dimensional radiotherapy techniques and Intensity Modulated Radiotherapy now allows higher radiation doses to be delivered. It is well-documented that the prostate is susceptible to both interfraction and intrafraction movements due to various physiological processes. Therefore there has been a recent general consensus that good immobilisation and electronic portal imaging is no longer sufficient to ensure accurate treatment verification. This idea has led to the concept of image-guided radiotherapy, which includes modalities such as cone-beam computed tomography and ultrasound to localise the prostate prior to treatment.There has been considerable research undertaken to determine the effectiveness of each of the image guided modalities and these studies have identified the benefit and limitations of each modality. Ultrasound is a non-invasive technique using a suprapubic ultrasound probe, which seems to be quite promising in terms of cost and time. However until large scales studies are performed which demonstrate the value of using ultrasound localisation, as an alternative to electronic portal imaging, it is likely that current practice will remain unchanged.
PROBER: oligonucleotide FISH probe design software
Authors: Navin Nicholas , Grubor Vladimir , Hicks Jim , Leibu Evan , Thomas Elizabeth , Troge Jennifer , Riggs Michael , Lundin Pär , Månér Susanne , Sebat Jonathan , Zetterberg Anders , Wigler Michael 
Published: June 2006

Abstract
PROBER is an oligonucleotide primer design software application that designs multiple primer pairs for generating PCR probes useful for fluorescence in situ hybridization (FISH). PROBER generates Tiling Oligonucleotide Probes (TOPs) by masking repetitive genomic sequences and delineating essentially unique regions that can be amplified to yield small (100–2000 bp) DNA probes that in aggregate will generate a single, strong fluorescent signal for regions as small as a single gene. TOPs are an alternative to bacterial artificial chromosomes (BACs) that are commonly used for FISH but may be unstable, unavailable, chimeric, or non-specific to small (10–100 kb) genomic regions. PROBER can be applied to any genomic locus, with the limitation that the locus must contain at least 10 kb of essentially unique blocks. To test the software, we designed a number of probes for genomic amplifications and hemizygous deletions that were initially detected by Representational Oligonucleotide Microarray Analysis of breast cancer tumors.
Availability:
Contact: navin@cshl.edu
Competitive Metagenomic DNA Hybridization Identifies Host-Specific Microbial Genetic Markers in Cow Fecal Samples
Authors: Shanks Orin C. , Santo Domingo Jorge W. , Lamendella Regina , Kelty Catherine A. , Graham James E. 
Published: June 2006

ABSTRACT

Several PCR methods have recently been developed to identify fecal contamination in surface waters. In all cases, researchers have relied on one gene or one microorganism for selection of host-specific markers. Here we describe the application of a genome fragment enrichment (GFE) method to identify host-specific genetic markers from fecal microbial community DNA. As a proof of concept, bovine fecal DNA was challenged against a porcine fecal DNA background to select for bovine-specific DNA sequences. Bioinformatic analyses of 380 bovine enriched metagenomic sequences indicated a preponderance of
Bacteroidales
-like regions predicted to encode membrane-associated and secreted proteins. Oligonucleotide primers capable of annealing to select
Bacteroidales
-like bovine GFE sequences exhibited extremely high specificity (>99%) in PCR assays with total fecal DNAs from 279 different animal sources. These primers also demonstrated a broad distribution of corresponding genetic markers (81% positive) among 148 different bovine sources. These data demonstrate that direct metagenomic DNA analysis by the competitive solution hybridization approach described is an efficient method for identifying potentially useful fecal genetic markers and for characterizing differences between environmental microbial communities.
The Alkyltert-Butyl Ether Intermediate 2-Hydroxyisobutyrate Is Degraded via a Novel Cobalamin-Dependent Mutase Pathway
Authors: Rohwerder Thore , Breuer Uta , Benndorf Dirk , Lechner Ute , Müller Roland H. 
Published: June 2006

ABSTRACTFuel oxygenates such as methyl and ethyltert-butyl ether (MTBE and ETBE, respectively) are degraded only by a limited number of bacterial strains. The aerobic pathway is generally thought to run viatert-butyl alcohol (TBA) and 2-hydroxyisobutyrate (2-HIBA), whereas further steps are unclear. We have now demonstrated for the newly isolated β-proteobacterial strains L108 and L10, as well as for the closely related strain CIP I-2052, that 2-HIBA was degraded by a cobalamin-dependent enzymatic step. In these strains, growth on substrates containing thetert-butyl moiety, such as MTBE, TBA, and 2-HIBA, was strictly dependent on cobalt, which could be replaced by cobalamin. Tandem mass spectrometry identified a 2-HIBA-induced protein with high similarity to a peptide whose gene sequence was found in the finished genome of the MTBE-degrading strainMethylibium petroleiphilumPM1. Alignment analysis identified it as the small subunit of isobutyryl-coenzyme A (CoA) mutase (ICM; EC 5.4.99.13), which is a cobalamin-containing carbon skeleton-rearranging enzyme, originally described only inStreptomycesspp. Sequencing of the genes of both ICM subunits from strain L108 revealed nearly 100% identity with the corresponding peptide sequences fromM. petroleiphilumPM1, suggesting a horizontal gene transfer event to have occurred between these strains. Enzyme activity was demonstrated in crude extracts of induced cells of strains L108 and L10, transforming 2-HIBA into 3-hydroxybutyrate in the presence of CoA and ATP. The physiological and evolutionary aspects of this novel pathway involved in MTBE and ETBE metabolism are discussed.