bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antiretroviral genotypic resistance in plasma RNA and whole blood DNA in HIV‐1 infected patients failing HAART
Authors: Saracino Annalisa , Gianotti Nicola , Marangi Marianna , Cibelli Donatella C. , Galli Andrea , Punzi Grazia , Monno Laura , Lazzarin Adriano , Angarano Gioacchino ,   on behalf of the Mutations, Salvage (MuSa) Study Group
Published: August 2008

AbstractThe extent to which HIV‐1 proviral DNA mutations cause clinically relevant antiretroviral resistance is still controversial. Paired plasma HIV‐1 RNA and whole blood DNA were compared in patients failing HAART to investigate if the additional knowledge of archived mutations could improve the selection of potentially active drugs. Seventy‐three HIV‐1‐infected patients with first/second HAART failure were studied before starting a new regimen based on RNA genotyping. Follow‐up data after a 12‐week therapy were available. DNA genotyping was retrospectively performed on stored whole blood samples and mutational profiles were compared to those from RNA. The mean number of IAS pol mutations was significantly higher in RNA (4.45 ± 2.76) than in DNA (2.88 ± 2.47) (P < 0.001). DNA genotyping provided a 6% increase in detection of resistance‐associated mutations. Among 64/73 patients showing discordant DNA/RNA profiles, 54 (84%) also differed for predicted active drugs. 16/73 (22%) patients had ≥1 mutation revealed by DNA genotyping alone, probably affecting therapy success in 2/16. However, neither RNA/DNA discordance nor detection of isolated DNA mutations were statistically associated with outcome. In conclusion, plasma RNA remains the elective choice for HIV genotyping in patients with therapy failure, even if the detection of proviral resistance‐associated mutations, not simultaneously found in RNA, is a frequent event. Therefore, in some cases DNA plus RNA genotyping might assist in choosing more accurately subsequent antiretroviral regimens. J. Med. Virol. 80:1695–1706, 2008. © 2008 Wiley‐Liss, Inc.
Viruses in community‐acquired pneumonia in children aged less than 3 years old: High rate of viral coinfection
Authors: Cilla Gustavo , Oñate Eider , Perez‐Yarza Eduardo G. , Montes Milagrosa , Vicente Diego , Perez‐Trallero Emilio 
Published: August 2008

AbstractThe occurrence of viral coinfections in childhood pneumonia has received little attention, probably because suitable detection methods have been lacking. Between November 2004 and October 2006, the presence of 14 respiratory viruses in children aged less than 3 years old with community‐acquired pneumonia were investigated using molecular or immunochromatographic techniques and/or viral culture. A total of 315 children (338 episodes) were included, and hospitalization was required in 178 episodes. At least one virus was detected in 66.9% of the episodes and simultaneous detection of two or more viruses was frequent (27% of the episodes with viral detection). The most frequently detected virus was respiratory syncytial virus (n = 67: 33 subgroup A, 33 subgroup B, 1 not typed), followed by human bocavirus (n = 48), rhinovirus (n = 46), human metapneumovirus (n = 39: 13 genotype A2, 8 B1, 5 B2, 1 A1, 12 not genotyped) and parainfluenza viruses (n = 38: 1 type 1, 3 type 2, 22 type 3, 11 type 4 and 1 not typed). The 14 viruses investigated were found in viral coinfections, which were more frequent in children aged less than 12 months. Except for adenovirus, the incidence of which was low, the percentage of viral coinfection ranged between 28.2% and 68.8%. Children with viral coinfection more frequently required hospital admission than those with single viral infection. It is concluded that viral coinfections are frequent in children aged less than 3 years old with community‐acquired pneumonia and can be a poor prognostic factor. J. Med. Virol. 80:1843–1849, 2008. © 2008 Wiley‐Liss, Inc.
HIV‐1 diversity among inmates of Italian prisons
Authors: Longo Benedetta , Novati Stefano , Montieri Stefania , Pontali Emanuele , Taglia Fabiana , Leo Guido , Babudieri Sergio , Starnini Giulio , Monarca Roberto , Suligoi Barbara , Rezza Giovanni , Ciccozzi Massimo ,   on behalf of the Italian Study Group on HIV in Prison (ISGHP)
Published: August 2008

AbstractIn Italy, the prevalence of non‐B HIV‐1 subtypes ranges reportedly from 5.4% to 12.6%, yet there are no data on their circulation in prisons, where the prevalence of HIV infection is high. A retrospective study was conducted to evaluate the circulation of non‐B subtypes and to characterize their determinants in five Italian prisons. To this end an aliquot of samples of blood was taken in the period 2001–2006 from all 262 HIV‐positive inmates in whom antiretroviral treatment had failed. Complete HIV‐1 PR and RT regions were sequenced for all samples and subjected to phylogenetic analysis; 250 (95.4%) sequences clustered with subtype B. The non‐B subtype was found in 4% of Italian prison inmates and 16.7% of non‐Italian prison inmates; the overall percentage increased from 1.8% for inmates infected in 1982–1990 to 4.4% in 1991–1999 and 21.9% in 2000–2006. Factors significantly associated with non‐B subtypes were an exposure to other than injecting drug use and a first positive HIV test in 2000–2006. Non‐B subtypes were distributed within five monophyletic clades. In all cases but one, it was possible to correlate the history of HIV‐exposure to the origin of the clade, with high bootstrap values. In conclusion, although the sample may not be representative of the prison inmate population in Italy, the data suggest strongly that the circulation of non‐B subtypes has apparently increased. Non‐B subtypes were found to have been associated with heterosexual contact and time of the first HIV‐positive test. Knowledge of the different subtypes circulating in prisons may be useful for tracking the epidemiology of HIV infection and for choosing antiretroviral therapy. J. Med. Virol. 80:1689–1694, 2008. © 2008 Wiley‐Liss, Inc.
Phylogenetic reconstruction of HCV genotype 1b dissemination in a small city centre: The Camporeale model
Authors: Ferraro Donatella , Genovese Domenico , Argentini Claudio , Giordano Viviana , Pizzillo Paola , Stroffolini Tommaso , Craxì Antonio , Rapicetta Maria , Di Stefano Rosa 
Published: August 2008

AbstractSeveral seroepidemiological population‐based surveys carried out in Italy have shown a high prevalence of hepatitis C virus (HCV) infection. Camporeale (CP), a small Sicilian town with a 10.4% prevalence of HCV mostly genotype 1b, probably represents a specific context, since intravenous drug addiction, and sexual promiscuity are almost absent. In order to reconstruct the pattern of introduction and diffusion of HCV in this ecological niche, the NS5 genomic region of 72 HCV genotype 1 isolates (39 from CP and 33 collected throughout Sicily) was amplified and sequenced. Sequences were aligned and analyzed by BioEdit, PAUP and BEAST, and their molecular evolution compared. Thirty‐eight HCV genotype 1b isolates from CP were associated in a monophyletic “transmission cluster.” By applying Monte Carlo Markov simulation, it was calculated that HCV was introduced between the end of the 1940s and the beginning of the 1950s. The phylogenetic distance between the CP cluster and other Sicilian isolates confirmed its uniqueness and the local diffusion from a common ancestor. The data obtained from classic phylogenetic analysis, combined with the application of the Bayesian analysis to the study of the coalescence of phylogenetic trees, have shown that, in CP, few HCV native strains have been transmitted in a limited length of time probably through iatrogenic routes, and then have not spread further. J. Med. Virol. 80:1723–1731, 2008. © 2008 Wiley‐Liss, Inc.
Prevalence and genotype identification of human JC virus in colon cancer in Taiwan
Authors: Lin Paul Yann , Fung Chiung‐Yau , Chang Fang‐Pei , Huang Wen‐Shih , Chen Wen‐Cheng , Wang Jeng‐Yi , Chang Deching 
Published: August 2008

AbstractAlthough JC virus (JCV), a human polyomavirus, has been detected in colon cancers, the association between JCV and colon cancer remains controversial. In Taiwan, the prevalence of JCV infection in colon cancer patients has not been reported. Thus, the purpose of this study was to investigate JCV infection in colon cancers in Taiwan. Formalin‐fixed, paraffin‐embedded tissues from 22 colon cancer patients were examined in this study. Nested PCR was performed to detect viral genomic DNA. The product of the nested PCR flanking the JCV regulatory region was sequenced further. Viral large tumor protein, LT, and late capsid protein, VP1, were examined by immunohistochemistry (IHC). Nested PCR revealed JCV genomic DNA in 86.4% (19/22) of the colon cancer tissue samples. Both rearranged and archetypal genotypes of JCV were identified. Expression of JCV LT was positive in 63.6% (14/22) of the examined colon cancer tissue samples but not in any adjacent normal region. Expression of viral capsid protein VP1 was not detected in any of the tissues examined. The current study demonstrates that JCV genomic DNA was present in the examined colon cancer tissues. The genotypes of JCV in colon cancer tissues were also identified. Expression of viral early protein but not structural capsid protein was detected in the examined colon cancer tissues. Furthermore, a high prevalence of JCV infection in colon cancer tissues in Taiwan was also demonstrated. J. Med. Virol. 80:1828–1834, 2008. © 2008 Wiley‐Liss, Inc.
Influence of signal‐peptide truncations on the functional expression of Escherichia coli γ ‐glutamyltranspeptidase
Authors: Lo Huei‐Fen , Chou Wei‐Mou , Chen Pei‐Jing , Lin Long‐Liu 
Published: August 2008

AbstractThe full‐length Escherichia coli γ ‐glutamyltranspeptidase (EcGGT) gene and five truncations lacking 33, 51, 54, 60, and 78 bp respectively at the 5′ end were prepared by polymerase chain reaction and cloned into the expression vector pQE‐30. Isopropyl‐β ‐D‐thiogalactopyranoside induction of E. coli M15 cells bearing the recombinant plasmids resulted in the intracellular production of the expressed proteins, EcGGT, EcGGT/ΔN11, EcGGT/ΔN17, EcGGT/ΔN18, EcGGT/ΔN20, and EcGGT/ΔN26. The overexpressed enzymes were purified to near homogeneity by Ni2+‐NTA resin. The specific activity for EcGGT, EcGGT/ΔN11 and EcGGT/ΔN17 was 5.3, 4.9, and 4.8 U/mg protein respectively, whereas the rest three enzymes had shown no GGT activity under the enzyme assay conditions. More than 94% of the activity was found in the cytoplasmic fraction of E. coli M15 cells harboring pQE‐EcGGT, pQE‐EcGGT/ΔN11 or pQE‐EcGGT/ΔN17. Western blot analysis confirmed that the majority of N‐terminally truncated enzymes were present in the cytoplasm. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Intervening sequences in 23S rRNA genes and 23S rRNA fragmentation in Taylorella asinigenitalis UCD‐1T strain
Authors: Tazumi Akihiro , Sekizuka Tsuyoshi , Moore John E. , Millar Cherie B. , Taneike Ikue , Matsuda Motoo 
Published: August 2008

AbstractPCR was performed with Taylorella asinigenitalis UCD‐1T using two primer pairs constructed in silico for the amplification of the intervening sequences (IVSs) in the first quarter and central regions of the 23S rRNA gene. Following TA cloning and sequencing, the strain was identified to carry heterogeneous and multiple IVSs. Two similar tandem repeat units of 25 and 24 base pairs (bp) with unknown function(s) were identified within the two IVSs in the central region. Secondary structure models of IVSs, containing stem and loop structures, were demonstrated. Although 16S rRNA and 4–5S RNA species were identified in the purified RNA fraction, no 23S rRNAs were evident, resulting in the occurrence of some smaller RNA fragments from approximately 500 to 1600 bp, in length. Thus, the 23S rRNA primary transcripts may be cleaved into some smaller fragments and IVSs. No IVS transcript was detected by northern blot hybridization analysis. The present and previous results strongly demonstrate the occurrence of heterogeneous and multiple IVSs in 23S rRNA gene sequences and 23S rRNA fragmentation, in T. asinigenitalis. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The surface layer protein of Bacillus thuringiensis CTC forms unique intracellular parasporal inclusion body
Authors: Zhu Chenguang , Yu Ziniu 
Published: August 2008

AbstractBacillus thuringiensis subsp. finitimus strain CTC forms round parasporal inclusion body. The inclusion body protein gene ctc has been cloned and characterized. Sequence homology analysis reveals that the amino acid sequence of CTC protein shows 87% identity with the surface layer (S‐layer) protein Sap (GenBank Z36946) in B. anthracis. In this report, transmission electron microscope observation showed that CTC formed intracellular parasporal inclusion body and sheet structure of S‐layer‐like protein at the spore phase. Furthermore, the ctc gene was transformed into an acrystalliferous B. thuringiensis strain BMB171. The resulting transformant could form parasporal body which had the same shape and molecular weight of protein with that of B. thuringiensis CTC. These results, together with the sequence homology analysis of ctc gene, confirmed that the unique intracellular parasporal inclusion body of B. thuringiensis was comprised of S‐layer protein. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Solution structure determination of oligoureas using methylene spin state selective NMR at 13C natural abundance
Authors: Guichard Gilles , Violette Aude , Chassaing Gérard , Miclet Emeric 
Published: August 2008

AbstractAbility of N,N′‐linked oligoureas containing proteinogenic side chains to adopt a stable helix conformation in solution has been described recently. NMR as well as circular dichroism (CD) spectroscopies were employed to gain insight into their specific fold. It is herein proposed to extend the structural information available on these peptidomimetics by an advantageous use of a methylene spin state selective NMR experiment. Homodecoupling provided by the pulse scheme made it possible to readily measure conformation‐dependent 3JHH constants that are difficult if not impossible to obtain with standard NMR experiments. Adding those couplings to the NMR restraints improved the quality of the structure calculations significantly, as judged by a ca 30% decrease of the root mean square deviation (RMSD) obtained over an ensemble of 20 structures. Moreover, accurate determination of individual 1JCH couplings within each methylene group revealed uniform values throughout the oligourea sequence, with 1JCH systematically slightly larger for the pro‐S hydrogen than for the pro‐R. As shown in this study, the methylene spin state selective NMR experiment displays a good intrinsic sensitivity and could therefore provide valuable structural information at 13C natural abundance for peptidomimetic molecules and foldamers bearing diastereotopic methylene protons. Copyright © 2008 John Wiley & Sons, Ltd.
Preparation of Pie‐Shaped and Rugged Aromatic Polyamide Particles
Authors: Yoshioka Yayoi , Asao Katsuya 
Published: August 2008

AbstractAromatic polyamide particles were prepared by reacting diamines and diacid chlorides in a reaction solution containing water. They consisted of submicron‐sized pie‐shaped or rugged spherical particles with a narrow size distribution. The surface morphology of these particles was found to vary with the volume of water added, the reaction solvent, and the monomer concentration, but the degree of crystallinity of the particles obtained was almost the same. In addition, the molecular weight of the resulting material depended on the volume of water added and the monomer concentration. During the particle formation process, the degree of crystallinity was set at the initial stage, and thereafter the morphology and the molecular weight changed gradually with reaction time.magnified image
Effect of phosphate electrolyte buffer on the dynamics of water in tendon and cartilage
Authors: Zheng ShaoKuan , Xia Yang 
Published: August 2008

AbstractA number of NMR spectroscopic and microscopic MRI (µMRI) techniques were used to study proton dynamics in canine tendon and articular cartilage immersed in normal saline solution (NaCl solution) and high‐concentration phosphate‐buffered saline (PBS) solution. In a proton CPMG experiment on tendons, the T2 relaxation of the tissue was found to be anisotropic and had two populations. When immersed in saline, the T2 values were short and their relative populations were anisotropic. When immersed in PBS, the T2 values increased and their relative populations became isotropic. These phenomena, also verified by proton double‐quantum‐filtered (DQF) NMR spectroscopy, were interpreted as the catalyzing effect of phosphate ions on proton exchange between water molecules. In the experiment on articular cartilage, the immersion of cartilage–bone blocks in PBS resulted in a significant reduction in the laminar appearance of cartilage on MRI (the magic angle effect). The quantitative T2 anisotropy by µMRI at 13 µm pixel resolution and DQF NMR spectroscopy confirmed the substantial effect of PBS on the water dynamics in cartilage tissue blocks. This preliminary study has two important implications. For in vitro cartilage research, this work confirms the importance of the salt solution in which the specimen is stored – not all salts have the same effect on the measurable quantities in NMR and MRI. For in vivo cartilage diagnosis, especially using whole‐body MRI scanners, this work suggests the possibility of using a suitable electrolyte as a novel contrast agent to assess the ultrastructural changes in cartilage due to tissue degradation. Copyright © 2008 John Wiley & Sons, Ltd.
Multiwall carbon nanotube films surface‐doped with electroceramics for sensor applications
Authors: Kukovecz Ákos , Smajda Rita , Őze Mariann , Schaefer Balázs , Haspel Henrik , Kónya Zoltán , Kiricsi Imre 
Published: August 2008

AbstractSelf‐supporting mats of multi‐wall carbon nanotubes (MWCNT buckypaper) are an interesting and versatile nanotube application platform. In the course of our explorations in this field we prepared MWCNT buckypapers with a surface density of 5.6 mg·cm–2 and modified their surface with pyroelectric LiNbO3 and piezoelectric KNbO3 crystals. The temperature and pressure sensitivity of the prepared devices was different than that of the undoped buckypapers: the temperature response increased, the pressure response decreased compared to undoped MWCNT mats. The described method seems to open a new pathway for buckypaper functionalization. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Boron doped graphene nanostructures
Authors: Quandt Alexander , Özdoğan Cem , Kunstmann Jens , Fehske Holger 
Published: August 2008

AbstractWe present results from an ab initio study of metallized semiconducting graphene nanostructures. Our model system consists of an alternating chain of quasi– planar B7 clusters embedded into a semiconducting armchair nanoribbon. We observe the appearance of overlapping bands around the Fermi‐level, with crystal momenta pointing into the direction of these boron chains. This observation could be a vantage point for the development of graphene nanodevices and integrated nanocircuits, based on existing technologies. Unit cell of B7‐doped armchair graphene nanoribbon. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Quantitative analysis of dispersion and doping of individual carbon nanotubes in water based solutions using absorption and Raman spectroscopy
Authors: Priya B. R. , Byrne H. J. 
Published: August 2008

AbstractThe concentration dependence of the dispersion of carbon nanotubes in water surfactant solution is monitored using absorption and Raman spectroscopy revealing a debundling below ∼0.07 g/l. A quantitative analysis of the doping of individual carbon nanotubes in surfactant at this concentration is conducted by varying the pH from 1 to 13 and monitoring the Raman spectrum. Mixed Gaussian and Lorentzian line shapes were fitted to the radial breathing modes and using a simple protonation model, an equilibrium constant Kp was obtained for each RBM. The protonation rate was related to the optical band gap of the tubes and the number of protons acting per entity was also calculated. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electrochemical functionalization of SWNT bundles in acid and salt media as observed by Raman and X‐ray photoelectron spectroscopy
Authors: Rafailov Peter M. , Thomsen Christian , Monev Milko , Dettlaff‐Weglikowska Urszula , Roth Siegmar 
Published: August 2008

AbstractWe carried out electrochemical functionalization of single‐walled carbon nanotube mats (buckypaper) in HCl and KCl aqueous solutions by exposing them to electrochemical potentials above the Cl– oxidation potential and high Faradaic currents. Formation of C‐Cl covalent bonds was established by X‐ray Photoelectron Spectroscopy (XPS). Combining results from Raman, XPS and conductivity measurements, we find a significantly higher degree of covalent functionalization in the HCl solution as compared to the KCl one. We also discuss the impact of electrochemical doping and functionalization on the morphology and the conductivity of the SWNT sample. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Carbon diffusion in CVD growth of carbon nanotubes on metal nanoparticles
Authors: Yazyev Oleg V. , Pasquarello Alfredo 
Published: August 2008

AbstractDiffusion of carbon is the crucial step in chemical vapor deposition (CVD) growth of carbon nanotubes (CNTs) on metal nanoparticles. Using first principles techniques we model the binding and diffusion of carbon atoms and dimers on late transition (Ni, Pd, Pt) and coinage (Cu, Ag, Au) metal catalysts. We consider various diffusion mechanisms including both surface and subsurface channels, finding the lowest activation barriers for carbon adatoms on nanoparticles of coinage metals. For these metals, our calculations further show that the diffusion is restricted to the nanoparticle surface when diatomic carbon is initially obtained from the decomposition of the precursor gas. In combination with the results for the binding of CNT fragments to metal nanoparticles, we conclude that coinage metal catalysts, in particular Cu, favor CVD growth of CNTs at low temperatures and with narrow chirality distributions. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Professional development of statisticians in the pharmaceutical sector: evolution over the past decade and into the future
Authors: Lewis Trevor 
Published: August 2008

AbstractThe adoption of The International Conference on Harmonization Tripartite Guideline: Statistical Principles for Clinical Trials (ICH‐E9) has provided a foundation for the application of statistical principles in clinical research and raised awareness of the value of a statistical contribution to the wider pharmaceutical R&D process. In addition, over the past decade globalization of the pharmaceutical R&D process and the measures taken to address reduced productivity and spiralling costs have impacted on the roles and career opportunities for statisticians working in the pharmaceutical sector. This has enhanced the need for continuing professional development to equip statisticians with the skills to fully contribute to creating innovative solutions. In the future, key areas of focus are the establishment of professional standards for statistical work and increasing the collaboration between statisticians working in industry, regulatory agencies and academia. In addition, the diversity of roles and potential career paths for statisticians embarking on a career in the pharmaceutical sector emphasizes the importance of mentoring and coaching. For the more experienced statisticians, there are unprecedented opportunities to lead and innovate. Copyright © 2008 John Wiley & Sons, Ltd.