bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disease model distortion in association studies
Authors: Vukcevic Damjan , Hechter Eliana , Spencer Chris , Donnelly Peter 
Published: March 2011

AbstractMost findings from genome‐wide association studies (GWAS) are consistent with a simple disease model at a single nucleotide polymorphism, in which each additional copy of the risk allele increases risk by the same multiplicative factor, in contrast to dominance or interaction effects. As others have noted, departures from this multiplicative model are difficult to detect. Here, we seek to quantify this both analytically and empirically. We show that imperfect linkage disequilibrium (LD) between causal and marker loci distorts disease models, with the power to detect such departures dropping off very quickly: decaying as a function of r4, where r2 is the usual correlation between the causal and marker loci, in contrast to the well‐known result that power to detect a multiplicative effect decays as a function of r2. We perform a simulation study with empirical patterns of LD to assess how this disease model distortion is likely to impact GWAS results. Among loci where association is detected, we observe that there is reasonable power to detect substantial deviations from the multiplicative model, such as for dominant and recessive models. Thus, it is worth explicitly testing for such deviations routinely. Genet. Epidemiol. 35: 278‐290, 2011.  © 2011 Wiley‐Liss, Inc.
Creating probabilistic maps of the face network in the adolescent brain: A multicentre functional MRI study
Authors: Tahmasebi Amir M. , Artiges Eric , Banaschewski Tobias , Barker Gareth J. , Bruehl Ruediger , Büchel Christian , Conrod Patricia J. , Flor Herta , Garavan Hugh , Gallinat Jürgen , Heinz Andreas , Ittermann Bernd , Loth Eva , Mareckova Klara , Martinot Jean‐Luc , Poline Jean‐Baptiste , Rietschel Marcella , Smolka Michael N. , Ströhle Andreas , Schumann Gunter , Paus Tomáš ,   The IMAGEN Consortium
Published: March 2011

AbstractLarge‐scale magnetic resonance (MR) studies of the human brain offer unique opportunities for identifying genetic and environmental factors shaping the human brain. Here, we describe a dataset collected in the context of a multi‐centre study of the adolescent brain, namely the IMAGEN Study. We focus on one of the functional paradigms included in the project to probe the brain network underlying processing of ambiguous and angry faces. Using functional MR (fMRI) data collected in 1,110 adolescents, we constructed probabilistic maps of the neural network engaged consistently while viewing the ambiguous or angry faces; 21 brain regions responding to faces with high probability were identified. We were also able to address several methodological issues, including the minimal sample size yielding a stable location of a test region, namely the fusiform face area (FFA), as well as the effect of acquisition site (eight sites) and scanner (four manufacturers) on the location and magnitude of the fMRI response to faces in the FFA. Finally, we provided a comparison between male and female adolescents in terms of the effect sizes of sex differences in brain response to the ambiguous and angry faces in the 21 regions of interest. Overall, we found a stronger neural response to the ambiguous faces in several cortical regions, including the fusiform face area, in female (vs. male) adolescents, and a slightly stronger response to the angry faces in the amygdala of male (vs. female) adolescents. Hum Brain Mapp, 2012. © 2011 Wiley Periodicals, Inc.
External light guidance for percutaneous dilatational tracheotomy
Authors: El‐Sayed Ivan H. , Ho James E. , Eisele David W. 
Published: March 2011

AbstractBackgroundPercutaneous dilatational tracheotomy (PDT) is considered a safe technique; however, there is still room for improvement. We present our initial experience with an external white light guide to position the endotracheal tube and guide needle placement during PDT.MethodsThis is a retrospective series of 15 consecutive patients undergoing external light–guided PDT. A white light source was placed on the anterior trachea wall externally and the transmitted light was identified in the tracheal lumen with a bronchoscopic to predict the needle entrance point.ResultsThe transmitted light was rapidly identified in all 15 patients, facilitated endotracheal tube tip placement in the subglottis in approximately 10 seconds in 13 of 15 patients, and predicted needle penetration into the trachea within 1 to 2 mm of the external light in all patients.ConclusionsExternal light guidance facilitates rapid, accurate placement of the needle through the tracheal wall and can reduce surgeon anxiety, especially in teaching situations. © 2011 Wiley Periodicals, Inc. Head Neck, 2011
TP53 Mutational signature for aristolochic acid: an environmental carcinogen
Authors: Moriya Masaaki , Slade Neda , Brdar Branko , Medverec Zvonimir , Tomic Karla , Jelaković Bojan , Wu Lin , Truong Sim , Fernandes Andrea , Grollman Arthur P. 
Published: March 2011

AbstractThis study was designed to establish the TP53 mutational spectrum of aristolochic acid (AA), examined in the context of endemic (Balkan) nephropathy, an environmental disease associated with transitional cell (urothelial) carcinomas of the upper urinary tract (UUC). Tumor tissue was obtained from residents of regions in Bosnia, Croatia and Serbia where endemic nephropathy has been prevalent for over 50 years. Fifty‐nine TP53 mutations were detected in 42 of the 97 tumors analyzed. Mutational spectra were dominated by A:T to T:A transversions with the mutated adenines located almost exclusively on the nontranscribed strand. This marked strand bias is attributed to selective processing of aristolactam‐dA adducts by transcription‐coupled nucleotide excision repair. Hotspots for A:T to T:A mutations include codons 131 and 179 and the 5′‐AG acceptor splice site of intron 6. The unique TP53 mutational signature for AA identified in this study can be used to explore the hypothesis that botanical products containing this human carcinogen and nephrotoxin are responsible, in part, for the high prevalence of UUC and chronic renal disease in countries where Aristolochia herbal remedies traditionally have been used for medicinal purposes.
Gene expression profiling of pituitary melanotrope cells during their physiological activation
Authors: Kuribara Miyuki , van Bakel Nick H.M. , Ramekers Dyan , de Gouw Daan , Neijts Roel , Roubos Eric W. , Scheenen Wim J.J.M. , Martens Gerard J.M. , Jenks Bruce G. 
Published: March 2011

AbstractThe pituitary melanotrope cells of the amphibian Xenopus laevis are responsible for the production of the pigment‐dispersing peptide α‐melanophore‐stimulating hormone, which allows the animal to adapt its skin color to its environment. During adaptation to a dark background the melanotrope cells undergo remarkable changes characterized by dramatic increases in cell size and secretory activity. In this study we performed microarray mRNA expression profiling to identify genes important to melanotrope activation and growth. We show a strong increase in the expression of the immediate early gene (IEG) c‐Fos and of the brain‐derived neurotrophic factor gene (BDNF). Furthermore, we demonstrate the involvement of another IEG in the adaptation process, Nur77, and conclude from in vitro experiments that the expression of both c‐Fos and Nur77 are partially regulated by the adenylyl cyclase system and calcium ions. In addition, we found a steady up‐regulation of Ras‐like product during the adaptation process, possibly evoked by BDNF/TrkB signaling. Finally, the gene encoding the 105‐kDa heat shock protein HSPh1 was transiently up‐regulated in the course of black‐background adaptation and a gene product homologous to ferritin (ferritin‐like product) was >100‐fold up‐regulated in fully black‐adapted animals. We suggest that these latter two genes are induced in response to cellular stress and that they may be involved in changing the mode of mRNA translation required to meet the increased demand for de novo protein synthesis. Together, our results show that microarray analysis is a valuable approach to identify the genes responsible for generating coordinated responses in physiologically activated cells. J. Cell. Physiol. 227: 288–296, 2012. © 2011 Wiley Periodicals, Inc.
Zinc Oxide Based Coatings for the UV‐Protection of Wood for Outdoor Applications
Authors: Weichelt Franziska , Beyer Mario , Emmler Rico , Flyunt Roman , Beyer Evelin , Buchmeiser Michael 
Published: March 2011

AbstractSummary: Nano‐sized zinc oxide (ZnO) was chosen as a suitable candidate for the UV‐protection of coatings. ZnO‐based acrylate coatings were applied to polycarbonate plates, glass plates and impregnated wood. Coated samples were artificially weathered (Xenon test) for at least 1500 hours and studied with regards to their optical and mechanical properties, such as color shifts (yellowing), as well as to changes in brightness, transparency or hydrophobicity. The prepared wood coatings showed reduced yellowing and improved optical properties.
LDH as Nanofiller: Organic Modification and Dispersion in Polymers
Authors: Costa F.R. , Leuteritz A. , Meinl J. , Wagenknecht U. , Heinrich G. 
Published: March 2011

AbstractSummary: Layered double hydroxide (LDH) is a relatively new class of layered crystalline clay materials to be used as nanofiller in various polymer matrices. We report here the organic modification of LDH by anionic surfactants having different sizes and functionalities. Subsequently, their dispersion in polymer is discussed and finally the characteristics of the polymer/LDH nanocomposites are investigated. LDH has been modified using regeneration method, which shows that irrespective of size and functionality of the anionic surfactant, organic modification can be carried out efficiently. However, it has been observed that alkyl sulfonate are more efficiently intercalated within LDH layers than other surfactants giving well defined crystal structure of the modified LDH. These modified LDH, when dispersed in polymers like maleic anhydride grafted polyethylene shows that not only the size of the surfactant, but also the functionality of the surfactant influences their dispersion in a non polar polymer matrix.
Ligand Efficiency Indices (LEIs): More than a Simple Efficiency Yardstick
Authors: Abad‐Zapatero Cele , Blasi Daniel 
Published: March 2011

AbstractThe concept of ligand efficiency and the usage of ligand efficiency values to assess the quality of fragments and compounds is becoming more accepted in the practice of medicinal chemistry. This is particularly true as it refers to the efficiency of ligands per unit size (i.e., binding affinity/number of non‐hydrogen atoms or binding affinity/MW). The use of the Ligand Efficiency Indices (LEIs) as variables for a Cartesian mapping of chemico‐biological space, the concept of AtlasCBS, has been presented in a recent publication with some initial drug‐discovery applications. In this communication, we present additional applications of the concept in three domains of drug discovery: i) analyze and compare the content of databases: inhibitors vs. drugs; ii) polypharmacology; and iii) applications to Fragment‐Based strategies. We suggest that the combined use of LEIs in a Cartesian representation of Chemico‐Biological Space (AtlasCBS) could be a useful tool in various aspects of drug‐discovery in the future.
A prognostic evaluation of vascular endothelial growth factor in children and young adults with osteosarcoma
Authors: Ługowska Iwona , Woźniak Wojciech , Klepacka Teresa , Michalak Elżbieta , Szamotulska Katarzyna 
Published: March 2011

AbstractBackgroundThe potential role of VEGF in osteosarcoma has been evaluated in several studies. The majority of them included heterogeneous and limited series of patients, giving conflicting results. The aim of presented study is to evaluate the prognostic role of VEGF‐A in biopsy samples of clinically homogeneous group of osteosarcoma patients with at least 5 years of follow up.Materials and MethodsVEGF‐A was assessed immunohistochemically in the pre‐treatment biopsy samples of 91 patients (mean age 14 years; range, 4–23 years) with primary, high‐grade, non‐metastatic osteosarcoma localized in extremities. The survival of each patient was assessed after at least 5‐year follow‐up period.ResultsVEGF‐A over 50% of positive tumor cells was observed in 39% of cases and was linked to patients age below 14‐year old (P = 0.025) and tumor size more than 8 cm (P = 0.054). VEGF‐A was associated with a significantly decreased both overall survival (P = 0.006) and progression‐free survival (P = 0.011). In the Cox proportional hazard model it was confirmed that VEGF‐A expression in the biopsy samples was an independent prognostic factor of unfavorable survival in osteosarcoma (HR 2.51; 95% CI: 1.12–5.66).ConclusionThe expression of VEGF‐A in the biopsy sample is the potential marker for predicting the course and outcome of osteosarcoma. Pediatr Blood Cancer 2011;57:63–68. © 2011 Wiley‐Liss, Inc.
Optical, electrical and morphological properties of transparent binary doped polyaniline thin films synthesized by in situ chemical bath deposition
Authors: Arenas Concepción , Sánchez Gabriela 
Published: March 2011

AbstractThe development of polymeric thin films has attracted attention in the optoelectronics field due to their transparency. The aim of the research presented was to obtain transparent polyaniline thin films by easy in situ oxidative polymerization of aniline with ammonium persulfate in the presence of a binary doping agent–poly(vinyl alcohol) mixture. Poly(acrylic acid), 2‐acrylamido‐2‐methyl‐1‐propanesulfonic acid or sodium dodecylsulfate were mixed with hydrochloric acid to form the binary doping agents. Polyaniline thin films were produced during aniline polymerization on Corning glass slides immersed in the mixture in order to study their optical, electrical and morphological properties. The optical absorption coefficient and the energy band gap were evaluated by optical transmission of the films in the UV‐visible spectral region. The optical absorption coefficient of all polyaniline films was of the order of 104 cm−1 with a maximum transmittance up to 80% at 550 nm. In order to investigate the effect of the mixture on the surface morphology and roughness of the films, atomic force microscopy was used. In general, surface roughness was reduced threefold by adding a mixture and optical transmission was increased by 20–30% without significantly affecting the absorption coefficient and the band gap of polyaniline. Islands and needle‐like structures on the film surfaces were obtained from various mixtures affecting the conductivity; for example, 0.17 S cm−1 was obtained from needle‐like morphology, while 1.9 × 10−4 S cm−1 was obtained from island morphology. Raman spectroscopy studies confirmed the presence of poly(vinyl alcohol) in the thin films. Copyright © 2011 Society of Chemical Industry
Cucurbit[7]uril moving on side chains of polypseudorotaxanes: Synthesis, characterization, and properties
Authors: Yang Hui , Hao Jingcheng , Tan Yebang 
Published: March 2011

AbstractNovel side chain polypseudorotaxanes with cucurbit[7]uril (CB[7]) threaded onto the side chains are synthesized from a water‐soluble polymer and CB[7] in water by simple stirring at room temperature. CB[7] beads could move from the hexyl groups to the benzyl and a part of viologen units in the side chains of polymer when the molar ratio of CB[7] to the monomer reaches from 1 to 2 as shown by 1H NMR studies, and it is considered that the hydrophobic and charge‐dipole interactions of CB[7] are the driving forces. The sizes of the polypseudorotaxanes with different molar ratio of CB[7] to 4VBVHeP in aqueous solution increase with increasing the molar ratio of CB[7] to 4VBVHeP as found by DLS and resonance light scattering, while the typical cyclic voltammograms and UV–vis data indicate that CB[7] are not threaded in the viologen units of P4VBVHeP, and the oxidation reduction characteristic of the polymer is remarkably affected by the addition of CB[7]. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
A novel method for the production of in vivo‐assembled, recombinant Escherichia coli RNA polymerase lacking the α C‐terminal domain
Authors: Twist Kelly‐Anne , Husnain Seyyed I. , Franke Josef D. , Jain Deepti , Campbell Elizabeth A. , Nickels Bryce E. , Thomas Mark S. , Darst Seth A. , Westblade Lars F. 
Published: March 2011

AbstractThe biochemical characterization of the bacterial transcription cycle has been greatly facilitated by the production and characterization of targeted RNA polymerase (RNAP) mutants. Traditionally, RNAP preparations containing mutant subunits have been produced by reconstitution of denatured RNAP subunits, a process that is undesirable for biophysical and structural studies. Although schemes that afford the production of in vivo‐assembled, recombinant RNAP containing amino acid substitutions, insertions, or deletions in either the monomeric β or β′ subunits have been developed, there is no such system for the production of in vivo‐assembled, recombinant RNAP with mutations in the homodimeric α‐subunits. Here, we demonstrate a strategy to generate in vivo‐assembled, recombinant RNAP preparations free of the α C‐terminal domain. Furthermore, we describe a modification of this approach that would permit the purification of in vivo‐assembled, recombinant RNAP containing any α‐subunit variant, including those variants that are lethal. Finally, we propose that these related approaches can be extended to generate in vivo‐assembled, recombinant variants of other protein complexes containing homomultimers for biochemical, biophysical, and structural analyses.
Identification and characterisation of ten glutathione S‐transferase genes from oriental migratory locust, Locusta migratoria manilensis (Meyen)
Authors: Qin Guohua , Jia Miao , Liu Ting , Xuan Tao , Yan Zhu Kun , Guo Yaping , Ma Enbo , Zhang Jianzhen 
Published: March 2011

AbstractBACKGROUND: Synthetic pyrethroids are the primary insecticides that are widely used for controlling Locusta migratoria manilensis (Meyen), a major pest in eastern and southern Asia and the Pacific region. In this paper, ten cDNAs encoding glutathione S‐transferases (GSTs) were sequenced and characterised in L. migratoria manilensis. The effects of deltamethrin on the ten GST gene expressions were studied.RESULTS: Phylogenetic analysis revealed nine GSTs in three different classes, including seven in sigma, one in delta and one in theta. The remaining GST (LmGSTu1) was unclassified. RT‐PCR analysis showed that most GST genes were expressed in all tissues examined, including the foregut, midgut, gastric caecum, hindgut, Malpighian tubules, fat bodies, muscles, spermaries and ovaries, except that LmGSTs2, LmGSTs4, LmGSTs7 and LmGSTu1 were expressed in several tissues. LmGSTu1 appeared to be the only gene whose expressions could not be detected in eggs. Real‐time quantitative PCR showed that deltamethrin at 0.08 and/or 0.12 µg mL−1 increased almost all ten GST gene expressions in third‐instar nymph locusts. However, deltamethrin at 0.16 and/or 0.2 µg mL−1 decreased the expressions of LmGSTd1, LmGSTs1, LmGSTs5 and LmGSTs6.CONCLUSION: The increases in GST gene expressions after deltamethrin exposure in L. migratoria manilensis might result in its elevating tolerance to other insecticides and xenobiotics. Copyright © 2011 Society of Chemical Industry
Temperature‐dependent grain growth and phase transformation in mixed anatase‐rutile nanocrystalline TiO2 films
Authors: Gnaser Hubert , Lösch Jörg , Orendorz Adam , Ziegler Christiane 
Published: March 2011

AbstractNanocrystalline TiO2 films were prepared from colloidal suspensions using a mixture of anatase and rutile TiO2 particles. Their structure was examined by X‐ray diffraction (XRD). The as‐prepared specimens exhibit the presence of both anatase and rutile crystallites with average sizes of ∼30 and ∼50 nm, respectively, as determined from their characteristic diffraction peaks in XRD. Isochronal annealing of the films for 90 min in air at temperatures of up to 1270 K effected clear structural changes: between 470 and 870 K, the crystallite sizes do not change, with the crystallites remaining in their original phase. For annealing temperatures Ta ≥ 970 K the anatase and rutile grain sizes increase, while above ∼1170 K, the anatase phase disappears and only crystallites in the rutile phase of TiO2 are observed. Their size increases further with increasing annealing temperature and reaches ∼150 nm at 1270 K. Concurrently, the weight fraction of rutile changes from an initial value of ∼0.09 (for 470−870 K) to unity (above 1170 K). At Ta = 970 K, the increase of the duration of annealing from 90 to 360 min leads to a moderate increase of the crystallite size. The results indicate that the transformation of anatase particles is governed by the concurrent occurrence of interface and surface nucleation processes.
Structural evolution of self‐assisted GaAs nanowires grown on Si(111)
Authors: Biermanns Andreas , Breuer Steffen , Davydok Anton , Geelhaar Lutz , Pietsch Ullrich 
Published: March 2011

AbstractGaAs nanowires are grown on Si(111) by self‐assisted molecular beam epitaxy, and the ratio between wurtzite and zinc‐blende phases is determined as function of nanowire length using asymmetric X‐ray diffraction. We show that under the applied growth conditions, nanowires grow in both phases during the initial stage of growth, whereas the zinc‐blende content increases with growth time and dominates in long nanowires. Compared to the zinc‐blende units, the vertical lattice parameter of the wurtzite segments is 0.7% larger, as measured by the positions of respective diffraction peaks. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effects of Lime Juice on Malaria Parasite Clearance
Authors: Adegoke S. A. , Oyelami O. A. , Olatunya O. S. , Adeyemi L. A. 
Published: March 2011

One hundred and twenty children with acute uncomplicated malaria who were managed at the children's outpatient department of the Wesley Guild Hospital, Ilesa (a unit of Obafemi Awolowo University Teaching Hospitals' Complex, Ile‐Ife, Osun state, Nigeria) were recruited into the study to determine the effects of lime juice on malaria parasite clearance. These children were randomized into treatment with World Health Organization recommended antimalarials (artemisinin combination therapy, ACT) either alone or with lime juice. Nine of them were lost to follow‐up, four were in the group that were managed with ACT and lime, and five in the group that were managed on ACT alone.The average (SD) time to achieve >75% reduction in parasite load was significantly lower in patients on ACT and lime; 30.5 ± 2.4 h against 38.6 ± 3.3 h for those on ACT alone (p < 0.001). Also, while a significantly higher proportion of children on antimalarial drugs and lime juice achieved complete parasite clearance by 72 h of therapy (p = 0.007), ten (18.2%) patients without lime had early treatment failure (p = 0.003). There were no side effects with the use of lime juice.It may therefore be inferred, from this preliminary work, that lime juice when used with the appropriate antimalarial may enhance malaria parasite clearance especially in those with uncomplicated malaria. Copyright © 2011 John Wiley & Sons, Ltd.
Alkali metal borides MeB (Me = Li, Na, K, Rb, Cs, Fr): CASPT2 calculations
Authors: Čukovičová Martina , Federič Jozef , Černušák Ivan 
Published: March 2011

AbstractThe binary alkali borides, which are yet to be studied experimentally are presented in this article. Ground and low‐lying excited states of MeB (Me = Li, Na, K, Rb, Cs, Fr) have been studied using multiconfigurational second‐order perturbation theory and coupled clusters techniques. We present the equilibrium bond lengths, harmonic frequencies, dissociation energies, and excitation energies. The manifold of the states contains potential energy curves of bound, weakly bound, and unbound species. The trends in molecular properties across the Group IA are discussed. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem 111:3438–3451, 2011