bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nested Hierarchal Organization of Conservation for MicroRNAs and Their Putative Targets to Drosophila melanogaster
Authors: Woodcock M. Ryan 
Published: May 2012

AbstractThis study examined microRNA network properties traced through taxonomic hierarchy considering both the acquisition of potential network targets and regulators. Primary literature review and database analyses were conducted to establish modules of conserved microRNAs across metazoan taxonomy. A hierarchical schema for the conservation of microRNAs and their putative targets to Drosophila melanogaster was engineered through comprehensive meta‐analysis, and conservation history of 90.39% of the total Drosophila dataset could be resolved through this hierarchical sampling regime; tracing from taxonomic order down to empire. The findings presented in this study represent a documentation of Drosophila microRNA regulatory network behavior thorough taxonomic hierarchy. MicroRNA regulatory network properties were found to transect taxonomic hierarchy. Newly acquired microRNAs from novel families reinforce the pre‐existing regulatory network, while expanding the target list to include a small number of novel genes. Lineage specific microRNAs were found to exhibit far fewer conserved targets than do the more broadly conserved microRNAs; even when considering only more recently emerged targets. There was a dramatic expansion in network complexity with the expansion of the microRNA repertoire, and this corresponds to the expansion in biological complexity.
Predicting Antigenicity of Proteins in a Bacterial Proteome; a Protein Microarray and Naïve Bayes Classification Approach
Authors: Liang Li , Felgner Philip L. 
Published: May 2012

AbstractDiscovery of novel antigens associated with infectious diseases is fundamental to the development of serodiagnostic tests and protein subunit vaccines against existing and emerging pathogens. Efforts to predict antigenicity have relied on a few computational algorithms predicting signal peptide sequences (SignalP), transmembrane domains, or subcellular localization (pSort). An empirical protein microarray approach was developed to scan the entire proteome of any infectious microorganism and empirically determine immunoglobulin reactivity against all the antigens from a microorganism in infected individuals. The current database from this activity contains quantitative antibody reactivity data against 35,000 proteins derived from 25 infectious microorganisms and more than 30 million data points derived from 15,000 patient sera. Interrogation of these data sets has revealed ten proteomic features that are associated with antigenicity, allowing an in silico protein sequence and functional annotation based approach to triage the least likely antigenic proteins from those that are more likely to be antigenic. The first iteration of this approach applied to Brucella melitensis predicted 37% of the bacterial proteome containing 91% of the antigens empirically identified by probing proteome microarrays. In this study, we describe a naïve Bayes classification approach that can be used to assign a relative score to the likelihood that an antigen will be immunoreactive and serodiagnostic in a bacterial proteome. This algorithm predicted 20% of the B. melitensis proteome including 91% of the serodiagnostic antigens, a nearly twofold improvement in specificity of the predictor. These results give us confidence that further development of this approach will lead to further improvements in the sensitivity and specificity of this in silico predictive algorithm.
Integration of Diverse Statistical Evidence of GeneTrait Association in Systems Biology Studies
Authors: Cheng Cheng 
Published: May 2012

AbstractThe rapid advancement of high‐throughput genomic assay technologies has generated large amounts of diverse genomic data in disparate human populations and diseases. These data provide a unique opportunity for biomedical investigators to systematically study multifaceted aspects of genes' involvement in the biological processes underlying important traits from the systems biology perspective. An important component in such a study is the inference that integrates diverse lines of statistical evidence for genetrait association from the observed trait values and the massive numbers of measured genomic features. A novel integrated statistical analysis procedure is developed in this paper and is illustrated by an application in studying childhood leukemia.
Prediction and Comparison of SalmonellaHuman and SalmonellaArabidopsis Interactomes
Authors: Schleker Sylvia , Garcia‐Garcia Javier , Klein‐Seetharaman Judith , Oliva Baldo 
Published: May 2012

AbstractSalmonellosis caused by Salmonella bacteria is a food‐borne disease and a worldwide health threat causing millions of infections and thousands of deaths every year. This pathogen infects an unusually broad range of host organisms including human and plants. A better understanding of the mechanisms of communication between Salmonella and its hosts requires identifying the interactions between Salmonella and host proteins. Proteinprotein interactions (PPIs) are the fundamental building blocks of communication. Here, we utilize the prediction platform BIANA to obtain the putative Salmonellahuman and SalmonellaArabidopsis interactomes based on sequence and domain similarity to known PPIs. A gold standard list of Salmonellahost PPIs served to validate the quality of the human model. 24,726 and 10,926 PPIs comprising interactions between 38 and 33 Salmonella effectors and virulence factors with 9,740 human and 4,676 Arabidopsis proteins, respectively, were predicted. Putative hub proteins could be identified, and parallels between the two interactomes were discovered. This approach can provide insight into possible biological functions of so far uncharacterized proteins. The predicted interactions are available via a web interface which allows filtering of the database according to parameters provided by the user to narrow down the list of suspected interactions. The interactions are available via a web interface at http://sbi.imim.es/web/SHIPREC.php.
Newborn Umbilical Cord Blood DNA Methylation and Gene Expression Levels Exhibit Limited Association with Birth Weight
Authors: Adkins Ronald M. , Tylavsky Frances A. , Krushkal Julia 
Published: May 2012

AbstractMost cases of fetal growth retardation are unexplained. These newborns are at high risk of serious illness or death in the neonatal period and exhibit significantly increased risk of specific chronic illnesses later in life. While there are several hypotheses to explain the well‐established association between low birth weight and later risk of disease, the true etiology is unknown. To search for molecular patterns that may explain the biological basis for reduced fetal growth in a clinically normal cohort, and possibly provide clues for the lifelong increased risk of disease, we surveyed genome‐wide DNA methylation and gene expression patterns in the umbilical cord blood of newborns born in Shelby County, TN. While we did not find genome‐wide significant associations of birth weight with either leukocytic gene expression or DNA methylation, we did find suggestive associations in several genes with known effects on pre‐ or postnatal growth and health. As with previous molecular epidemiological studies of birth weight, we did not sample the most biologically relevant tissues in the newborn. However, our discovery of biologically plausible associations in a peripheral tissue suggests that further studies of tissues key to fetal growth regulation are warranted.
Fluorine‐Directed β‐Galactosylation: Chemical Glycosylation Development by Molecular Editing
Authors: Durantie Estelle , Bucher Christoph , Gilmour Ryan 
Published: May 2012

AbstractValidation of the 2‐fluoro substituent as an inert steering group to control chemical glycosylation is presented. A molecular editing study has revealed that the exceptional levels of diastereocontrol in glycosylation processes by using 2‐fluoro‐3,4,6‐tri‐O‐benzyl glucopyranosyl trichloroacetimidate (TCA) scaffolds are a consequence of the 2R,3S,4S stereotriad. This study has also revealed that epimerization at C4, results in a substantial enhancement in β‐selectivity (up to β/α 300:1).
Effect of serum lipoproteins on stereoselective halofantrine metabolism by rat hepatocytes
Authors: Patel Jigar P. , Hamdy Dalia A. , El‐kadi A. O. , Brocks Dion R. 
Published: May 2012

AbstractExperimental hyperlipidemia has shown to decrease cytochrome P450 3A4 and 2C11 expression and to increase liver concentrations and the plasma protein binding of halofantrine (HF) enantiomers. The present study examined the effect of hyperlipidemic (HL) serum on the metabolism of HF enantiomers by primary rat hepatocytes. Hepatocytes from normolipidemic (NL) and HL (poloxamer 407 treated) rats were incubated with rac‐HF in cell media with or without additional rat serum (5%). In those incubations with rat serum, the hepatocytes were preincubated or coincubated with serum from NL or HL rats. Rat serum‐free hepatocyte incubations served as controls. Stereospecific assays were used to measure HF and desbutylhalofantrine (its major metabolite) enantiomer concentrations in whole well contents (cells + media). Concentrations of desbutylhalofantrine were not measurable. The disappearance (apparent metabolism) of (−)‐HF exceeded that of antipode, but HF metabolism did not differ between hepatocytes from NL and HL rats. Coincubation of HL rat serum with NL hepatocytes caused a significant decrease in the disappearance of (−)‐HF, whereas in HL hepatocytes, a substantially decreased apparent metabolism was noted for both enantiomers. Compared with NL serum, (−)‐HF disappearance was significantly lowered upon preincubation of NL hepatocytes with HL serum. A combination of factors including diminished drug metabolizing or lipoprotein receptor expression, and increased plasma protein binding in the wells, may have contributed to a decrease in apparent metabolism of the HF enantiomers in the presence of lipoproteins from HL rat serum. Chirality 24:558–565, 2012. © 2012 Wiley Periodicals, Inc.
A study on semiflows generated by cooperative full‐range CNNs
Authors: Di Marco Mauro , Forti Mauro , Grazzini Massimo , Nistri Paolo , Pancioni Luca 
Published: May 2012

ABSTRACTThe paper considers the full‐range (FR) model of cellular neural networks (CNNs) characterized by ideal hard‐limiter nonlinearities with two vertical segments in the current–voltage characteristic. It is shown that when the FRCNNs are cooperative, i.e., there are excitatory interconnections between distinct neurons, the generated solution semiflow is monotone and that monotonicity implies some fundamental restrictions on the geometry of omega‐limit sets. The result on monotonicity is a generalization to the class of differential inclusions describing the dynamics of FRCNNs of a classic result due to Kamke for cooperative ordinary differential equations. The paper also points out difficulties to use the standard theory of eventually strongly monotone (ESM) semiflows for addressing convergence of FRCNNs. By means of counterexamples, it is shown that, even assuming the irreducibility of the interconnections, the semiflow generated by a cooperative FRCNN is not ESM; furthermore, also the limit set dichotomy can be violated. Copyright © 2012 John Wiley & Sons, Ltd.
Photocatalytic and Photoelectrocatalytic Degradation of the Explosive RDX by TiO2 Thin Films Prepared by CVD and Anodic Oxidation of Ti
Authors: Tian Fang , Hitchman Michael L. , Shamlian Sarkis H. 
Published: May 2012

AbstractTwo kinds of TiO2 films prepared by CVD and by anodization of titanium mesh are compared for the photocatalytic (PC) and photoelectrocatalytic (PEC) degradation of RDX aqueous solutions illuminated under a 200 W UV light. The PC activity of anodically formed TiO2 is lower than that with CVD‐produced TiO2. The PC efficiencies of degradation of RDX with both anodized and CVD films are improved by applying a potential of 1 V versus saturated calomel electrode (SCE), with up to 95% of RDX being destroyed in two hours by a CVD‐produced TiO2 film, and 81% by anodized TiO2. Chemical analysis shows that during RDX degradation, nitrite is the first mineralized product which is further oxidized to nitrate.
New sources of retinoic acid synthesis revealed by live imaging of an Aldh1a2‐GFP reporter fusion protein throughout zebrafish development
Authors: Pittlik Silke , Begemann Gerrit 
Published: May 2012

AbstractBackground: Regulation of synthesis and turnover of retinoic acid (RA) is an important mechanism that controls the activity of RA signaling during vertebrate development. During embryonic patterning, the dynamic expression patterns of the aldh1a2 gene, which encodes a retinaldehyde dehydrogenase, provide the major source of RA, whereas the only other retinaldehyde dehydrogenase in teleosts, aldh1a3, is expressed later and locally restricted. Aldh1a2‐mediated RA synthesis has been shown to also regulate adult cell fates, such as during heart and fin regeneration. However, only very few other sites of postembryonic RA synthesis in vertebrates are known. We generated transgenic lines in zebrafish by BAC recombineering that express a fusion protein of Aldh1a2 and green fluorescent protein (GFP) under the control of endogenous aldh1a2 regulatory sequences (aldh1a2:gfp). Results:
aldh1a2:gfp reports the complete endogenous expression pattern in embryos and rescues embryonic lethality in aldh1a2 mutants. We identify novel postembryonic sources of RA synthesis, including lateral line support cells, in kidney‐derived organs that regulate calcium homeostasis, and in perichordal cells during vertebral development. Conclusions: The novel aldh1a2 reporter line is driven by the complete set of regulatory sequences required for zebrafish development, reports novel sources of RA synthesis, and identifies the source of RA that promotes vertebral ossification. Developmental Dynamics 241:1205–1216, 2012. © 2012 Wiley Periodicals, Inc.
Highly Oxidized Semiconducting Coordination Polymers – Coupled Oxidation and Coordination of Guanidine Electron Donors
Authors: Trumm Christine , Stang Simone , Eberle Benjamin , Kaifer Elisabeth , Wagner Norbert , Beck Johannes , Bredow Thomas , Meyerbröker Nikolaus , Zharnikov Michael , Hübner Olaf , Himmel Hans‐Jörg 
Published: May 2012

AbstractRedox and coordination processes are coupled in the course of reactions of the organic electron donors 1,2,4,5‐tetrakis(tetramethylguanidino)benzene (1) and 1,2,4,5‐tetrakis(N,N′‐dimethyl‐N,N′‐ethyleneguanidino)benzene (2) with silver salts. Experiments with several different silver salts show that the product structure is significantly affected by the properties of the anion in these salts. Chain polymers are the products of reactions with AgPF6 or AgBF4, in which dicationic organic building blocks are connected by silver ions. Experiments with AgNO3 yielded either dinuclear complexes (with 1) or 2D networks (with 2). If the salt Ag[Al{OC(CF3)3}4], featuring a weakly coordinating anion, was used, simple silver‐free salts of the guanidine dication were obtained. The thermal stability, optical properties, and electrical conductivity were studied in detail for the product polymer {[(1)Ag](PF6)3}n. From the temperature dependence of the electric conductivity, this compound was found to be a semiconductor with a band gap of approximately 3 eV. The experiments were complemented by quantum chemical calculations at density‐functional‐theory level on the band structure of this and a related polymer. The electronic situation was further analyzed with the aid of molecular model complexes, which were either synthesized or calculated.
Multifunctional TiO2‐Coated Ag Nanowire Arrays as Recyclable SERS Substrates for the Detection of Organic Pollutants
Authors: Zhou Ying , Chen Jin , Zhang Li , Yang Liangbao 
Published: May 2012

AbstractA novel method to prepare TiO2‐coated Ag nanowire arrays for use as multifunctional surface enhanced Raman scattering (SERS) active substrates is introduced. Such an array is made by the synthesis of an Ag nanowire array utilizing an anodic aluminum oxide (AAO) template, followed by coating of the Ag wires with a layer of titania that is several nanometers thick. Employing these TiO2‐coated Ag nanowire substrates in the detection of organic contaminants allows high SERS enhancement to be achieved. Moreover, owing to the high photocatalytic activity of titania, the substrate can degrade target molecules into small inorganic molecules under UV irradiation, and in this manner the arrays are able to self‐clean. The unique properties of this integrated substrate enable it to exhibit its feasibility as an analytical tool for the assessment of environmental pollution and thus to assist in the detection and disposal of contaminants.
A Vanadium‐Based Chemical Oscillator: Identification of Chemical Species Responsible for the Redox Reaction and Construction of a Simplified Model
Authors: Kanamori Kan , Kataoka Hiroshi , Matsugo Seiichi 
Published: May 2012

AbstractTo identify the chemical species involved in a unique, vanadium‐based chemical oscillator reaction, products derived from indole in the oscillation solution were isolated and characterized. NMR and mass spectra showed that 3,3‐dichloro‐2‐oxoindole and isatin were formed during the oscillation process. The formation of these two compounds suggests that peroxo species such as CHCl2OO· and CHCl2OOH play a key role in the construction of the oscillation system. A skeletal model for the system is proposed based on these findings.
Influence of Structure and Organic‐Inorganic Phase Interactions on Coating Mechanical Properties in the Ternary Goethite:Poly(HEMA):Silica System (Eur. J. Inorg. Chem. 16/2012)
Authors: Chemin Nicolas , Rozes Laurence , Chanéac Corinne , Cassaignon Sophie , Le Bourhis Eric , Jolivet Jean‐Pierre , Barthel Etienne , Sanchez Clément 
Published: May 2012

AbstractThe back cover picture highlights the mechanical and optical properties of a hybrid silica‐PHEMA coating on glass reinforced by using goethite nanorods in relation with the local structure at the interface. We demonstrate the possibility to finely tune the final mechanical properties by adjusting the coating silica content. In this hybrid nanocomposite, goethite particles exhibit interesting stress relaxation functions, which prevent crack formation in the films whilst reaching high silica content in the hybrid matrix. Details are discussed in the article by N. Chemin, C. Chanéac et al. on p. 2675 ff. magnified image
Three‐Component Coupling of Aldehydes, Amines, and Alkynes Catalyzed by Oxidized Copper Nanoparticles on Titania (Eur. J. Org. Chem. 16/2012)
Authors: Albaladejo María José , Alonso Francisco , Moglie Yanina , Yus Miguel 
Published: May 2012

AbstractThe cover picture shows an example of diastereoselective aldehyde/amine/alkyne coupling catalyzed by copper nanoparticles supported on titania under solvent‐free conditions. The background picture depicts a panoramic view from Cerro Campanario (1052 m) in Bariloche (Río Negro, Argentina). This is one of the most beautiful and fascinating views in the region including: the East Perito Moreno's lake (aldehyde), West Perito Moreno's lake (amine), Trebol's pool (alkyne), Nahuel Huapi's lake (background), Llao Llao's peninsula and hotel, and the surrounding hills (López and Capilla in the foreground). Details are discussed in the article by F. Alonso et al. on p. 3093 ff. magnified image
Electrochemistry and Simultaneous Detection of Metabolites of Purine Nucleotide Based on Large Mesoporous Carbon Modified Electrode
Authors: Liu Lina , Wang Huan , Bo Xiangjie , Yang Li , Guo Liping 
Published: May 2012

AbstractA large mesoporous carbon modified glassy carbon electrode (LMC/GCE) was prepared. The morphology and structure of the LMC were characterized. The LMC/GCE was used to investigate the electrochemical behaviors of metabolites of purine nucleotide, uric acid (UA), xanthine (XA) and hypoxanthine (HX). The LMC/GCE exhibited high electrocatalytic activity towards the three compounds when compared with those obtained at the GCE. Furthermore, the LMC/GCE realized simultaneous determination of UA, XA and HX at a physiological pH of 7.0 with wide linear range and low detection limit. The electrocatalytic activity of the LMC/GCE towards guanine (G) and adenine (A) was also investigated.
Effects of Redox Couple on the Response of Polypyrrole‐Based Electrochemical DNA Sensors
Authors: Booth Marsilea Adela , Harbison SallyAnn , Travas‐Sejdic Jadranka 
Published: May 2012

AbstractMuch research‐to‐date exists to create sensitive and selective DNA sensors. A variety of approaches are adopted, including those involving polypyrrole and electrical impedance spectroscopy. Combined these are able to sense as well as aptly transduce signals. Many such sensors employ ferri/ferrocyanide to exhibit surface hybridization. This redox reporter, though with merits, can prove disadvantageous. To this end, a comparative study was performed with the redox reporter hydroquinone. For comparison purposes ferri/ferrocyanide indicated greater sensitivity, suggested to arise from inherent charge. Conversely, with hydroquinone steric hindrance is the main influencing factor. Such a study aims to guide design of analogous sensors.
Energy and the environment: How will EPA's newest regulations affect electric markets?
Authors: Lesser Jonathan A. 
Published: May 2012

AbstractLast December, the US Environmental Protection Agency (EPA) put the finishing touches on new regulations to reduce emissions of mercury and other air toxics, primarily from coal‐fired power plants.1 Regulations targeting coal‐fired power plants are nothing new, really, as coal has been Public Enemy No. 1 for many environmentalists and environmental regulators for many years. The air toxics rule joins several others, including rules governing movements of air pollutants between states, disposal of coal ash, and discharges of cooling water.
Secular changes in personality: study on 75‐year‐olds examined in 1976–1977 and 2005–2006
Authors: Billstedt E. , Waern M. , Duberstein P. , Marlow T. , Hellström T. , Östling S. , Skoog I. 
Published: May 2012

ObjectiveIn order to study secular changes in personality factors neuroticism and extroversion, representative population samples of non‐demented 75‐year‐olds underwent psychiatric examinations in 1976–1977 (total n = 223, 138 women, 85 men) and 2005–2006 (total n = 556, 322 women and 234 men).MethodsEysenck Personality Inventory was used at both occasions. Demographic factors (educational level, marital status, having children) were registered.ResultsSeventy‐five‐year‐olds examined in 2005–2006 had higher values on extroversion and lower values on the Lie scale compared with those examined in 1976–1977. Neuroticism did not differ between the two birth cohorts. Neuroticism scores were higher in women than in men both in 1976–1977 and 2005–2006, and Lie score was higher in women than in men in 2005–2006.ConclusionsOur findings suggest that present cohorts of 75‐year‐olds are more extroverted and less prone to respond in a socially desirable manner than those born three decades earlier. Neuroticism levels remained unchanged, suggesting this trait may be less influenced by environmental factors than the other traits studied. Copyright © 2012 John Wiley & Sons, Ltd.