bluuebunny/crossref_metadata_2025_split huggingface dataset:
Depletion of eIF4G from yeast cells narrows the range of translational efficiencies genome-wide
Authors: Park Eun-Hee , Zhang Fan , Warringer Jonas , Sunnerhagen Per , Hinnebusch Alan G 
Published: January 2011

Abstract

Background
Eukaryotic translation initiation factor 4G (eIF4G) is thought to influence the translational efficiencies of cellular mRNAs by its roles in forming an eIF4F-mRNA-PABP mRNP that is competent for attachment of the 43S preinitiation complex, and in scanning through structured 5' UTR sequences. We have tested this hypothesis by determining the effects of genetically depleting eIF4G from yeast cells on global translational efficiencies (TEs), using gene expression microarrays to measure the abundance of mRNA in polysomes relative to total mRNA for ~5900 genes.

Results
Although depletion of eIF4G is lethal and reduces protein synthesis by ~75%, it had small effects (less than a factor of 1.5) on the relative TE of most genes. Within these limits, however, depleting eIF4G narrowed the range of translational efficiencies genome-wide, with mRNAs of better than average TE being translated relatively worse, and mRNAs with lower than average TE being translated relatively better. Surprisingly, the fraction of mRNAs most dependent on eIF4G display an average 5' UTR length at or below the mean for all yeast genes.

Conclusions
This finding suggests that eIF4G is more critical for ribosome attachment to mRNAs than for scanning long, structured 5' UTRs. Our results also indicate that eIF4G, and the closed-loop mRNP it assembles with the m7 G cap- and poly(A)-binding factors (eIF4E and PABP), is not essential for translation of most (if not all) mRNAs but enhances the differentiation of translational efficiencies genome-wide.
Insects in confined swine operations carry a large antibiotic resistant and potentially virulent enterococcal community
Authors: Ahmad Aqeel , Ghosh Anuradha , Schal Coby , Zurek Ludek 
Published: January 2011

Abstract

Background
Extensive use of antibiotics as growth promoters in the livestock industry constitutes strong selection pressure for evolution and selection of antibiotic resistant bacterial strains. Unfortunately, the microbial ecology and spread of these bacteria in the agricultural, urban, and suburban environments are poorly understood. Insects such as house flies (Musca domestica) and German cockroaches (Blattella germanica) can move freely between animal waste and food and may play a significant role in the dissemination of antibiotic resistant bacteria within and between animal production farms and from farms to residential settings.

Results
Enterococci from the digestive tract of house flies (n = 162), and feces of German cockroaches (n = 83) and pigs (n = 119), collected from two commercial swine farms were isolated, quantified, identified, and screened for antibiotic resistance and virulence. The majority of samples (93.7%) were positive for enterococci with concentrations 4.2 ± 0.7 × 104 CFU/house fly, 5.5 ± 1.1 × 106 CFU/g of cockroach feces, and 3.2 ± 0.8 × 105 CFU/g of pig feces. Among all the identified isolates (n = 639) Enterococcus faecalis was the most common (55.5%), followed by E. hirae (24.9%), E. faecium (12.8%), and E. casseliflavus (6.7%). E. faecalis was most prevalent in house flies and cockroaches, and E. hirae was most common in pig feces. Our data showed that multi-drug (mainly tetracycline and erythromycin) resistant enterococci were common from all three sources and frequently carried antibiotic resistance genes including tet(M) and erm(B) and Tn916/1545 transposon family. E. faecalis frequently harbored virulence factors gelE, esp, and asa1. PFGE analysis of selected E. faecalis and E. faecium isolates demonstrated that cockroaches and house flies shared some of the same enterococcal clones that were detected in the swine manure indicating that insects acquired enterococci from swine manure.

Conclusions
This study shows that house flies and German cockroaches in the confined swine production environment likely serve as vectors and/or reservoirs of antibiotic resistant and potentially virulent enterococci and consequently may play an important role in animal and public health.
Functional mapping of reaction norms to multiple environmental signals through nonparametric covariance estimation
Authors: Yap John S , Li Yao , Das Kiranmoy , Li Jiahan , Wu Rongling 
Published: January 2011

Abstract

Background
The identification of genes or quantitative trait loci that are expressed in response to different environmental factors such as temperature and light, through functional mapping, critically relies on precise modeling of the covariance structure. Previous work used separable parametric covariance structures, such as a Kronecker product of autoregressive one [AR(1)] matrices, that do not account for interaction effects of different environmental factors.

Results
We implement a more robust nonparametric covariance estimator to model these interactions within the framework of functional mapping of reaction norms to two signals. Our results from Monte Carlo simulations show that this estimator can be useful in modeling interactions that exist between two environmental signals. The interactions are simulated using nonseparable covariance models with spatio-temporal structural forms that mimic interaction effects.

Conclusions
The nonparametric covariance estimator has an advantage over separable parametric covariance estimators in the detection of QTL location, thus extending the breadth of use of functional mapping in practical settings.
Immunologically reactive M. leprae antigens with relevance to diagnosis and vaccine development
Authors: Sampaio Lucas H , Stefani Mariane MA , Oliveira Regiane M , Sousa Ana LM , Ireton Greg C , Reed Steven G , Duthie Malcolm S 
Published: January 2011

Abstract

Background
Leprosy is a chronic infectious disease caused by Mycobacterium leprae that can manifest a wide variety of immunological and clinical outcomes ranging from potent humoral responses among borderline lepromatous (BL) and lepromatous (LL) patients to strong cellular responses among tuberculoid (TT) and borderline tuberculoid (BT) patients. Until recently, relatively little has been known about the immune responses to individual proteins of M. leprae recognized during leprosy.

Methods
The immune reactivity to a panel of 33 M. leprae recombinant proteins was evaluated among leprosy patients and controls from a high endemic area for leprosy (Goiania/GO, Central Brazil). Serum IgG responses were measured by ELISA (45 participants/group) and T cell responses (20 participants/group) were evaluated by IFN-gamma production in 24 hours whole blood cultures with antigen (whole blood assay-WBA). Study groups were newly diagnosed, untreated TT/BT and BL/LL leprosy patients classified by Ridley Jopling criteria and household contacts of BL/LL patients (HHC). Control groups were HIV-1 negative pulmonary tuberculosis patients (TB) and healthy individuals from the same endemic area (EC). In silico predictions indicated the level of identity of M. leprae proteins with homologues in other mycobacteria and the presence of T cell and B cell epitopes.

Results
Despite the prediction that all proteins would be reactive, 16 of 33 (48%) of the single proteins tested were immunogenic (recognized in WBA or ELISA) and seventeen were non-immunogenic (not recognized in either assay). Among the 16 immunogenic proteins, 9 were considered leprosy specific in WBA inducing cell-mediated IFN-gamma secretion from TT/BT patients and HHC. Three of these proteins were also leprosy specific in serology being recognized by serum IgG from LL/BL patients. Seven of the immunogenic proteins were not leprosy specific.

Conclusions
New M. leprae antigens recognized by antibody responses of BL/LL patients and cellular responses of TT/BT leprosy patients were identified. An improved serological diagnostic test for leprosy could be developed by incorporating these IgG-reactive antigens to the current PGL-I based tests. Moreover our data indicate that the WBA is a robust, relatively simple and user friendly format for a T cell based diagnostic test. The field use of these test formats in leprosy endemic countries could contribute to early leprosy diagnosis before the development of deformities and disabilities.
Graphical analysis of pH-dependent properties of proteins predicted using PROPKA
Authors: Rostkowski Michał , Olsson Mats HM , Søndergaard Chresten R , Jensen Jan H 
Published: January 2011

Abstract

Background
Charge states of ionizable residues in proteins determine their pH-dependent properties through their pKa values. Thus, various theoretical methods to determine ionization constants of residues in biological systems have been developed. One of the more widely used approaches for predicting pKa values in proteins is the PROPKA program, which provides convenient structural rationalization of the predicted pKa values without any additional calculations.

Results
The PROPKA Graphical User Interface (GUI) is a new tool for studying the pH-dependent properties of proteins such as charge and stabilization energy. It facilitates a quantitative analysis of pKa values of ionizable residues together with their structural determinants by providing a direct link between the pKa data, predicted by the PROPKA calculations, and the structure via the Visual Molecular Dynamics (VMD) program. The GUI also calculates contributions to the pH-dependent unfolding free energy at a given pH for each ionizable group in the protein. Moreover, the PROPKA-computed pKa values or energy contributions of the ionizable residues in question can be displayed interactively. The PROPKA GUI can also be used for comparing pH-dependent properties of more than one structure at the same time.

Conclusions
The GUI considerably extends the analysis and validation possibilities of the PROPKA approach. The PROPKA GUI can conveniently be used to investigate ionizable groups, and their interactions, of residues with significantly perturbed pKa values or residues that contribute to the stabilization energy the most. Charge-dependent properties can be studied either for a single protein or simultaneously with other homologous structures, which makes it a helpful tool, for instance, in protein design studies or structure-based function predictions. The GUI is implemented as a Tcl/Tk plug-in for VMD, and can be obtained online at http://propka.ki.ku.dk/~luca/wiki/index.php/GUI_Web.
Comparison of Dietary Control and Atorvastatin on High Fat Diet Induced Hepatic Steatosis and Hyperlipidemia in Rats
Authors: Ji Guiyuan , Zhao Xihong , Leng Liang , Liu Peiyi , Jiang Zhuoqin 
Published: January 2011

AbstractBackgroundTreatment with atorvastatin (ATO) or dietary control has been demonstrated to benefit patients with non-alcoholic fatty liver disease (NAFLD) and hyperlipidemia. However, little is known on whether combination of dietary control and ATO treatment could enhance the therapeutic effect.MethodsWe employed a rat model of NAFLD to examine the therapeutic efficacy of dietary control and/or ATO treatment. Sprague-Dawley rats were fed with normal chow diet as normal controls or with high fat diet (HFD) for 12 weeks to establish NAFLD. The NAFLD rats were randomized and continually fed with HFD, with normal chow diet, with HFD and treated with 30 mg/kg of ATO or with normal chow diet and treated with the same dose of ATO for 8 weeks. Subsequently, the rats were sacrificed and the serum lipids, aminotranferase, hepatic lipids, and liver pathology were characterized. The relative levels of fatty acid synthesis and β-oxidation gene expression in hepatic tissues were measured by quantitative real-time polymerase chain reaction (qRT-PCR). Hepatic expression of hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase was determined by Western blot assay.ResultsWhile continual feeding with HFD deteriorated NAFLD and hyperlipidemia, treatment with dietary control, ATO or ATO with dietary control effectively improved serum and liver lipid metabolism and liver function. In comparison with ATO treatment, dietary control or combined with ATO treatment significantly reduced the liver weight and attenuated the HFD-induced hyperlipidemia and liver steatosis in rats. Compared to ATO treatment or dietary control, combination of ATO and dietary control significantly reduced the levels of serum total cholesterol and low density lipoprotein cholesterol (LDL-C). However, the combination therapy did not significantly improve triglyceride and free fatty acid metabolism, hepatic steatosis, and liver function, as compared with dietary control alone.ConclusionsATO treatment effectively improved NAFLD-related hyperlipidemia and inhibited liver steatosis, accompanied by modulating the expression of genes for regulating lipid metabolism. ATO enhanced the effect of dietary control on reducing the levels of serum total cholesterol and LDL-C, but not triglyceride, free fatty acid and hepatic steatosis in HFD-induced fatty liver and hyperlipidemia in rats.
Effects of low-temperature capping on the optical properties of GaAs/AlGaAs quantum wells
Authors: Jo Masafumi , Duan Guotao , Mano Takaaki , Sakoda Kazuaki 
Published: January 2011

AbstractWe study the effects of low-temperature capping (200-450°C) on the optical properties of GaAs/AlGaAs quantum wells. Photoluminescence measurements clearly show the formation of abundant nonradiative recombination centers in an AlGaAs capping layer grown at 200°C, while there is a slight degradation of the optical quality in AlGaAs capping layers grown at temperatures above 350°C compared to that of a high-temperature capping layer. In addition, the optical quality can be restored by post-growth annealing without any structural change, except for the 200°C-capped sample.
Characterization of MHz pulse repetition rate femtosecond laser-irradiated gold-coated silicon surfaces
Authors: Sivakumar Manickam , Venkatakrishnan Krishnan , Tan Bo 
Published: January 2011

AbstractIn this study, MHz pulse repetition rate femtosecond laser-irradiated gold-coated silicon surfaces under ambient condition were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction analysis (XRD), and X-ray photoelectron spectroscopy (XPS). The radiation fluence used was 0.5 J/cm2 at a pulse repetition rate of 25 MHz with 1 ms interaction time. SEM analysis of the irradiated surfaces showed self-assembled intermingled weblike nanofibrous structure in and around the laser-irradiated spots. Further TEM investigation on this nanostructure revealed that the nanofibrous structure is formed due to aggregation of Au-Si/Si nanoparticles. The XRD peaks at 32.2°, 39.7°, and 62.5° were identified as (200), (211), and (321) reflections, respectively, corresponding to gold silicide. In addition, the observed chemical shift of Au 4f and Si 2p lines in XPS spectrum of the irradiated surface illustrated the presence of gold silicide at the irradiated surface. The generation of Si/Au-Si alloy fibrous nanoparticles aggregate is explained by the nucleation and subsequent condensation of vapor in the plasma plume during irradiation and expulsion of molten material due to high plasma pressure.
Formation and reinforcement of clusters composed of C60 molecules
Authors: Kurosu Shunji , Fukuda Takahiro , Shibuya Yuichi , Maekawa Toru 
Published: January 2011

AbstractWe carry out two experiments: (1) the formation of clusters composed of C60 molecules via self-assembly and (2) the reinforcement of the clusters. Firstly, clusters such as fibres and helices composed of C60 molecules are produced via self-assembly in supercritical carbon dioxide. However, C60 molecules are so weakly bonded to each other in the clusters that the clusters are broken by the irradiation of electron beams during scanning electron microscope observation. Secondly, UV photons are irradiated inside a chamber in which air is filled at 1 atm and the above clusters are placed, and it was found that the clusters are reinforced; that is, they are not broken by electron beams any more. C60 molecules located at the surface of the clusters are oxidised, i.e. C60O
n
molecules, where n = 1, 2, 3 and 4, are produced according to time-of-flight mass spectroscopy. It is supposed that oxidised C60 molecules at the surface of the clusters may have an important role for the reinforcement, but the actual mechanism of the reinforcement of the clusters has not yet been clearly understood and therefore is an open question.
Improvement of performance of InAs quantum dot solar cell by inserting thin AlAs layers
Authors: Hu Dongzhi , McPheeters Claiborne CO , Yu Edward T , Schaadt Daniel M 
Published: January 2011

AbstractA new measure to enhance the performance of InAs quantum dot solar cell is proposed and measured. One monolayer AlAs is deposited on top of InAs quantum dots (QDs) in multistack solar cells. The devices were fabricated by molecular beam epitaxy. In situ annealing was intended to tune the QD density. A set of four samples were compared: InAs QDs without in situ annealing with and without AlAs cap layer and InAs QDs in situ annealed with and without AlAs cap layer. Atomic force microscopy measurements show that when in situ annealing of QDs without AlAs capping layers is investigated, holes and dashes are present on the device surface, while capping with one monolayer AlAs improves the device surface. On unannealed samples, capping the QDs with one monolayer of AlAs improves the spectral response, the open-circuit voltage and the fill factor. On annealed samples, capping has little effect on the spectral response but reduces the short-circuit current, while increasing the open-circuit voltage, the fill factor and power conversion efficiency.
Formation of Ge-Sn nanodots on Si(100) surfaces by molecular beam epitaxy
Authors: Mashanov Vladimir , Ulyanov Vladimir , Timofeev Vyacheslav , Nikiforov Aleksandr , Pchelyakov Oleg , Yu Ing-Song , Cheng Henry 
Published: January 2011

AbstractThe surface morphology of Ge0.96Sn0.04/Si(100) heterostructures grown at temperatures from 250 to 450°C by atomic force microscopy (AFM) and scanning tunnel microscopy (STM) ex situ has been studied. The statistical data for the density of Ge0.96Sn0.04 nanodots (ND) depending on their lateral size have been obtained. Maximum density of ND (6 × 1011 cm-2) with the average lateral size of 7 nm can be obtained at 250°C. Relying on the reflection of high energy electron diffraction, AFM, and STM, it is concluded that molecular beam growth of Ge1-x
Sn
x
heterostructures with the small concentrations of Sn in the range of substrate temperatures from 250 to 450°C follows the Stranski-Krastanow mechanism. Based on the technique of recording diffractometry of high energy electrons during the process of epitaxy, the wetting layer thickness of Ge0.96Sn0.04 films is found to depend on the temperature of the substrate.
Electrical behavior of multi-walled carbon nanotube network embedded in amorphous silicon nitride
Authors: Stavarache Ionel , Lepadatu Ana-Maria , Teodorescu Valentin Serban , Ciurea Magdalena Lidia , Iancu Vladimir , Dragoman Mircea , Konstantinidis George , Buiculescu Raluca 
Published: January 2011

AbstractThe electrical behavior of multi-walled carbon nanotube network embedded in amorphous silicon nitride is studied by measuring the voltage and temperature dependences of the current. The microstructure of the network is investigated by cross-sectional transmission electron microscopy. The multi-walled carbon nanotube network has an uniform spatial extension in the silicon nitride matrix. The current-voltage and resistance-temperature characteristics are both linear, proving the metallic behavior of the network. The I-V curves present oscillations that are further analyzed by computing the conductance-voltage characteristics. The conductance presents minima and maxima that appear at the same voltage for both bias polarities, at both 20 and 298 K, and that are not periodic. These oscillations are interpreted as due to percolation processes. The voltage percolation thresholds are identified with the conductance minima.
Preparation and characterization of spindle-like Fe3O4 mesoporous nanoparticles
Authors: Zhang Shaofeng , Wu Wei , Xiao Xiangheng , Zhou Juan , Ren Feng , Jiang Changzhong 
Published: January 2011

AbstractMagnetic spindle-like Fe3O4 mesoporous nanoparticles with a length of 200 nm and diameter of 60 nm were successfully synthesized by reducing the spindle-like α-Fe2O3 NPs which were prepared by forced hydrolysis method. The obtained samples were characterized by transmission electron microscopy, powder X-ray diffraction, attenuated total reflection fourier transform infrared spectroscopy, field emission scanning electron microscopy, vibrating sample magnetometer, and nitrogen adsorption-desorption analysis techniques. The results show that α-Fe2O3 phase transformed into Fe3O4 phase after annealing in hydrogen atmosphere at 350°C. The as-prepared spindle-like Fe3O4 mesoporous NPs possess high Brunauer-Emmett-Teller (BET) surface area up to ca. 7.9 m2 g-1. In addition, the Fe3O4 NPs present higher saturation magnetization (85.2 emu g-1) and excellent magnetic response behaviors, which have great potential applications in magnetic separation technology.
Resonant frequency of gold/polycarbonate hybrid nano resonators fabricated on plastics via nano-transfer printing
Authors: Dechaumphai Edward , Zhang Zhao , Siwak Nathan P , Ghodssi Reza , Li Teng 
Published: January 2011

AbstractWe report the fabrication of gold/polycarbonate (Au/PC) hybrid nano resonators on plastic substrates through a nano-transfer printing (nTP) technique, and the parametric studies of the resonant frequency of the resulting hybrid nano resonators. nTP is a nanofabrication technique that involves an assembly process by which a printable layer can be transferred from a transfer substrate to a device substrate. In this article, we applied nTP to fabricate Au/PC hybrid nano resonators on a PC substrate. When an AC voltage is applied, the nano resonator can be mechanically excited when the AC frequency reaches the resonant frequency of the nano resonator. We then performed systematic parametric studies to identify the parameters that govern the resonant frequency of the nano resonators, using finite element method. The quantitative results for a wide range of materials and geometries offer vital guidance to design hybrid nano resonators with a tunable resonant frequency in a range of more than three orders of magnitude (e.g., 10 KHz-100 MHz). Such nano resonators could find their potential applications in nano electromechanical devices. Fabricating hybrid nano resonators via nTP further demonstrates nTP as a potential fabrication technique to enable a low-cost and scalable roll-to-roll printing process of nanodevices.
Two novel hierarchical homogeneous nanoarchitectures of TiO2 nanorods branched and P25-coated TiO2 nanotube arrays and their photocurrent performances
Authors: Hu Anzheng , Cheng Cuixia , Li Xin , Jiang Jian , Ding Ruimin , Zhu Jianhui , Wu Fei , Liu Jinping , Huang Xintang 
Published: January 2011

AbstractWe report here for the first time the synthesis of two novel hierarchical homogeneous nanoarchitectures of TiO2nanorods branched TiO2nanotube arrays (BTs) and P25-coated TiO2nanotube arrays (PCTs) using two-step method including electrochemical anodization and hydrothermal modification process. Then the photocurrent densities versus applied potentials of BTs, PCTs, and pure TiO2nanotube arrays (TNTAs) were investigated as well. Interestingly, at -0.11 V and under the same illumination condition, the photocurrent densities of BTs and PCTs show more than 1.5 and 1 times higher than that of pure TNTAs, respectively, which can be mainly attributed to significant improvement of the light-absorbing and charge-harvesting efficiency resulting from both larger and rougher surface areas of BTs and PCTs. Furthermore, these dramatic improvements suggest that BTs and PCTs will achieve better photoelectric conversion efficiency and become the promising candidates for applications in DSSCs, sensors, and photocatalysis.