bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential methylation of the micro‐RNA 7b gene targets postnatal maturation of murine neuronal Mecp2 gene expression
Authors: Chen Yongjun , Shin Bo‐Chul , Thamotharan Shanthie , Devaskar Sherin U. 
Published: September 2013

ABSTRACTDNA methylation and microRNAs (miRNAs) play crucial roles in maturation of postnatal mouse neurons. Aberrant DNA methylation and/or altered miRNA expression cause postnatal neurodevelopmental disorders. In general, DNA methylation in the 5′‐flanking region suppresses gene expression through recruitment of methyl‐CpG binding domain proteins (MBPs) to the cytosine residues of CpG dinucleotides. X‐linked MeCP2 (methyl‐CpG binding protein 2), a member of MBPs, is a methylation‐associated transcriptional repressor with other functions in the central nervous system (CNS). miRNAs negatively regulate gene expression by targeting the 3′‐untranslated region (3′UTR). Some miRNA genes harboring or being embedded in CpG islands undergo methylation‐mediated silencing. One such miRNA is miR‐7b which is differentially expressed through stages of neurodevelopment. In our present study, we focused on a canonical CpG island located in the 5′‐flanking region of the murine miR‐7b gene. Hypermethylation of this CpG island down‐regulates miR‐7b while recruiting MeCP2 to the methylated CpG dinucleotides. Meanwhile, Mecp2, a target of miR‐7b, was up‐regulated due to lack of restrain exerted by miR‐7b during maturation of postnatal (PN) mouse neurons between PN3 and PN14. Our results indicate that miR‐7b is a direct downstream gene transcriptional target while also being a negative post‐transcriptional regulator of Mecp2 expression. We speculate that this bidirectional feed‐back autoregulatory function of miR‐7b and Mecp2 while linking DNA methylation and miRNA action maintains the homeostatic control of gene expression necessary during postnatal maturation of mammalian neurons. © 2013 Wiley Periodicals, Inc. Develop Neurobiol 74: 407–425, 2014
Elevated CO2 affects embryonic development and larval phototaxis in a temperate marine fish
Authors: Forsgren Elisabet , Dupont Sam , Jutfelt Fredrik , Amundsen Trond 
Published: September 2013

AbstractAs an effect of anthropogenic CO2 emissions, the chemistry of the world's oceans is changing. Understanding how this will affect marine organisms and ecosystems are critical in predicting the impacts of this ongoing ocean acidification. Work on coral reef fishes has revealed dramatic effects of elevated oceanic CO2 on sensory responses and behavior. Such effects may be widespread but have almost exclusively been tested on tropical reef fishes. Here we test the effects elevated CO2 has on the reproduction and early life history stages of a temperate coastal goby with paternal care by allowing goby pairs to reproduce naturally in an aquarium with either elevated (ca 1400 μatm) CO2 or control seawater (ca 370 μatm CO2). Elevated CO2 did not affect the occurrence of spawning nor clutch size, but increased embryonic abnormalities and egg loss. Moreover, we found that elevated CO2 significantly affected the phototactic response of newly hatched larvae. Phototaxis is a vision‐related fundamental behavior of many marine fishes, but has never before been tested in the context of ocean acidification. Our findings suggest that ocean acidification affects embryonic development and sensory responses in temperate fishes, with potentially important implications for fish recruitment.
Why to account for finite sites in population genetic studies and how to do this with Jaatha 2.0
Authors: Mathew Lisha A. , Staab Paul R. , Rose Laura E. , Metzler Dirk 
Published: September 2013

AbstractWith the advent of next‐generation sequencing technologies, large data sets of several thousand loci from multiple conspecific individuals are available. Such data sets should make it possible to obtain accurate estimates of population genetic parameters, even for complex models of population history. In the analyses of large data sets, it is difficult to consider finite‐sites mutation models (FSMs). Here, we use extensive simulations to demonstrate that the inclusion of FSMs is necessary to avoid severe biases in the estimation of the population mutation rate θ, population divergence times, and migration rates. We present a new version of Jaatha, an efficient composite‐likelihood method for estimating demographic parameters from population genetic data and evaluate the usefulness of Jaatha in two biological examples. For the first application, we infer the speciation process of two wild tomato species, Solanum chilense and Solanum peruvianum. In our second application example, we demonstrate that Jaatha is readily applicable to NGS data by analyzing genome‐wide data from two southern European populations of Arabidopsis thaliana. Jaatha is now freely available as an R package from the Comprehensive R Archive Network (CRAN).
Wetted‐wall corona discharge induced degradation of sulfadiazine antibiotics in aqueous solution
Authors: Rong Shaopeng , Sun Yabing 
Published: September 2013

AbstractBACKGROUNDSulfadiazine, is a potent antibacterial agent belonging to the sulfonamide class of antibiotics and is widely used as veterinary and human medicine, has been detected in contaminated water and soils. A cylindrical wetted‐wall corona discharge was applied for the removal of sulfadiazine. The target water was made to flow as a film over the surface of the electrode; the radicals generated at the gas–liquid interface discharge can efficiently reach the flowing‐water film surface.RESULTSInitial concentrations of 10 mg L‐1 sulfadiazine can all be removed within 30 min under discharge conditions of 100 W. The degradation of sulfadiazine can be enhanced by the addition of hydrogen radical scavengers, but can be inhibited by adding hydroxyl radical scavengers. Both kinds of radical scavengers can increase the concentrations of H2O2. The wetted‐wall corona discharge was ineffective in mineralization, but it can be enhanced by CCl4. Based on the results of LC–MS analysis, six intermediates were identified and the proposed evolutionary process was investigated.CONCLUSIONSWetted‐wall corona discharge can effectively degrade sulfadiazine in aqueous solution. These results are helpful for exploring new efficient technology and the evolutionary mechanism for antibiotics treatment. © 2013 Society of Chemical Industry
Alanine‐derivatized β‐cyclodextrin bonded silica: structure and adsorption selectivity
Authors: He Kaichen , Qiu Fengxian , Rong Xinshan , Qin Jiao , Yan Jie , Yang Dongya 
Published: September 2013

AbstractBACKGROUNDMany drug, pharmaceutical and flavoring compounds are racemic mixtures with chiral isomers having nearly identical physical and chemical properties. Phenylalanine is an aromatic alpha‐amino acid that exists in two isomeric forms: D‐phenylalanine (D‐Phe) and L‐phenylalanine (L‐Phe). Due to the different biological natures and pharmacological activities of both enantiomers, it is important to use them in their pure forms for specific therapeutic uses. This work has focused on using novel chiral recognition materials for the chiral separation of racemic phenylalanine.RESULTSThe static adsorption experiments indicate that prepared β‐cyclodextrin‐bonded silica (CD/SiO2), L‐alanine‐derivatized β‐cyclodextrin‐bonded silica and D‐alanine‐derivatized β‐cyclodextrin‐bonded silica (L‐Ala‐CD/SiO2 and D‐Ala‐CD/SiO2) materials have significantly higher adsorption capacity for D‐phenylalanine (D‐Phe) compared with L‐phenylalanine (L‐Phe), and the selectivity coefficient of CD/SiO2, L‐Ala‐CD/SiO2 and D‐Ala‐CD/SiO2 are 1.99, 1.84 and 3.48, respectively. The equilibrium data were well represented by Langmuir isotherm models. CD/SiO2, L‐Ala‐CD/SiO2 and D‐Ala‐CD/SiO2 were applied in four cycle's regeneration without significant loss in adsorption capacity.CONCLUSIONSD‐Ala‐CD/SiO2 has high recognition and binding affinity for D‐Phe molecule. The prepared chiral materials could be applied to chiral separation of the racemic phenylalanine acid solution. © 2013 Society of Chemical Industry
Advances in the development and application of ferrate(VI) for water and wastewater treatment
Authors: Jiang Jia‐Qian 
Published: September 2013

AbstractFerrate(VI) ion has the formula FeO42−, and possesses unique properties, vs. strong oxidising potential and simultaneous generation of ferric coagulating species. For this reason, a number of studies have been carried out to investigate the preparation, characterisation and application of ferrate(VI) for water and wastewater treatment. These studies revealed that ferrate(VI) can disinfect microorganisms, partially degrade and/or oxidise organic and inorganic impurities, and remove suspended/colloidal particulate materials in a single dosing and mixing unit process. Most recently, research groups globally have reported using ferrate(VI) to treat emerging micropollutants in water purification processes. Work has not only been limited to fundamental studies but has been driven by the ideas of putting the application of ferrate(VI) into practice; the advantages of the application of ferrate(VI) over existing water and wastewater treatment methods should be shown as should other benefits to the water industry of its use. This paper thus reviews advances in the preparation and use of ferrate(VI), discusses the potential full scale application of ferrate(VI) in water purification and recommends required future research in order to implement ferrate(VI) in practice. © 2013 Society of Chemical Industry
Stable aquaculture of the Japanese lancelet Branchiostoma japonicum for 7 years
Authors: Yasui Kinya , Igawa Takeshi , Kaji Takao , Henmi Yasuhisa 
Published: September 2013

ABSTRACTDespite advances in the study on animal evolution in the last two decades, paucity of experimental data on cephalochordates comparable to those on the other chordates hinders an integrative understanding of chordate evolutionary history. To obtain lancelet data under well‐controlled experiments, laboratory cultures of lancelets have been performed at several institutions. In a mass culture started in 2005, we have obtained up to three consecutive generations of Branchiostoma japonicum. Using sand substratum, survival rates of laboratory lancelets until maturation have improved to greater than 30%, much higher than compared to previously, and for adults the annual average survival rate was 82.3%. The high survival rate allows maintaining animals at least 6 years and potentially longer. Water temperatures lower than 23°C obviously reduced the frequency of spawning even after the onset of spawning period, and 1–2 days after changing the temperature at 25°C animals became spawned well. We also observed obvious sex reversal from male to female in individuals that had been cultured for 3 years or more. Our continuous culture has provided sufficient materials for vital experiments on early development and for studying metamorphosis, as well as for the conservation of wild populations. The subculture of successive laboratory generations will provide a valuable resource for genetic studies. J. Exp. Zool. (Mol. Dev. Evol.) 320B: 538–547, 2013. © 2013 Wiley Periodicals, Inc.
Assessment of inflammation with a very small iron‐oxide particle in a murine model of reperfused myocardial infarction
Authors: Protti Andrea , Dong Xuebin , Andia Marcelo E. , Yu Bin , Dokukina Kate , Chaubey Sanjay , Phinikaridou Alkystis , Vizcay‐Barrena Gema , Taupitz Matthias , Botnar Rene M. , Shah Ajay M. 
Published: September 2013

PurposeTo investigate a very small iron‐oxide particle (VSOP) in a mouse model of acute ischemia‐reperfusion to access the mechanism of such particles in areas of myocardial inflammation.Materials and MethodsAnimals were injected with VSOP at several time points, in a mouse model of acute myocardial infarction (MI), before and after MI. MRI was used to localize areas of VSOP enhancement, evaluate VSOP areas extension, and determine the related T2* values. Histology, electron microscopy, macrophage counting, and Evan's Blue staining were also performed.ResultsWe found that areas of VSOP uptake decreased from 1 to 8 days post‐MI while the related T2* values increased. T2* and VSOP areas, defined from MRI data, correlated well between 1 and 3 days post‐MI but not at 7 days after injection. Histological analysis and electron microscopy showed colocalization of macrophages with areas of VSOP staining. However, there was no correlation between number of macrophages and the extension of the VSOP areas achieved by MR. We found that only areas of increased permeability (assessed by Evan's Blue staining) showed colocalization of macrophages and VSOP uptake.ConclusionThis study demonstrates that VSOP allows the assessment of myocardial inflammation associated with increased permeability during infarct healing in a mouse model of ischemia‐reperfusion. J. Magn. Reson. Imaging 2014;39:598–608. © 2013 Wiley Periodicals, Inc.
Validation of an MRI‐based method to assess patellofemoral joint contact areas in loaded knee flexion in vivo
Authors: McWalter Emily J. , O'Kane Colm M. , FitzPatrick David P. , Wilson David R. 
Published: September 2013

PurposeTo develop and validate short axial and sagittal MRI scans (<1min) to assess in vivo patellofemoral contact areas in loaded knee flexion.Materials and MethodsContact area was assessed in four cadaver knee specimens from axial and sagittal scans using two contact area extraction techniques (delineation and intersection) and three calculation techniques (slice thickness multiplication, linear interpolation, and spline interpolation). Error was expressed as the mean absolute and percentage difference from a dye staining‐based reference standard. Intrareader and intrasubject repeatability, expressed as the mean standard deviation, was determined.ResultsContact area assessments from the sagittal MRI scans using the delineation and slice thickness multiplication technique had the smallest error (47.7 ± 38.1 mm2 or 10.7%). The intrareader repeatability from assessments using the sagittal scans was smaller than those using the axial scans when the delineation method was used (<9.4 ± 4.3 mm2 and <15.4 ± 14.1 mm2, respectively). The intrasubject repeatability of the assessment from the sagittal scan was less than 39.9 ± 23.0 mm2.ConclusionThis protocol yields assessments of contact area in less than 1 minute that have errors similar to those made using scans many times longer and can be used in series with kinematic scans to carry out simultaneous assessments in vivo to study patellofemoral joint disease. J. Magn. Reson. Imaging 2014;39:978–987. © 2013 Wiley Periodicals, Inc.
More than biofuels – Potential uses of microalgae as sources of high‐value lipids
Authors: Lee Chang Kim Jye , Nichols Peter D. , Blackburn Susan I. 
Published: September 2013

AbstractCultivation of microalgae has potential in producing a feedstock for biofuels and, in addition, high‐value lipid bioproducts such as long‐chain (⪈C20, LC) omega‐3 oils, carotenoid pigments and squalene, as well as other non‐lipid materials including exopolysaccharide. The high‐value LC omega‐3 oils have been conventionally sourced from fish. This paper provides a perspective on our recent study of the heterotrophic growth of thraustochytrids for their wider biotechnological potential, including as a source of a range of higher value lipids in addition to biofuels.
MR and CT based treatment planning for mTHPC mediated interstitial photodynamic therapy of head and neck cancer: Description of the method
Authors: Karakullukcu Baris , van Veen Robert L.P. , Aans Jan Bonne , Hamming‐Vrieze Olga , Navran Arash , Teertstra H. Jelle , van den Boom Ferrie , Niatsetski Yuri , Sterenborg H.J.C.M. , Tan I. Bing 
Published: September 2013

AbstractBackground and ObjectiveInterstitial photodynamic therapy is a potentially important tool in the management of voluminous or deep‐seated recurrent head and neck cancers.Study Design/MethodsThe described treatment algorithm in this manuscript consists of the treatment simulation, implantation of light sources, verification, modification of the treatment plan if necessary, and illumination. The tumor is delineated on imaging sections (CT, MRI, and/or PET/CT) and the treatment is simulated by virtually introducing light sources to the tumor volume on specially modified brachytherapy software. This enables us to determine if the treatment is technically feasible, and information about approximate number and location of light sources necessary. Following implantation of catheters in which the light sources will be introduced, CT or MR scan is performed to verify the actual location of the implanted catheters. The verification‐CT is imported to the software and co‐registered with pre‐treatment images to observe the deviations from the simulation. The simulation is run again with the actual position of the light sources to determine if any additional light sources are necessary and adaptation of the source length in order to cover the tumor volume (modification). Thereafter the tumor is illuminated.ResultsThis method has the potential to help with identifying iPDT feasible patients by simulating before the actual treatment. The suboptimal placement of light sources can be identified and corrected. The simulations were documented and saved for subsequent evaluation of the technique.ConclusionThe proposed technique can help standardize and document iPDT. Lasers Surg. Med. 45:517–523, 2013. © 2013 Wiley Periodicals, Inc.
Dose–response plasma appearance of coffee chlorogenic and phenolic acids in adults
Authors: Renouf Mathieu , Marmet Cynthia , Giuffrida Francesca , Lepage Mélissa , Barron Denis , Beaumont Maurice , Williamson Gary , Dionisi Fabiola 
Published: September 2013

ScopeCoffee contains phenolic compounds, mainly chlorogenic acids (CGAs). Even though coffee intake has been associated with some health benefits in epidemiological studies, the bioavailability of coffee phenolics is not fully understood.Objective and study designWe performed a dose–response study measuring plasma bioavailability of phenolics after drinking three increasing, but still nutritionally relevant doses of instant pure soluble coffee. The study design was a one treatment (coffee) three‐dose randomized cross‐over design, with a washout period of 2 wks between visits.ResultsCGAs, phenolic acids, and late‐appearing metabolites all increased with increasing ingested dose. Hence, the sum of area under the curve was significantly higher for the medium to low dose, and high to medium dose, by 2.23‐ and 2.38‐fold, respectively. CGAs were not well absorbed in their intact form, regardless of the dose. CGA and phenolic acids appeared rapidly in plasma, indicating an early absorption in the gastrointestinal tract. Late‐appearing metabolites were the most abundant, regardless of the dose.ConclusionThis study confirmed previous findings about coffee bioavailability but also showed that coffee phenolics appear in a positive dose–response manner in plasma when drank at nutritionally relevant doses.
Activation of pluripotency genes by a nanotube‐mediated protein delivery system
Authors: Cho Seong Je , Choi Hyun Woo , Cho Jaegeol , Jung Suntae , Seo Han Geuk , Do Jeong Tae 
Published: September 2013

SummaryThe overexpression of cell reprogramming factors (Oct4, Sox2, Klf4, Nanog, and c‐Myc) allows differentiated cells to revertto an earlier developmental stage. Differentiated cells can also be reprogrammed by directly delivering reprogramming proteins tagged with cell‐penetrating peptides, which allow the proteins to pass through the cell membrane and into the cytoplasm–although this method has been an inefficient process. Here, we describe a novel technique for delivering reprogramming proteins into cells using titanium oxide (TiO2) nanotubes, which show no cytotoxic effects and do not affect cell proliferation. TiO2 nanotubes successfully transferred the above‐mentioned reprogramming factors into differentiated somatic cells. After 3 weeks of treatment with protein‐conjugated nanotubes, the somatic cells adopted an embryonic stem cell‐like morphology and expressed activated Oct4‐green fluorescent protein, a pluripotency biomarker. Our results indicate that TiO2 nanotubes can be used to directly deliver reprogramming factors into somatic cells to induce pluripotency. Mol. Reprod. Dev. 80: 1000–1008, 2013. © 2013 Wiley Periodicals, Inc.
Enabling hyperpolarized 129Xe MR spectroscopy and imaging of pulmonary gas transfer to the red blood cells in transgenic mice expressing human hemoglobin
Authors: Freeman Matthew S. , Cleveland Zackary I. , Qi Yi , Driehuys Bastiaan 
Published: September 2013

PurposeHyperpolarized (HP) 129Xe gas in the alveoli can be detected separately from 129Xe dissolved in pulmonary barrier tissues (blood plasma and parenchyma) and red blood cells (RBCs) of humans, allowing this isotope to probe impaired gas uptake. Unfortunately, mice, which are favored as lung disease models, do not display a unique RBC resonance, thus limiting the preclinical utility of 129Xe MR. Here we overcome this limitation using a commercially available strain of transgenic mice that exclusively expresses human hemoglobin.MethodsDynamic HP 129Xe MR spectroscopy, and three‐dimensional radial MRI of gaseous and dissolved 129Xe were performed in both wild‐type (C57BL/6) and transgenic mice.ResultsUnlike wild‐type animals, transgenic mice displayed two dissolved 129Xe NMR peaks at 198 and 217 ppm, corresponding to 129Xe dissolved in barrier tissues and RBCs, respectively. Moreover, signal from these resonances could be imaged separately, using a 1‐point variant of the Dixon technique.ConclusionIt is now possible to examine the dynamics and spatial distribution of pulmonary gas uptake by the RBCs of mice using HP 129Xe MR spectroscopy and imaging. When combined with ventilation imaging, this ability will enable translational “mouse‐to‐human” studies of impaired gas exchange in a variety of pulmonary diseases. Magn Reson Med 70:1192–1199, 2013. © 2013 Wiley Periodicals, Inc.
Susceptibility map‐weighted imaging (SMWI) for neuroimaging
Authors: Gho Sung‐Min , Liu Chunlei , Li Wei , Jang Ung , Kim Eung Yeop , Hwang Dosik , Kim Dong‐Hyun 
Published: September 2013

PurposeTo propose a susceptibility map‐weighted imaging (SMWI) method by combining a magnitude image with a quantitative susceptibility mapping (QSM) ‐based weighting factor thereby providing an alternative contrast compared with magnitude image, susceptibility‐weighted imaging, and QSM.MethodsA three‐dimensional multi‐echo gradient echo sequence is used to obtain the data. The QSM was transformed to a susceptibility mask that varies in amplitude between zero and unity. This mask was multiplied several times with the original magnitude image to create alternative contrasts between tissues with different susceptibilities. A temporal domain denoising method to enhance the signal‐to‐noise ratio was further applied. Optimal reconstruction processes of the SMWI were determined from simulations.ResultsTemporal domain denoising enhanced the signal‐to‐noise ratio, especially at late echoes without spatial artifacts. From phantom simulations, the optimal number of multiplication and threshold values was chosen. Reconstructed SMWI created different contrasts based on its weighting factors made from paramagnetic or diamagnetic susceptibility tissue and provided an excellent delineation of microhemorrhage without blooming artifacts typically caused by the nonlocal property of phase.ConclusionSMWI presents an alternative contrast for susceptibility‐based imaging. The validity of this method was demonstrated using in vivo data. This proposed method together with denoising allows high‐quality reconstruction of susceptibility‐weighted image of human brain in vivo. Magn Reson Med 72:337–346, 2014. © 2013 Wiley Periodicals, Inc.