bluuebunny/crossref_metadata_2025_split huggingface dataset:
Concise Review: The Involvement ofSOX2in Direct Reprogramming of Induced Neural Stem/Precursor Cells
Authors: Maucksch Christof , Jones Kathryn S. , Connor Bronwen 
Published: July 2013

AbstractSince induced pluripotent stem cells were first generated from mouse embryonic fibroblasts in 2006, somatic cell reprogramming has become a powerful and valuable tool in many fields of biomedical research, with the potential to lead to the development of in vitro disease models, cell-based drug screening platforms, and ultimately novel cell therapies. Recent research has now demonstrated the direct conversion of fibroblasts into stem, precursor, or mature cell types that are committed in their fate within a specific lineage, such as hematopoietic precursors or mature neurons. This has been achieved by ectopic expression of defined, tissue-specific transcription factors. Several studies have demonstrated direct reprogramming of mouse and human fibroblasts into immature neural stem or precursor cells, either by transient expression of the four pluripotency genes OCT3/4, KLF4, SOX2, and C-MYC or by application of different combinations of up to 11 neural transcription factors. Interestingly, in all of these studies SOX2 was introduced alone or in combination with other transcription factors. In this review we discuss the different combinations of ectopic transcription factors used to generate neural stem/precursor cells from somatic cells, with particular emphasis on SOX2 and its potential to act as a master regulator for reprogramming to a neural precursor state.
Quantification of microRNA Expression with Next‐Generation Sequencing
Authors: Eminaga Seda , Christodoulou Danos C. , Vigneault Francois , Church George M. , Seidman J.G. 
Published: July 2013

AbstractRapid advancement of next‐generation sequencing technologies has made it possible to study expression profiles of microRNAs (miRNAs) comprehensively and efficiently. Multiplexing miRNA libraries by barcoding can significantly reduce sequencing cost per sample without compromising library quality. This unit provides a step‐by‐step protocol for isolating miRNAs and constructing multiplexed miRNA libraries. Also described is a custom computational pipeline for analyzing the multiplexed miRNA library sequencing reads generated by Illumina‐based technology. Curr. Protoc. Mol. Biol. 103:4.17.1–4.17.14. © 2013 by John Wiley & Sons, Inc.
John R. Delaney Receives 2012 Athelstan Spilhaus Award: Citation
Authors: Leinen Margaret 
Published: July 2013

AbstractJohn R. Delaney received the Athelstan Spilhaus Award at the 2012 AGU Fall Meeting Honors Ceremony, held on 5 December 2012 in San Francisco, Calif. The award honors “individuals who have devoted portions of their lives to expressing the excitement, significance, and beauty of the Earth and space sciences to the general public.”
Working With Strainmeter Data
Authors: Hodgkinson Kathleen , Agnew Duncan , Roeloffs Evelyn 
Published: July 2013

AbstractThe Plate Boundary Observatory (PBO), the geodetic component of the U.S. National Science Foundation–funded Earthscope program, includes 75 borehole and 6 laser strainmeters (http://pbo.unavco.org). The strainmeters are installed at several locations: on the Cascadia forearc in Washington state and on Vancouver Island, Canada; in arrays of two to nine instruments along the North American–Pacific plate boundary in California; at Mount St. Helens; and in Yellowstone National Park. For deformation signals seconds to weeks in duration, strainmeters have a resolution and a signal‐to‐noise ratio superior to those of seismometers and GPS. However, this high sensitivity can introduce nontectonic signals into strain data, presenting data interpretation challenges, especially for borehole strainmeters.
High‐Resolution Satellite Data Open for Government Research
Authors: Neigh Christopher S. R. , Masek Jeffrey G. , Nickeson Jaime E. 
Published: July 2013

U.S. satellite commercial imagery (CI) with resolution less than 1 meter is a common geospatial reference used by the public through Web applications, mobile devices, and the news media. However, CI use in the scientific community has not kept pace, even though those who are performing U.S. government research have access to these data at no cost. Previously, studies using multiple CI acquisitions from IKONOS‐2, Quickbird‐2, GeoEye‐1, WorldView‐1, and WorldView‐2 would have been cost prohibitive. Now, with near‐global submeter coverage and online distribution, opportunities abound for future scientific studies. This archive is already quite extensive (examples are shown in Figure 1) and is being used in many novel applications.
Scientists observe near‐inertial wave trapped in Gulf Stream eddy
Authors: Schultz Colin 
Published: July 2013

AbstractDuring a research cruise in September 2009, Joyce et al. detected for the first time the existence of a near‐inertial wave trapped within most of a 90 kilometer‐diameter warm‐core eddy in the Gulf Stream. Just as oceanic gravitational waves are driven by the counterbalancing forces of gravity and buoyancy, inertial waves are driven by the wind and the inertial Coriolis force. The downward propagating wave that the authors detected was bounded by the clockwise‐rotating eddy.
Structure evolution of ultra high molecular weight polyethylene/montmorillonite nanocomposite fibers prepared by melt spinning
Authors: Zhang Qiang , Wang Qingzhao , Chen Yong 
Published: July 2013

ABSTRACTNanocomposite fibers of ultra high molecular weight polyethylene (UHMWPE) and organic montmorillonite (OMMT) were successfully prepared by a melt‐spinning process. The evolution of the microstructures of the nanocomposite fibers in the drawing process was preliminarily studied by X‐ray diffraction (XRD), differential scanning calorimetry, and small‐angle X‐ray scatters. With the increase of draw ratio values, the crystallinity of the nanocomposite fibers increased, the grain size decreased, and the folded chain crystals gradually transformed into extended chain crystals. The results suggested the evolution of the nanocomposite fibers was similar with that of the fibers made by gel‐spun drawing process. The addition of OMMT in UHMWPE improved the fluidity of the composites yet without affecting the crystal structure of UHMWPE in the drawing process. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 130: 3930–3936, 2013
A New V‐Shaped Organic Fluorescent Compound Integrated with Crystallization‐Induced Emission Enhancement and IntramolecularCharge Transfer
Authors: Gu Pei‐Yang , Zhang You‐Hao , Liu Gao‐Yan , Ge Jian‐Feng , Xu Qing‐Feng , Zhang Qichun , Lu Jian‐Mei 
Published: July 2013

AbstractThe emission behavior of a new V‐shaped organic fluorescent compound (p,p′‐bis(2‐aryl‐1,3,4‐oxadiazol‐5‐yl)diphenyl sulfone (OZA-SO), consisting of diethylamino (donor) and sulfone (acceptor) units, has been studied in various polar solvents and with different morphologies. As expected, there is the gradual transition from the locally excited state to the intramolecular charge‐transfer (ICT) state with the increasing solvent polarity. The photoluminescence intensity of OZA-SO initially decreases with a low water fraction (fw), owing to ICT effect, and then increases with a high fw, owing to crystallization‐induced emission enhancement. At the same time, the fluorescence lifetime of OZA-SO increases from 0.062 ns in dimethylformamide (DMF) to 5.80 ns in a solution containing 90 % water, and then to 7.49 ns in a solution containing 60 % water. Furthermore, the solid‐state emission of OZA-SO can be tuned reversibly from green to yellow by fuming/grinding or fuming/heating owing to morphological changes. This color‐switchable feature of OZA-SO may have potential applications in optical‐recording and temperature‐sensing materials.
Structure, function, and tethering of DNA‐binding domains in σ54 transcriptional activators
Authors: Vidangos Natasha , Maris Ann E. , Young Anisa , Hong Eunmi , Pelton Jeffrey G. , Batchelor Joseph D. , Wemmer David E. 
Published: July 2013

ABSTRACTWe compare the structure, activity, and linkage of DNA‐binding domains (DBDs) from σ54 transcriptional activators and discuss how the properties of the DBDs and the linker to the neighboring domain are affected by the overall properties and requirements of the full proteins. These transcriptional activators bind upstream of specific promoters that utilize σ54‐polymerase. Upon receiving a signal the activators assemble into hexamers, which then, through adenosine triphosphate (ATP) hydrolysis, drive a conformational change in polymerase that enables transcription initiation. We present structures of the DBDs of activators nitrogen regulatory protein C 1 (NtrC1) and Nif‐like homolog 2 (Nlh2) from the thermophile Aquifex aeolicus. The structures of these domains and their relationship to other parts of the activators are discussed. These structures are compared with previously determined structures of the DBDs of NtrC4, NtrC, ZraR, and factor for inversion stimulation. The N‐terminal linkers that connect the DBDs to the central domains in NtrC1 and Nlh2 were studied and found to be unstructured. Additionally, a crystal structure of full‐length NtrC1 was solved, but density of the DBDs was extremely weak, further indicating that the linker between ATPase and DBDs functions as a flexible tether. Flexible linking of ATPase and DBDs is likely necessary to allow assembly of the active hexameric ATPase ring. The comparison of this set of activators also shows clearly that strong dimerization of the DBD only occurs when other domains do not dimerize strongly. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 1082–1096, 2013.
Weak operator binding enhances simulated lac repressor‐mediated DNA looping
Authors: Colasanti Andrew V. , Grosner Michael A. , Perez Pamela J. , Clauvelin Nicolas , Lu Xiang‐Jun , Olson Wilma K. 
Published: July 2013

ABSTRACTThe 50th anniversary of Biopolymers coincides closely with the like celebration of the discovery of the Escherichia coli (lac) lactose operon, a classic genetic system long used to illustrate the influence of biomolecular structure on function. The looping of DNA induced by the binding of the Lac repressor protein to sequentially distant operator sites on DNA continues to serve as a paradigm for understanding long‐range genomic communication. Advances in analyses of DNA structures and in incorporation of proteins in computer simulations of DNA looping allow us to address long‐standing questions about the role of protein‐mediated DNA loop formation in transcriptional control. Here we report insights gained from studies of the sequence‐dependent contributions of the natural lac operators to Lac repressor‐mediated DNA looping. Novel superposition of the ensembles of protein‐bound operator structures derived from NMR measurements reveals variations in DNA folding missed in conventional structural alignments. The changes in folding affect the predicted ease with which the repressor induces loop formation and the ways that DNA closes between the protein headpieces. The peeling of the auxiliary operators away from the repressor enhances the formation of loops with the 92‐bp wildtype spacing and hints of a structural reason behind their weak binding. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 1070–1081, 2013.
The changing dielectric properties of CHO cells can be used to determine early apoptotic events in a bioprocess
Authors: Braasch Katrin , Nikolic‐Jaric Marija , Cabel Tim , Salimi Elham , Bridges Greg E. , Thomson Doug J. , Butler Michael 
Published: July 2013

ABSTRACTTo ensure maximum productivity of recombinant proteins it is desirable to prolong cell viability during a mammalian cell bioprocess, and therefore important to carefully monitor cell density and viability. In this study, five different and independent methods of monitoring were applied to Chinese hamster ovary (CHO) cells grown in a batch culture in a controlled bioreactor to determine cell density and/or cell viability. They included: a particle counter, trypan blue exclusion (Cedex), an in situ bulk capacitance probe, an off‐line fluorescent flow cytometer, and a prototype dielectrophoretic (DEP) cytometer. These various techniques gave similar values during the exponential growth phase. However, beyond the exponential growth phase the viability measurements diverged. Fluorescent flow cytometry with a range of fluorescent markers was used to investigate this divergence and to establish the progress of cell apoptosis: the cell density estimates by the intermediate stage apoptosis assay agreed with those obtained by the bulk capacitance probe and the early stage apoptosis assay viability measurements correlated well with the DEP cytometer. The trypan blue assay showed higher estimates of viable cell density and viability compared to the capacitance probe or the DEP cytometer. The DEP cytometer measures the dielectric properties of individual cells and identified at least two populations of cells, each with a distinct polarizability. As verified by comparison with the Nexin assay, one population was associated with viable (non‐apoptotic) cells and the other with apoptotic cells. From the end of the exponential through the stationary and decline stages there was a gradual shift of cell count from the viable into the apoptotic population. However, the two populations maintained their individual dielectric properties throughout this shift. This leads to the conclusion that changes in bulk dielectric properties of cultures might be better modeled as shifts in cells between different dielectric sub‐populations, rather than assuming a homogeneous dielectric population. This shows that bulk dielectric probes are sensitive to the early apoptotic changes in cells. DEP cytometry offers a novel and unique technology for analyzing and characterizing mammalian cells based on their dielectric properties, and suggests a potential application of the device as a low‐cost, label‐free, electronic monitor of physiological changes in cells. Biotechnol. Bioeng. 2013;110: 2902–2914. © 2013 Wiley Periodicals, Inc.
Recasting Stigma as a Dialogical Concept: A Case Study of Rural‐to‐Urban Migrants in China
Authors: Guan Jian , Liu Li 
Published: July 2013

ABSTRACTThe present study explores stigma against rural‐to‐urban migrants in China, drawing on a dialogical approach. It investigates the processes of stigmatization from two sides: that of the stigmatizer and that of the stigmatized. Open‐ended individual interviews were conducted with 138 participants (60 urban residents and 78 rural‐to‐urban migrants) in Tianjin, China. Findings from this study indicate that migrants were stigmatized by urban residents as having an unattractive physical appearance, potential perils of disease or crime, and discredited places of origin. Such stigma was embedded in China's unique hukou system and generated from a social categorization of superior and inferior groups. Migrants reported a number of coping strategies to counter such stigma: blaming fate, stigma reversal and upward mobility. However, migrants did not view themselves contemptuously and expressed positive feelings about their lives as migrants. They regarded internal migration as a way of pursuing happiness. Overall, urban residents stigmatized migrants legitimated by the hukou system, while migrants were surprisingly resilient against stigma, and did not internalize it, due to their economics‐driven internal migration. This study underscores that stigma in a given society is dialogically interdependent with its socio‐cultural context and that the perspectives of both the stigmatizer and the stigmatized need to be taken into consideration. Copyright © 2013 John Wiley & Sons, Ltd.
Mechanistic Study of the Oxidative Steam Reforming of EtOH on Rh(111): The Importance of the Oxygen Effect
Authors: Syu Cih‐Ying , Wang Jeng‐Han 
Published: July 2013

AbstractThis study extensively investigates the catalytic mechanism and oxygen effect in the oxidative steam reforming (OSR) of EtOH on Rh(111) by using plane‐wave density functional theory (DFT) and kinetic calculations. The mechanistic results show that both surface acetaldehyde (CH3CHO*) and oxametallacycle (CH2CH2O*) species from CαH and CβH bond scissions of surface ethoxy (CH3CH2O*) groups, respectively, are key intermediates. Both of these species can quickly decomposed into surface carbon (C*), methylidyne (CH*), and carbon monoxide (CO*) species, owing to energetic preferences. However, the removal of the adspecies in the formation of major products CO(g) and CO2(g) through high‐barrier oxidation steps are considered the rate‐determining steps in the overall catalytic process. In the study of the oxygen effect, surface oxygen (O*) species might slightly elevate the barriers for EtOH decomposition, but can lower the barriers for the rate‐limiting oxidation steps. The kinetic calculations, which well‐predict the experimental observations, indicate that the rates of those oxidation steps can be further increased at high oxygen pressures. These results conclude that the oxygen effect plays a crucial role in the OSR of EtOH on Rh‐based catalysts and further implies that the catalytic performance can be improved by using promoters, which have better oxidative capability, and by increasing the oxygen content, which can assist the oxidation process.
Cobalt‐Catalyzed CH Bond Functionalizations with Aryl and Alkyl Chlorides
Authors: Punji Benudhar , Song Weifeng , Shevchenko Grigory A. , Ackermann Lutz 
Published: July 2013

AbstractInexpensive cobalt catalysts derived from N‐heterocylic carbenes (NHC) allowed efficient catalytic CH bond arylations on heteroaryl‐substituted arenes with widely available aryl chlorides, which set the stage for the preparation of sterically hindered tri‐ortho‐substituted biaryls. Likewise, challenging direct alkylations with β‐hydrogen‐containing primary and even secondary alkyl chlorides proceeded on pyridyl‐ and pyrimidyl‐substituted arenes and heteroarenes. The cobalt‐catalyzed CH bond functionalizations occurred efficiently at ambient reaction temperature with excellent levels of site‐selectivities and ample scope. Mechanistic studies highlighted that electron‐deficient aryl chlorides reacted preferentially, while the arenes kinetic CH bond acidity was found to largely govern their reactivity.
Encapsulation of Metalloporphyrins in a Self‐Assembled Cubic M8L6 Cage: A New Molecular Flask for Cobalt–Porphyrin‐Catalysed Radical‐Type Reactions
Authors: Otte Matthias , Kuijpers Petrus F. , Troeppner Oliver , Ivanović‐Burmazović Ivana , Reek Joost N. H. , de Bruin Bas 
Published: July 2013

AbstractThe synthesis of a new, cubic M8L6 cage is described. This new assembly was characterised by using NMR spectroscopy, DOSY, TGA, MS, and molecular modelling techniques. Interestingly, the enlarged cavity size of this new supramolecular assembly allows the selective encapsulation of tetra(4‐pyridyl)metalloporphyrins (MII(TPyP), M=Zn, Co). The obtained encapsulated cobalt–porphyrin embedded in the cubic zinc–porphyrin assembly is the first example of a catalytically active encapsulated transition‐metal complex in a cubic M8L6 cage. The substrate accessibility of this system was demonstrated through radical‐trapping experiments, and its catalytic activity was demonstrated in two different radical‐type transformations. The reactivity of the encapsulated CoII(TPyP) complex is significantly increased compared to free CoII(TPyP) and other cobalt–porphyrin complexes. The reactions catalysed by this system are the first examples of cobalt–porphyrin‐catalysed radical‐type transformations involving diazo compounds which occur inside a supramolecular cage.
Eichhornia crassipes Cleans Wetlands by Enhancing the Nitrogen Removal and Modulating Denitrifying Bacteria Community
Authors: Yi Neng , Gao Yan , Long Xiao‐hua , Zhang Zhi‐yong , Guo Jun‐yao , Shao Hong‐bo , Zhang Zhen‐hua , Yan Shao‐hua 
Published: July 2013

AbstractThe role of floating macrophytes on modulating the microbial nitrogen removal is not well understood. In this study, the cultivation of Eichhornia crassipes in eutrophic water may affect the nitrogen (N) fate by modulating the denitrifying bacteria diversity and abundance. The gaseous N losses via denitrification were estimated by 15N stable isotope tracing and the diversity and abundance of denitrifying genes (nirS, nirK, and nosZ) were investigated by molecular tools. The denaturing gradient gel electrophoresis (DGGE) profiles showed that the diversity of denitrifying genes in the treatments with E. crassipes was significantly higher than that in the treatment without E. crassipes. The real‐time PCR (qPCR) results showed the trend of denitrifier abundance in the entire system was in the order of N‐ER (nitrate with just root of E. crassipes) and A‐ER (ammonia with just root of E. crassipes) > N‐R (nitrate with E. crassipes) and A‐R (ammonia with E. crassipes) > N‐W (nitrate without plant) and A‐W (ammonia without plant). The gaseous 15N losses via denitrification were significantly and positively related to the abundance of nirK, nirS, and nosZ genes. The results indicated that cultivation of E. crassipes in eutrophic water could increase the diversity and abundance of denitrifying bacteria, resulting in more N being removed as gases via denitrification.
Accuracy of multiparametric magnetic resonance imaging in confirming eligibility for active surveillance for men with prostate cancer
Authors: Stamatakis Lambros , Siddiqui M. Minhaj , Nix Jeffrey W. , Logan Jennifer , Rais‐Bahrami Soroush , Walton‐Diaz Annerleim , Hoang Anthony N. , Vourganti Srinivas , Truong Hong , Shuch Brian , Parnes Howard L. , Turkbey Baris , Choyke Peter L. , Wood Bradford J. , Simon Richard M. , Pinto Peter A. 
Published: July 2013

BACKGROUNDActive surveillance (AS) is an attempt to avoid overtreatment of clinically insignificant prostate cancer (PCa); however, patient selection remains controversial. Multiparametric prostate magnetic resonance imaging (MP‐MRI) may help better select AS candidates.METHODSWe reviewed a cohort of men who underwent MP‐MRI with MRI/Ultrasound fusion–guided prostate biopsy and selected potential AS patients at entry using Johns Hopkins criteria. MP‐MRI findings were assessed, including number of lesions, dominant lesion diameter, total lesion volume, prostate volume, and lesion density (calculated as total lesion volume/prostate volume). Lesions were assigned a suspicion score for cancer by MRI. AS criteria were reapplied based on the confirmatory biopsy, and accuracy of MP‐MRI in predicting AS candidacy was assessed. Logistic regression modeling and chi‐square statistics were used to assess associations between MP‐MRI interpretation and biopsy results.RESULTSEighty‐five patients qualified for AS with a mean age of 60.2 years and mean prostate‐specific antigen level of 4.8 ng/mL. Of these, 25 patients (29%) were reclassified as not meeting AS criteria based on confirmatory biopsy. Number of lesions, lesion density, and highest MRI lesion suspicion were significantly associated with confirmatory biopsy AS reclassification. These MRI‐based factors were combined to create a nomogram that generates a probability for confirmed AS candidacy.CONCLUSIONAs clinicians counsel patients with PCa, MP‐MRI may contribute to the decision‐making process when considering AS. Three MRI‐based factors (number of lesions, lesion suspicion, and lesion density) were associated with confirmatory biopsy outcome and reclassification. A nomogram using these factors has promising predictive accuracy for which future validation is necessary. Cancer 2013;119:3359–66. Published 2013. This article is a U.S. Government work and is in the public domain in the USA