bluuebunny/crossref_metadata_2025_split huggingface dataset:
Site‐Specific Protein Labeling with SNAP‐Tags
Authors: Cole Nelson B. 
Published: October 2013

ABSTRACTSite‐specific labeling of cellular proteins with chemical probes is a powerful tool for studying protein function in living cells. A number of small peptide and protein tags have been developed that can be labeled with synthetic probes with high efficiencies and specificities and provide flexibility not available with fluorescent proteins. The SNAP‐tag is a modified form of the DNA repair enzyme human O6‐alkylguanine‐DNA‐alkyltransferase, and undergoes a self‐labeling reaction to form a covalent bond with O6‐benzylguanine (BG) derivatives. BG can be modified with a wide variety of fluorophores and other reporter compounds, generally without affecting the reaction with the SNAP‐tag. In this unit, basic strategies for labeling SNAP‐tag fusion proteins, both for live cell imaging and for in vitro analysis, are described. This includes a description of a releasable SNAP‐tag probe that allows the user to chemically cleave the fluorophore from the labeled SNAP‐tag fusion. In vitro labeling of purified SNAP‐tag fusions is briefly described. Curr. Protoc. Protein Sci. 73:30.1.1‐30.1.16. © 2013 by John Wiley & Sons, Inc.
Harvesting, Isolation, and Functional Assessment of Primary Vagal Ganglia Cells
Authors: Dubuis Eric , Grace Megan , Wortley Michael A. , Birrell Mark A. , Belvisi Maria G. 
Published: October 2013

AbstractAirway sensory nerves play an important defensive role in the lungs, being central in mediating protective responses like cough and bronchoconstriction. In some cases, these responses become excessive, hypersensitive, and deleterious. Understanding the normal function of airway nerves and phenotype changes associated with disease will help in developing new therapeutics for treating chronic obstructive pulmonary disease and chronic cough. Guinea pigs, and to a lesser extent ferrets, are commonly employed for studying the cough reflex because they have a cough response similar to humans. While rats and mice do not exhibit a cough response, they do possess sensory nerves that respond to the same range of tussive stimuli as guinea pigs and humans. Described in this unit are protocols for harvesting guinea pig, mouse, and rat sensory nerve cell bodies to assess molecular and functional changes associated with pulmonary disease, and to identify new targets for therapeutic intervention. Curr. Protoc. Pharmacol. 62:12.15.1‐12.15.27. © 2013 by John Wiley & Sons, Inc.
2′‐Hydroxy Protection of Ribonucleosides as 2‐Cyano‐2,2‐Dimethylethanimine‐N‐Oxymethyl Ethers in Solid‐Phase Synthesis of RNA Sequences
Authors: Cieślak Jacek , Ausín Cristina , Grajkowski Andrzej , Beaucage Serge L. 
Published: October 2013

AbstractThe reaction of 2′‐O‐aminooxymethylribonucleosides with 2‐cyano‐2‐methyl propanal leads to the formation of stable and yet reversible 2′‐O‐(2‐cyano‐2,2‐dimethylethanimine‐N‐oxymethyl)ribonucleosides in post‐purification yields of 54% to 82%. Phenoxyacetylation of the exocyclic amino functions of these ribonucleosides proceeds in yields of 74% to 89%, and subsequent 5′‐O‐dimethoxytritylation and 3′‐O‐phosphitylation of the corresponding N‐phenoxyacetylated ribonucleosides provide the fully protected ribonucleoside phosphoramidite monomers in isolated yields of 69% to 88%. These ribonucleoside phosphoramidites are employed in solid‐phase synthesis of three chimeric RNA sequences, each differing in purine/pyrimidine content. The stepwise coupling efficiency of the ribonucleoside phosphoramidites (as 0.15 M solutions in acetonitrile) averages 99% over a coupling time of 180 s when 5‐benzylthio‐1H‐tetrazole is used as an activator. Upon completion of RNA chain assembly, removal of the nucleobase‐ and phosphate‐protecting groups and release of sequences from the solid support are carried out under standard basic conditions. Finally, the 2′‐O‐(2‐cyano‐2,2‐dimethylethanimine‐N‐oxymethyl) protective groups are cleaved from the RNA sequences by treatment with 0.5 M tetra‐n‐butylammonium fluoride in dry DMSO for 24 to 48 hr at 55°C without releasing RNA‐alkylating side‐products. Characterization of the fully deprotected RNA sequences by PAGE, enzymatic hydrolysis, and MALDI‐TOF mass spectrometry confirms the identity and high quality of these sequences. Curr. Protoc. Nucleic Acid Chem. 54:3.22.1‐3.22.28. © 2013 by John Wiley & Sons, Inc.
Towards Functional Orthogonalisation of Protein Complexes: Individualisation of GroEL Monomers Leads to Distinct Quasihomogeneous Single Rings
Authors: Billerbeck Sonja , Calles Belén , Müller Christian L. , de Lorenzo Victor , Panke Sven 
Published: October 2013

AbstractThe essential molecular chaperonin GroEL is an example of a functionally highly versatile cellular machine with a wide variety of in vitro applications ranging from protein folding to drug release. Directed evolution of new functions for GroEL is considered difficult, due to its structure as a complex homomultimeric double ring and the absence of obvious molecular engineering strategies. In order to investigate the potential to establish an orthogonal GroEL system in Escherichia coli, which might serve as a basis for GroEL evolution, we first successfully individualised groEL genes by inserting different functional peptide tags into a robustly permissive site identified by transposon mutagenesis. These peptides allowed fundamental aspects of the intracellular GroEL complex stoichiometry to be studied and revealed that GroEL single‐ring complexes, which assembled in the presence of several functionally equivalent but biochemically distinct monomers, each consist almost exclusively of only one type of monomer. At least in the case of GroEL, individualisation of monomers thus leads to individualisation of homomultimeric protein complexes, effectively providing the prerequisites for evolving an orthogonal intracellular GroEL folding machine.
Zwitterionic Moieties from the Huisgen Reaction: A Case Study with Amphiphilic Dendritic Assemblies
Authors: Ramireddy Rajasekhar R. , Subrahmanyam Ayyagari V. , Thayumanavan S. 
Published: October 2013

AbstractSupramolecular nano‐assemblies that reduce nonspecific interactions with biological macromolecules, such as proteins, are of great importance for various biological applications. Recently, zwitterionic materials have been shown to reduce nonspecific interactions with biomolecules, owing both to their charge neutrality and their ability to form a strong hydration layer around zwitterions via electrostatic interactions. Here, new triazole‐based zwitterionic moieties are presented that are incorporated as the hydrophilic functionalities in facially amphiphilic dendrons. The amphiphilic zwitterionic dendrons spontaneously self‐assemble in aqueous solutions forming micelle‐type aggregates, which were confirmed by DLS, TEM, and fluorescence techniques. The structural and functional characteristics of the zwitterionic dendrons are also compared with the corresponding charge‐neutral PEG‐based dendrons and anionic carboxylate‐based dendrons. Surface‐charge measurements, temperature sensitivity and evaluation of interactions of these assemblies with proteins form the bases for these comparisons.
Lack of tyramine pressor response effect with oral CX157: A specific reversible MAOI
Authors: Burch Daniel , Asgharnejad Mahnaz , Gerson William , Fielding Robert M. , Azzaro Albert J. 
Published: October 2013

AbstractThis Phase 1, single‐center, double‐blind, placebo‐controlled, three‐period study assessed cardiovascular safety of CX157, a specific Reversible Inhibitor of Monoamine Oxidase A (RIMA), following the oral administration of tyramine. In Period 1, the sensitivity of each subject to orally administered tyramine was established by determining the dose of tyramine that elevates SBP ≥30 mmHg on ≥3 consecutive occasions (i.e., TYR303). Twelve subjects qualified for randomization in Period 2 during which an oral CX157 Modified Release Tablet (125 mg [N = 10]) or placebo (N = 2) were administered twice per day for 6 days to reach steady state. In Period 3, CX157 and placebo were administered with oral tyramine in fed state with daily increases in the tyramine dose of 20, 40, and 80 mg in an attempt to achieve the TYR303. CX157 Modified Release Tablet, 125 mg administered twice per day (250 mg daily dose), was not associated with a tyramine reaction (i.e., TYR303). It is generally agreed that a high tyramine meal would contain up to 40 mg of dietary tyramine. These data obtained with CX157 provide an adequate margin of safety with respect to tyramine interaction and suggest that future studies can be conducted without the need for dietary tyramine restrictions.
Stable Cycling of Fe2O3 Nanorice as an Anode through Electrochemical Porousness and the Solid–Electrolyte Interphase Thermolysis Approach
Authors: Liang Jianwen , Wei Denghu , Cheng Qiushi , Zhu Yongchun , Li Xiaona , Fan Long , Zhang Jingjing , Qian Yitai 
Published: October 2013

AbstractA new thread for improving the cycling stability of Fe2O3 nanorice is proposed through combining the electrochemical porousness (EP) effect and solid–electrolyte interphase (SEI) thermolysis approach. Starting from solid Fe2O3 nanorice, this process could be applied to prepare porous Fe2O3 nanorice with a good coating of a porous SEI thermolysis layer composed of carbon and Li2O. The interconnecting pores and full coating of the SEI thermolysis layer provides not only mechanical resistance of the Fe2O3 nanorice against pulverization, but also high electrical and ionic conductivity over the electrode throughout long cell cycles. This method results in the enhancement of cycling ability and capacity, which is demonstrated by comparison with the starting Fe2O3 nanorice. After the EP and SEI thermolysis approach, the Fe2O3 nanorice exhibits an energy capacity retention about of 680 mAh g−1 at a current density of 1000 mA g−1 over 250 cycles, which is more than 82 % of the initial reversible capacity. Moreover, it also has an excellent rate capability and high coulombic efficiency. This strategy provides a simple and convenient route toward stable charge/discharge cycling for not only Fe2O3, but also for other electrode materials that are subject to large volume changes and low charge voltages. At the same time, it also contributes to a fundamental understanding of improved cycling stability and reversible capacity for electrode materials.
A case of gallbladder perforation detected by sonography after a blunt abdominal trauma
Authors: Hongo Maiko , Ishida Hideaki , Naganuma Hiroko , Yoshioka Hiroshi , Kasuya Takamitu , Niwa Makoto 
Published: October 2013

ABSTRACTGallbladder (GB) perforation is a very rare posttraumatic abdominal injury. It is potentially life‐threatening, and good outcome requires early diagnosis. We present a case of isolated posttraumatic GB perforation in which the precise sonographic (US) diagnosis led us to apply proper management. Color Doppler US showed a clear to‐and‐fro flow signal passing through the perforation site, and contrast‐enhanced US confirmed the presence of a small defect in the GB wall. When examining posttraumatic patients, the possibility of GB perforation must be kept in mind. Color Doppler US and contrast‐enhanced US are the examinations of choice to detect the perforation site and show bile movement through the perforation. © 2013 Wiley Periodicals, Inc. J Clin Ultrasound 42:301–304, 2014
Evolutionary analysis of HBV “S” antigen genetic diversity in Iranian blood donors: A nationwide study
Authors: Pourkarim Mahmoud Reza , Sharifi Zohre , Soleimani Ali , Amini‐Bavil‐Olyaee Samad , Elsadek Fakhr Ahmed , Sijmons Steven , Vercauteren Jurgen , Karimi Gharib , Lemey Philippe , Maes Piet , Alavian Seyed Moayed , Van Ranst Marc 
Published: October 2013

AbstractThe genetic diversity of the HBV S gene has a significant impact on the prophylaxis and treatment of hepatitis B infection. The effect of selective pressure on this genetic alteration has not yet been studied in Iranian blood donors. To explore HBV evolution and to analyze the effects and patterns of hepatitis B surface antigen (HBsAg) mutations on blood screening assays, 358 Iranian blood donors diagnosed as asymptomatic HBV carriers were enrolled in this nationwide study. Large S and partial S genes were amplified and sequenced. HBV (sub) genotypes and synonymous and nonsynonymous mutations were investigated. The impact of naturally occurring mutations on HBsAg ELISA results was explored. Phylogenetic analyses revealed that isolated strains were of genotype D. The dominant subgenotype/subtype was D1/ayw2. Deletions and naturally occurring stop codons in the pre‐S1 and major hydrophilic region (MHR) were identified. In total, 32.8% of the studied strains harbored 195 single or multiple mutations in the MHR, the majority of which were located at the first loop of the “a determinant” domain. The ayw2 subtype showed a significant effect on the ELISA signal/cut‐off value and carried fewer mutations in the MHR. Nonsynonymous/synonymous substitution value indicated that negative selection was the dominant evolutionary force in the HBV S gene. This nationwide study revealed that mutation frequency of HBsAg among Iranian blood donors was much higher than previous reports from the different local regions. These findings regarding the significant differences in reactivity of ELISA among different subtypes of HBV and its correlation with the number of mutations at the MHR will be valuable to public health authorities. J. Med. Virol. 86:144–155, 2014. © 2013 Wiley Periodicals, Inc.
Uvular injury during the perioperative period in patients undergoing general anesthesia
Authors: Pamnani Anup , Faggiani Susan L. , Hood Melanie , Kacker Ashutosh , Gadalla Farida 
Published: October 2013

ObjectiveThe purpose of this study was to evaluate the incidence and causes of uvular injury in the patients that received general anesthesia in the perioperative period.Study DesignA 4‐year retrospective review of cases of uvular injury and their resolution was conducted in adult patients who received general anesthesia at our institution.MethodsAn extensive review was conducted of the quality assurance (QA) database maintained by the Department of Anesthesiology at our tertiary academic medical center. The database was searched for cases of uvular injury that occurred in adult patients undergoing general anesthesia that between January 2007 and December 2010. The medical records of identified patients were then obtained to evaluate the presentation, treatment and ultimate resolution of injury.ResultsTen cases of uvular injury were reported in the 28,788 general anesthetics conducted over a 3‐year period in adult patients. This correlates to an incidence of 0.034%. Uvular injury occurred in mostly male patients (80%) during elective cases in the supine position. All cases were associated with endotracheal intubation. Additional objects, such as gastric tubes and esophageal temperature probes, were placed in the pharynx of 80% of these patients. Urologic procedures were associated with 50% of reported cases. Treatment ranged from observation to medical therapy. There were no permanent symptoms in any of the patients.ConclusionUvular injury is a relatively rare complication that occurs in patients during the perioperative period who receive general anesthesia. While endotracheal intubation is closely associated with this type of injury, further study is required to elucidate the mechanism and other associated etiologic factors.Level of Evidence4. Laryngoscope, 124:196–200, 2014
5α‐reductase type 3 enzyme in benign and malignant prostate
Authors: Titus Mark A. , Li Yun , Kozyreva Olga G. , Maher Varun , Godoy Alejandro , Smith Gary J. , Mohler James L. 
Published: October 2013

AbstractBACKGROUNDCurrently available 5α‐reductase inhibitors are not completely effective for treatment of benign prostate enlargement, prevention of prostate cancer (CaP), or treatment of advanced castration‐recurrent (CR) CaP. We tested the hypothesis that a novel 5α‐reductase, 5α‐reductase‐3, contributes to residual androgen metabolism, especially in CR‐CaP.METHODSA new protein with potential 5α‐reducing activity was expressed in CHO‐K1 cellsandTOP10 E. coli for characterization. Protein lysates and total mRNA were isolated from preclinical and clinical tissues. Androgen metabolism was assessed using androgen precursors and thin layer chromatography or liquid chromatography tandem mass spectrometry.RESULTSThe relative mRNA expression for the three 5α‐reductase enzymes in clinical samples of CR‐CaP was 5α‐reductase‐3 ≫ 5α‐reductase‐1 > 5α‐reductase‐2. Recombinant 5α‐reductase‐3 protein incubations converted testosterone, 4‐androstene‐3,17‐dione (androstenedione) and 4‐pregnene‐3,20‐dione (progesterone) to dihydrotestosterone, 5α‐androstan‐3,17‐dione, and 5α‐pregnan‐3,20‐dione, respectively. 5α‐Reduced androgen metabolites were measurable in lysates from androgen‐stimulated (AS) CWR22 and CR‐CWR22 tumors and clinical specimens of AS‐CaP and CR‐CaP pre‐incubated with dutasteride (a bi‐specific inhibitor of 5α‐reductase‐1 and 2).CONCLUSIONHuman prostate tissues contain a third 5α‐reductase that was inhibited poorly by dutasteride at high androgen substrate concentration in vitro, and it may promote DHT formation in vivo, through alternative androgen metabolism pathways when testosterone levels are low. Prostate 74:235–249, 2014. © 2013 Wiley Periodicals, Inc.
Bridging vs. Chelating Coordination Modes of Vinylsilanes in CuI π‐Complexes: Structure and Stability
Authors: Dużak Tomasz , Zarychta Bartosz , Olijnyk Volodymyr 
Published: October 2013

AbstractTwo new copper(I) olefin complexes, [Cu6Cl6(MTrVS)2] (1) and [Cu2Cl2(DMVSP)2] (2), of tridentate bridging methyltrivinylsilane (MTrVS) and bidentate chelating 2‐[dimethyl(vinyl)silyl]pyridine (DMVSP) have been synthesized and characterized by single‐crystal X‐ray structure analysis, IR and 1H NMR spectroscopy. It has been shown that using the alkenylsilanes with required electronic properties, molecular symmetry and conformational flexibility, it is possible to control the formation of optimal copper(I) halide oligomers. The obtained results, together with relevant literature data, also illustrate how the coordination mode of vinylsilanes is related to Cu–(C=C) bond strengthening and, consequently, to stability of the organometallic compounds. In particular, we suggest that, together with Cu–Cα distance shortening accompanied by a segmentation of π‐conjugated chelate ring, complex shows an increased lability to form probably an alkenylcopper intermediate in the homocoupling reaction of alkenyl(2‐pyridyl)silanes. At the same time, no appreciable reduction of thermal stability of π‐conjugated chelate complex 2 with respect to bridged compound 1 emerges.
Hidden burrow plugs and their function in the tiger beetle, Cosmodela batesi (Coleoptera, Cicindelidae)
Authors: Lin Shou-Wang , Okuyama Toshinori 
Published: October 2013

Abstract
Tiger beetle larvae excavate and live in underground burrows, whose openings they sometimes plug with soil. This study documents the burrow plugging behavior of the tiger beetle, Cosmodela batesi (Fleutiaux), in the field. We also tested the function of burrow plugs in the laboratory. In the field, C. batesi more frequently made a plug when it rained. Most larvae made plugs inside their burrows (rather than at the soil surface), and the use of an endoscope was necessary to detect these sub-surface plugs. In the laboratory, flooding was simulated by artificially introducing water into specially-made arenas. Water filled the entire burrow when there was no plug, whereas plugged burrows maintained air chambers inside. When a plug was broken with a wire, burrows filled up with water. The burrowing and plugging behavior described in this study is likely an important adaptation of C. batesi to its habitat.
Mirror-symmetric exact coherent states in plane Poiseuille flow
Authors: Nagata M. , Deguchi K. 
Published: October 2013

AbstractTwo new families of exact coherent states are found in plane Poiseuille flow. They are obtained from the stationary and the travelling-wave mirror-symmetric solutions in plane Couette flow by a homotopy continuation. They are characterized by the mirror symmetry inherited from those continued solutions in plane Couette flow. The first family arises from a saddle-node bifurcation and the second family bifurcates by breaking the top–bottom symmetry of the first family. We find that both families exist below the minimum saddle-node-point Reynolds number known to date (Waleffe, Phys. Fluids, vol. 15, 2003, pp. 1517–1534).
Fragmented Liberalization in the Chinese Automotive Industry: The Political Logic behind Beijing Hyundai's Success in the Chinese Market
Authors: Oh Seung-Youn 
Published: October 2013

AbstractThis paper explains the extraordinary rise of the Beijing Hyundai Motor Company (BHMC), a joint venture between a state-owned enterprise run by the Beijing municipal government and Hyundai Motor Company. Within the span of three years, the BHMC soared to become China's second-ranked automotive manufacturer in terms of units sold. I highlight the role of the Beijing municipal government in creating favourable market conditions for the BHMC during its initial operation phase (2002–2005). The Beijing municipal government selectively adopted protectionist measures and liberalizing measures to promote its locally based company. I characterize this practice asfragmented liberalization,a system through which sub-national governments discriminately apply WTO or central government regulations to promote their local joint venture partner. In so doing, I also challenge the existing assumption that multinational companies are the drivers of economic liberalization, by showing Hyundai's support for local protectionism and industrial policy at the sub-national level.
A consistent semantics of self-adjusting computation
Authors: ACAR UMUT A. , BLUME MATTHIAS , DONHAM JACOB 
Published: October 2013

AbstractThis paper presents a semantics of self-adjusting computation and proves that the semantics is correct and consistent. The semantics introduces memoizing change propagation, which enhances change propagation with the classic idea of memoization to enable reuse of computations even when memory is mutated via side effects. During evaluation, computation reuse via memoization triggers a change-propagation algorithm that adapts the reused computation to the memory mutations (side effects) that took place since the creation of the computation. Since the semantics includes both memoization and change propagation, it involves both non-determinism (due to memoization) and mutation (due to change propagation). Our consistency theorem states that the non-determinism is not harmful: any two evaluations of the same program starting at the same state yield the same result. Our correctness theorem states that mutation is not harmful: Self-adjusting programs are compatible with purely functional programming. We formalize the semantics and its meta-theory in the LF logical framework and machine check our proofs using Twelf.