bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microwave‐Assisted Phosphitylation of DNA and RNA Nucleosides and Their Analogs
Authors: Efthymiou Tim , Krishnamurthy Ramanarayanan 
Published: March 2015

AbstractMicrowave‐assisted chemical phosphitylation of novel nucleoside analogs containing a ribulose sugar unit was successful with yields ranging from 50% to 79% using 2‐cyanoethyl‐N,N‐diisopropyl chlorophosphoramidite as the phosphitylating reagent. The resultant phosphoramidite products remained intact, with no signs of degradation over extended reaction times (up to 60 min) at an elevated temperature (65°C). When the same microwave‐mediated phosphitylating protocols were applied to canonical DNA and RNA nucleoside monomers as substrates, using either 2‐cyanoethyl‐N,N,‐diisopropyl chlorophosphoramidite or 2‐cyanoethyl‐N,N,N′,N′‐tetraisopropyl phosphane with an activator, 40% to 90% yields of DNA and RNA phosphoramidites were obtained within 10 to 15 min. These results demonstrate that microwave‐assisted phosphitylation is an efficient alternative to standard phosphitylating conditions that can be expanded and refined to include a variety of substrates. © 2015 by John Wiley & Sons, Inc.
Characterization of Thioether‐Linked Protein Adducts of DNA Using a Raney‐Ni‐Mediated Desulfurization Method and Liquid Chromatography‐Electrospray‐Tandem Mass Spectrometry
Authors: Chowdhury Goutam , Guengerich F. Peter 
Published: March 2015

AbstractThis unit contains a complete procedure for the detection and structural characterization of DNA protein crosslinks (DPCs). The procedure also describes an approach for the quantitation of the various structurally distinct DPCs. Although various methods have been described in the literature for labile DPCs, characterization of nonlabile adducts remain a challenge. Here we present a novel approach for characterization of both labile and non‐labile adducts by the use of a combination of chemical, enzymatic, and mass spectrometric approaches. A Raney Ni‐catalyzed reductive desulfurization method was used for removal of the bulky peptide adducts, enzymatic digestion was used to digest the protein to smaller peptides and DNA to nucleosides, and finally LC‐ESI‐tandem mass spectrometry (MS) was utilized for detection and characterization of nucleoside adducts. © 2015 by John Wiley & Sons, Inc.
Investigating Protein Structure and Evolution with SCOP2
Authors: Andreeva Antonina , Howorth Dave , Chothia Cyrus , Kulesha Eugene , Murzin Alexey G. 
Published: March 2015

AbstractSCOP2 is a successor to the Structural Classification of Proteins (SCOP) database that organizes proteins of known structure according to their structural and evolutionary relationships. It was designed to provide a more advanced framework for the classification of proteins. The SCOP2 classification is described in terms of a directed acyclic graph in which each node defines a relationship of particular type that is represented by a region of protein structure and sequence. The SCOP2 data are accessible via SCOP2‐Browser and SCOP2‐Graph. This protocol unit describes different ways to explore and investigate the SCOP2 evolutionary and structural groupings. © 2015 by John Wiley & Sons, Inc.
Expression Data Analysis with Reactome
Authors: Jupe Steve , Fabregat Antonio , Hermjakob Henning 
Published: March 2015

AbstractThe Reactome database of curated biological pathways provides a tool for visualizing user‐supplied expression data as an overlay on pathway diagrams, thereby affording an effective means to examine expression of the constituents of the pathway and determine whether all that are necessary are present. Several experiments can be visualized in succession, to determine whether expression changes with experimental conditions, a useful feature for examining a time‐course, dose‐response, or disease progression. © 2015 by John Wiley & Sons, Inc.
A method to derive maps of ionospheric conductances, currents, and convection from the Swarm multisatellite mission
Authors: Amm O. , Vanhamäki H. , Kauristie K. , Stolle C. , Christiansen F. , Haagmans R. , Masson A. , Taylor M. G. G. T. , Floberghagen R. , Escoubet C. P. 
Published: March 2015

AbstractThe European Space Agency (ESA) Swarm spacecraft mission is the first multisatellite ionospheric mission with two low‐orbiting spacecraft that are flying in parallel at a distance of ~100–140 km, thus allowing derivation of spatial gradients of ionospheric parameters not only along the orbits but also in the direction perpendicular to them. A third satellite with a higher orbit regularly crosses the paths of the lower spacecraft. Using the Swarm magnetic and electric field instruments, we present a novel technique that allows derivation of two‐dimensional (2‐D) maps of ionospheric conductances, currents, and electric field in the area between the trajectories of the two lower spacecraft, and even to some extent outside of it. This technique is based on Spherical Elementary Current Systems. We present test cases of modeled situations from which we calculate virtual Swarm data and show that the technique is able to reconstruct the model electric field, horizontal currents, and conductances with a very good accuracy. Larger errors arise for the reconstruction of the 2‐D field‐aligned currents (FAC), especially in the area outside of the spacecraft orbits. However, even in this case the general pattern of FAC is recovered, and the magnitudes are valid in an integrated sense. Finally, using an MHD model run, we show how our technique allows estimation of the ionosphere‐magnetosphere coupling parameter K, if conjugate observations of the magnetospheric magnetic and electric field are available. In the case of a magnetospheric multisatellite mission (e.g., the ESA Cluster mission) several K estimates at nearby points can be generated.
Upper thermospheric responses to forcing from above and below during 1–10 April 2010: Results from an ensemble of numerical simulations
Authors: Hagan M. E. , Häusler K. , Lu G. , Forbes J. M. , Zhang X. 
Published: March 2015

AbstractIn this report we examine the spatial and temporal variability of the quiescent thermosphere leading up to and after the 5 April 2010 geomagnetic disturbance. We attribute the dominant driver of this variability to a combination of tides generated in situ and in the troposphere, stratosphere, and mesosphere. We identify nonmigrating tidal signatures attributable to the latter source that are ubiquitous, persistent, and significant at all thermospheric latitudes. Further, these perturbations underlie the upper atmospheric response to solar geomagnetic disturbances and are measurably altered, along with their migrating counterparts, during the storm. Our investigation is centered on a series of National Center for Atmospheric Research thermosphere‐ionosphere‐mesosphere‐electrodynamics general circulation model simulations during 1–10 April 2010, including an optimal simulation with lower boundary forcing based on Modern‐Era Retrospective Analysis for Research and Application reanalysis data and upper boundary forcing based on satellite and ground magnetometer measurements and the Assimilative Mapping of Ionospheric Electrodynamics procedure and three diagnostic simulations. The differences between the optimal and diagnostic simulations allow us to quantify thermospheric variability attributable to solar geomagnetic forcing and dynamical effects propagating into the thermosphere from below. We find that they can be comparable at high latitudes for some nonmigrating tidal components.
Decadal changes in South Pacific sea surface temperatures and the relationship to the Pacific decadal oscillation and upper ocean heat content
Authors: Linsley Braddock K. , Wu Henry C. , Dassié Emilie P. , Schrag Daniel P. 
Published: March 2015

AbstractDecadal changes in Pacific sea surface temperatures (SSTs) and upper ocean heat content (OHC) remain poorly understood. We present an annual average composite coral Sr/Ca‐derived SST time series extending back to 1791 from Fiji, Tonga, and Rarotonga (FTR) in the Pacific Decadal Oscillation (PDO) sensitive region of the southwest Pacific. Decadal SST maxima between 1805 and 1830 Common Era (C.E.) indicate unexplained elevated SSTs near the end of the Little Ice Age. The mean period of decadal SST variability in this region has a period near 25 years. Decades of warmer (cooler) FTR SST co‐occur with PDO negative (positive) phases since at least ~1930 C.E. and positively correlate with South Pacific OHC (0–700 m). FTR SST is also inversely correlated with decadal changes in equatorial Pacific SST as measured by coral Sr/Ca. Collectively, these results support the fluctuating trade wind‐shallow meridional overturning cell mechanism for decadal modulation of Pacific SSTs and OHC.
Multiple carriers of Q noble gases in primitive meteorites
Authors: Marrocchi Yves , Avice Guillaume , Estrade Nicolas 
Published: March 2015

AbstractThe main carrier of primordial heavy noble gases in chondrites is thought to be an organic phase, known as phase Q, whose precise characterization has resisted decades of investigation. Indirect techniques have revealed that phase Q might be composed of two subphases, one of them associated with sulfide. Here we provide experimental evidence that noble gases trapped within meteoritic sulfides present chemically and thermally driven behavior patterns that are similar to Q gases. We therefore suggest that phase Q is likely composed of two subcomponents: carbonaceous phases and sulfides. In situ decay of iodine at concentration levels consistent with those reported for meteoritic sulfides can reproduce the 129Xe excess observed for Q gases relative to fractionated solar wind. We suggest that the Q‐bearing sulfides formed at high temperature and could have recorded the conditions that prevailed in the chondrule‐forming region(s).
Interannual variability of tropical cyclone activity and regional Hadley circulation over the Northeastern Pacific
Authors: Zhang Gan , Wang Zhuo 
Published: March 2015

AbstractThe interannual variability of the regional Hadley circulation (HC) and tropical cyclone (TC) activity over the Northeastern Pacific (NEP) was investigated. The interannual variability of the HC in the NEP hurricane season is found dominated by a mode (M1EP) regulating the strength and meridional extent of the Intertropical Convergence Zone. M1EP has a more robust correlation with NEP TC activity than the El Niño–Southern Oscillation sea surface temperature indices. The strong correlation is attributed to the impacts of M1EP on environmental conditions. In addition, the leading mode of the Atlantic HC, which has an anticorrelation with M1EP, also strongly impacts NEP TC activity. The findings, together with Zhang and Wang (2013), highlight the role of the HC in controlling the variability of TC activity as well as the interbasin connection between the NEP and the Atlantic. The regional HC is thus recommended as a useful metric to benchmark models in simulating TC activity.
Hunts, Heinz, and Fries Priming ‘Ketchup’: The Effects of Lexicality on Brand Name–Product Associations and Brand Memory
Authors: Coane Jennifer H. , Monahan Kayleigh T. , Termonen Miia‐Liisa 
Published: March 2015

SummaryBrand names should be memorable and easy to associate with the product. The present study investigated how brand name lexicality affects accessibility in memory. In Experiment 1, participants completed a primed lexical decision task (LDT) in which primes were real‐word brands (RWB; e.g., SATURN), nonword brands (NWB; e.g., KIA), or semantic associates (e.g., TIRE) and targets were product categories (e.g., car). NWB primes resulted in equivalent priming as semantic primes and were recalled more than RWBs in a free‐recall task. In Experiment 2, participants completed an unprimed LDT or brand decision task (BDT). In LDT, high NWB error rates reflected greater familiarity. In BDT, many RWBs were not recognized as brands. In Experiment 3, a primed BDT with brand names as targets indicated that NWBs and RWBs are equally primed by a related category label. Overall, NWBs appear to be more familiar and memorable, possibly because of distinctiveness. Copyright © 2015 John Wiley & Sons, Ltd.
Palladium‐Catalyzed One‐Pot Sonogashira Coupling, exo‐dig Cyclization and Hydride Transfer Reaction: Synthesis of Pyridine‐Substituted Pyrroles
Authors: Shekarrao Kommuri , Kaishap Partha Pratim , Gogoi Sanjib , Boruah Romesh C. 
Published: March 2015

AbstractAn efficient palladium(II)‐catalyzed method for the synthesis of alkylated pyridine‐substituted pyrroles has been developed by a one‐pot three component reaction of β‐bromovinyl aldehydes, primary amines and 2‐alkynylpyridines in good yields. The reactions can also provide an efficient route to 2‐picolinoylpyrroles by slightly altering the reaction conditions.magnified image
MUMAB: A Conversation With the Past
Authors: Wade Andrew D. , Beckett Ronald G. , Conlogue Gerald J. , Gonzalez Ramon , Wade Ronn , Brier Bob 
Published: March 2015

ABSTRACTIn May of 1994, Drs. Bob Brier and Ronn Wade produced the first modern mummy embalmed in the ancient Egyptian tradition. MUMAB (Mummy, University of Maryland At Baltimore) has been studied over the intervening 18 years as part of the Mummy Replication Project, including high‐resolution computed tomography scanning, magnetic resonance imaging, and histological examination. The radiological study of MUMAB is combined here with the firsthand discussion of the processes that resulted in the mummy's radiographic appearance. This allows for a close examination of the assumptions made in the radiological study of ancient Egyptian mummified human remains in a way not possible for the ancient remains themselves. Anat Rec, 298:954–973, 2015. © 2015 Wiley Periodicals, Inc.
Radioiodine remnant ablation in low‐risk differentiated thyroid cancer patients who had R0 dissection is an over treatment
Authors: Bal Chandrasekhar , Ballal Sanjana , Soundararajan Ramya , Chopra Saurav , Garg Aayushi 
Published: March 2015

AbstractLow‐risk (LR) differentiated thyroid cancer (DTC) patients should be ablated or not, albeit, with small dose of radioiodine is highly controversial. We hypothesized that those LR DTC patients who were surgically ablated need no radioiodine remnant ablation (RRA). This study aims to evaluate the long‐term outcome in these two groups of patients. Retrospective cohort study conducted from January 1991 to December 2012. Based on extent of surgical resection and histopathology, LR DTC patients were classified as Gr‐1: 169 patients, who were surgically ablated; Gr‐2: 153 patients, who had significant remnant in thyroid bed. Basal parameters were comparable between two groups except pretherapy 24 h radioiodine uptake (0.16 ± 0.01% vs. 5.64 ± 0.46%; P < 0.001). No patient received RRA in Gr‐1; Gr‐2 patients were administered 30 mCi 131I. Total number of events (recurrence, persistent, and progression of disease), with median follow up of 10.3 years, was observed in 10/322 (3.1%) of LR DTC patients. Only one patient had disease recurrence from Gr‐1, who became disease‐free after radioiodine therapy. Similarly, one patient from 126, who was ablated with single dose of RRA, had recurrence from Gr‐2. However, 8/27 (29.7%) patients from Gr‐2 had persistent disease; even two of them subsequently developed disease progression, who failed first‐dose of RRA. The event‐free survival rates were 99.4% and 94.1% (P = 0.006) in Gr‐1 and Gr‐2, respectively. RRA is an overtreatment in surgically ablated LR DTC patients. Successfully ablated RRA patients also had similar long‐term outcome, however, those who failed, should be re‐stratified as intermediate‐risk category, and managed aggressively.
RuII, OsII, and IrIII Complexes with Chelating Pyridyl–Mesoionic Carbene Ligands: Structural Characterization and Applications in Transfer Hydrogenation Catalysis
Authors: Bolje Aljoša , Hohloch Stephan , van der Meer Margarethe , Košmrlj Janez , Sarkar Biprajit 
Published: March 2015

AbstractChelating ligands with one pyridine donor and one mesoionic carbene donor are fast establishing themselves as privileged ligands in homogeneous catalysis. The synthesis of several new IrIII–Cp*‐ and OsII–Cym complexes (Cp*=pentamethylcyclopentadienyl, Cym=p‐cymene=4‐isopropyl‐toluene) derived from chelating pyridyltriazolylidenes where the additional pyridine donor was incorporated via the azide part of the triazole is presented. Furthermore, different 4‐substituted phenylacetylene building blocks have been used to introduce electronic fine‐tuning in the ligands. The ligands thus can be generally described as 4‐(4‐R‐phenyl)‐3‐methyl‐1‐(pyridin‐2‐yl)‐1H‐1,2,3‐triazol‐5‐ylidene (with R being H (L1), Me (L2), OMe (L3), CN (L4), CF3 (L5), Br (L6) or NO2 (L7)). The corresponding complexes (Ir‐1 to Ir‐7 and Os‐1 to Os‐7) were characterized by standard spectroscopic methods, and the expected three‐legged, piano‐stool type coordination was unambiguously confirmed by X‐ray diffraction analysis of selected compounds. Together with RuII analogues previously reported by us, a total of 21 complexes were tested as (pre)catalysts for the transfer hydrogenation of carbonyl groups, showing a remarkable reactivity even at very low catalyst loadings. The electronic effects of the ligands as well as different substrates were investigated. Some mechanistic elucidations are also presented.
Factors Influencing the Regioselectivity of the Oxidation of Asymmetric Secondary Amines with Singlet Oxygen
Authors: Ushakov Dmitry B. , Plutschack Matthew B. , Gilmore Kerry , Seeberger Peter H. 
Published: March 2015

AbstractAerobic amine oxidation is an attractive and elegant process for the α functionalization of amines. However, there are still several mechanistic uncertainties, particularly the factors governing the regioselectivity of the oxidation of asymmetric secondary amines and the oxidation rates of mixed primary amines. Herein, it is reported that singlet‐oxygen‐mediated oxidation of 1° and 2° amines is sensitive to the strength of the α‐CH bond and steric factors. Estimation of the relative bond dissociation energy by natural bond order analysis or by means of one‐bond CH coupling constants allowed the regioselectivity of secondary amine oxidations to be explained and predicted. In addition, the findings were utilized to synthesize highly regioselective substrates and perform selective amine cross‐couplings to produce imines.
Efficient Synthesis of Triarylamines Catalyzed by Copper(I) Diazabutadiene Complexes
Authors: Liu Yuhua , Yang Lianming 
Published: March 2015

AbstractCuprous chloride was coordinated by diazabutadiene (DAB‐R) ligands to form Cu(I)‐(DAB‐R) complexes, most of which have a 1:1 ratio of Cu to DAB‐R as reported. In the case of a special DAB‐iPP, N,N′‐bis(2,6‐diisopropylphenyl)‐1,4‐diaza‐1,3‐butadiene, an unexpected composition of complex was found with the formula Cu(I)Cl(DAB)2. When employed as catalyst for triarylamine synthesis from the coupling of aryl halides with primary and secondary arylamines, the new Cu(I)‐(DAB‐iPP) complex displayed high efficiency.
Supramolecular Prodrug Micelles Constructed by Drug‐Drug Conjugate with Water Soluble Pillar[6]arene for Controllable and Rapid Drug Release
Authors: Cao Yu , Zou Xiaochun , Xiong Shuhan , Li Yan , Shen Yingzhong , Hu Xiaoyu , Wang Leyong 
Published: March 2015

AbstractThe first attempt of constructing supramolecular prodrug micelles based on the host‐guest interaction between water‐soluble pillar[6]arene (WP6) and a novel doxorubicin (DOX)‐based drug‐drug conjugate (G) is reported, in which the drug‐drug conjugate is synthesized by conjugating anticancer drug DOX with another drug isoniazide via the acid‐cleavable hydrazone bond. The obtained WP6⊃G micelles are stable under physiological conditions, whereas the cumulative release of DOX is approximate to 100% within 30 min at pH 5.5 by simulating the endo‐lysosomal environment at 37°C. Therefore, this WP6‐based prodrug micelles can achieve efficient DOX accumulation in the acidic tumor cells within a short period of time, which is very important and valuable; meanwhile it can also reduce the unexpected premature burst release under physiological condition. Furthermore, cellular internalization and localization experiments demonstrated that these prodrug micelles enter cancer cells mainly via endocytosis and can lead to significant drug accumulation in SKOV3 cancer cells, implying its promising future for cancer therapy.
Low‐Valent Titanium‐Mediated Enantioselective Synthesis of Quinazolinone Alkaloids Circumdatins F, H, and Analogs
Authors: Luo Shi‐Peng , Geng Hui , Wang Yu , Huang Pei‐Qiang 
Published: March 2015

AbstractWe report the concise and protecting‐group‐free enantioselective total syntheses of circumdatins F and H. In view of the extreme importance of analogs of quinazolinone alkaloids in drug research and discovery, four analogs of bioactive quinazolinobenzodiazepine alkaloids, including demethoxycircumdatin H (12) and N‐demethylbenzomalvin A (13), have been synthesized. The method is based on the low‐valent titanium‐promoted intramolecular reductive coupling of imides with o‐nitrobenzimides, which yielded quinazolino[3,2‐a][1,4]benzodiazepines under mild conditions. In addition, heptacyclic dehydraasperlicin E (16) has been synthesized from asperlicin C by a NCS‐mediated dehydra‐cyclization reaction.
Complexation of Linear Aliphatic Ester, Aldehyde and Ketone Guests by Per‐ethylated Pillar[5]arene
Authors: Lou Xiaobing , Chen Huanqing , Jia Xueshun , Li Chunju 
Published: March 2015

AbstractThe complexation of four neutral guest molecules containing carbon‐oxygen double bonds, i.e., 1,6‐diacetoxyhexane (1), dimethyl hexanedioate (2), hexanal (3), and 2‐hexanone (4), by per‐ethylated pillar[5]arene is reported. These guests show remarkably different binding affinities. For example, ester 1 could be fully engulfed by the host cavity to form a [2]pseudorotaxane‐type inclusion complex, while for 2, no obvious host‐guest interaction was observed.
A Pillar[6]arene‐[2]pseudorotaxane Based pH‐Sensitive Molecular Switch
Authors: Chen Huanqing , Jia Xueshun , Li Chunju 
Published: March 2015

AbstractA novel pH‐responsive [2]pseudorotaxane based on ethylated pillar[6]arene and bis(1,2,3‐triazolium)butane cation was constructed. The dethreading and rethreading could be reversibly controlled by adding base and acid, i.e., the deprotonation and reprotonation of the guest. In contrast, such responsible switching behavior does not occur for the complexation between the guest and ethylated pillar[5]arene, since both the cationic axle and the deprotonated one can be strongly bound by ethylated pillar[5]arene. Furthermore, the bis(1,2,3‐triazolium)butane⊂pillar[6]arene‐[2]pseudorotaxane can also disassemble upon the addition of competitive ethylated pillar[5]arene.
Computational prediction of manually gated rare cells in flow cytometry data
Authors: Qiu Peng 
Published: March 2015

AbstractRare cell identification is an interesting and challenging question in flow cytometry data analysis. In the literature, manual gating is a popular approach to distill flow cytometry data and drill down to the rare cells of interest, based on prior knowledge of measured protein markers and visual inspection of the data. Several computational algorithms have been proposed for rare cell identification. To compare existing algorithms and promote new developments, FlowCAP‐III put forward one computational challenge that focused on this question. The challenge provided flow cytometry data for 202 training samples and two manually gated rare cell types for each training sample, roughly 0.02 and 0.04% of the cells, respectively. In addition, flow cytometry data for 203 testing samples were provided, and participants were invited to computationally identify the rare cells in the testing samples. Accuracy of the identification results was evaluated by comparing to manual gating of the testing samples. We participated in the challenge, and developed a method that combined the Hellinger divergence, a downsampling trick and the ensemble SVM. Our method achieved the highest accuracy in the challenge. © 2015 International Society for Advancement of Cytometry