bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lattice dynamics and structure of GeTe, SnTe and PbTe
Authors: Bauer Pereira Paula , Sergueev Ilya , Gorsse Stéphane , Dadda Jayaram , Müller Eckhard , Hermann Raphaël P. 
Published: December 2012

AbstractThe lattice dynamics in the IV–VI compounds GeTe, SnTe and PbTe were studied by 125Te and 119Sn nuclear inelastic scattering and the obtained partial density of phonon states were compared with published theoretical calculations. The phase purity and structure were characterized by high energy X‐ray diffraction. The effect of the atomic arrangement, rhombohedral for GeTe and cubic for SnTe and PbTe, is visible in the density of phonon states. Vibrational properties are found to be in good agreement with available calculated data and the softer character of the NaCl‐type structures in comparison with the rhombohedral GeTe is confirmed.
Lipid profiling for early diagnosis and progression of colorectal cancer using direct‐infusion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry
Authors: Li Fang , Qin Xuzhen , Chen Haiquan , Qiu Ling , Guo Yumei , Liu Hui , Chen Guoqiang , Song Gaoguang , Wang Xiaodong , Li Fenjie , Guo Shuai , Wang Baohua , Li Zhili 
Published: December 2012

RATIONALEColorectal cancer (CRC) has attracted increasing attention due to its common occurrence and worldwide distribution.METHODSDirect‐infusion positive and negative ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (DI‐ESI(±)‐FTICR MS) was applied to analyze the serum metabolites from 52 CRC patients and 52 healthy controls. Metabolites whose inter‐group intensities were determined to be statistically significant by univariate and multivariate statistical analyses were further identified by a combination of the Human Metabolome Database, accurate mass measurement, isotopic abundance distribution simulation, and tandem mass spectrometry. Orthogonal partial least square discriminant analysis (OPLS‐DA), based on the data from DI‐ESI(±)‐FTICR MS, revealed a remarkable discrimination among early stage patients, late stage patients, and healthy controls.RESULTSA total of 15 differentially expressed metabolites were identified and categorized into four lipid classes. Each lipid class demonstrated specific changing trends in CRC progression. Biomarker panel 1 containing palmitic amide, oleamide, hexadecanedioic acid, octadecanoic acid, eicosatrienoic acid, LPC(18:2), LPC(20:4), LPC(22:6), myristic acid and LPC(16:0) achieved excellent diagnostic accuracy with area under the ROC curve (AUC) of 0.991, a sensitivity of 0.981 and a specificity of 1.000 for differentiating early stage patients from healthy controls, which was better than the carcinoembryonic antigen biomarker.CONCLUSIONSOur study revealed that the consideration of CRC stages would be necessary in diagnostic biomarker discovery, as well as that attention should be paid to the facile loss of methyl chloride from the [M + Cl]– form of LPC(16:0) in its tandem mass spectrum. Copyright © 2012 John Wiley & Sons, Ltd.
The determination of flavonoids in Wikstroemia indica C. A. Mey. by liquid chromatography with photo‐diode array detection and negative electrospray ionization tandem mass spectrometry
Authors: Ko Yen‐Chen , Feng Hai‐Tung , Lee Ren‐Jye , Lee Maw‐Rong 
Published: December 2012

RATIONALEFlavonoids in the medicinal plant Wikstroemia indica C. A. Mey. are present in trace amounts and found in complex matrices. An efficient and sensitive method is necessary for the rapid identification of such biomolecules.METHODSFlavonoids were extracted with methanol via ultrasonic‐assisted extraction and analyzed by liquid chromatography with photo‐diode array detection and tandem mass spectrometry. The extract was analyzed and compounds were identified using negative electrospray ionization data‐dependent tandem mass spectrometry.RESULTSThe results confirmed the presence of three flavonoid compounds, seven biflavonoid compounds, and one coumarin‐like compound, daphnoretin, in the extracts of different plant parts of W. indica. The method detection limit was evaluated down to 5 µg/g using kaempfol as a reference standard.CONCLUSIONSThe proposed method offers a rapid and reliable analysis for the determination of flavonoids in medicinal plants. Copyright © 2012 John Wiley & Sons, Ltd.
Electron transfer followed by collision‐induced dissociation (NET‐CID) for generating sequence information from backbone‐modified oligonucleotide anions
Authors: Gao Yang , McLuckey Scott A. 
Published: December 2012

RATIONALEOligonucleotides with 2'‐modifications and/or phosphorothioate (PS) backbones are prone to undergo limited backbone fragmentation upon ion trap collision‐induced dissociation (CID). For better identification and characterization of chemically modified oligonucleotides, a more universal fragmentation method is desirable.METHODSGas‐phase dissociation of various 2'‐position‐modified oligonucleotides and mixed‐backbone oligonucleotides (MBOs) has been studied by ion trap CID of the radical anion species formed via electron transfer ion/ion reactions.RESULTSFor 2'‐modified mix‐mer radical anions, complete sequence information was generated with non‐complementary d/w‐ion series, while a/z‐ions were observed randomly with relatively low intensity. The 2'‐position modification, which has been observed to affect CID patterns of oligonucleotide anions, did not exhibit any observable influence on the dissociation patterns of oligonucleotide radical anions. For MBOs comprised of DNA nucleotides, ion trap CID of even‐electron species generated complementary a‐B/w‐type ions and multiple fragment types at the phosphorothioate (PS) linkages. For MBOs comprised of 2'‐OMe‐modified nucleotides, only PS bond cleavage was observed for ion trap CID of doubly deprotonated precursor ions. Negative electron transfer reaction with or without supplemental activation of MBOs gave rise to a/d/w‐type fragments similar to those of the 2'‐modified mix‐mers. PS bonds were observed to be more fragile under the electron detachment process, and phosphodiester (PO) bond cleavages were noted upon further collisional activation.CONCLUSIONSNET‐CID proved to be an efficient method of generating full sequence information for 2'‐modifications and/or mixed‐backbone oligonucleotides. Copyright © 2012 John Wiley & Sons, Ltd.
5‐Amino‐1‐naphthol, a novel 1,5‐naphthalene derivative matrix suitable for matrix‐assisted laser desorption/ionization in‐source decay of phosphorylated peptides
Authors: Osaka Issey , Sakai Mami , Takayama Mitsuo 
Published: December 2012

RATIONALEAlthough matrix‐assisted laser desorption/ionization in‐source decay (MALDI‐ISD) is an important method for post‐translational modification (PTM) analysis, the conventional matrices, 2,5‐dihydroxybenzoic acid (2,5‐DHB) and 1,5‐diaminonaphthalene (1,5‐DAN), are poor in terms of the fragment ion yields of the phosphorylated peptides. The use of 5‐amino‐1‐naphthol (5,1‐ANL) as a novel matrix for ISD of phosphorylated peptides in MALDI time‐of‐flight mass spectrometry (TOFMS) is described here.METHODSWe have evaluated the ion yields of ISD fragments obtained from phosphorylated peptides using three 1,5‐naphthalene derivatives as MALDI‐ISD matrices, i.e., 5,1‐ANL, 1,5‐DAN and 1,5‐dihydroxynaphthalene (1,5‐DHN). The signal‐to‐noise ratio (S/N) of c'‐series ions obtained from these matrices was used to estimate their suitability for MALDI‐ISD of non‐modified and phosphorylated peptides.RESULTSThe order of the S/N values of the ISD fragments for non‐modified and phosphorylated peptides were 1,5‐DAN > 5,1‐ANL > 1,5‐DHN and 5,1‐ANL > 1,5‐DHN > 1,5‐DAN, respectively.CONCLUSIONSThe newly introduced matrix 5,1‐ANL gave highest ion yields of ISD fragments from mono‐, di‐, and tetraphosphorylated peptides, while 1,5‐DAN was poor in the ISD ion yields for phosphorylated peptides. Copyright © 2012 John Wiley & Sons, Ltd.
Novel laser spectroscopic technique for continuous analysis of N2O isotopomers – application and intercomparison with isotope ratio mass spectrometry
Authors: Köster Jan Reent , Well Reinhard , Tuzson Béla , Bol Roland , Dittert Klaus , Giesemann Anette , Emmenegger Lukas , Manninen Albert , Cárdenas Laura , Mohn Joachim 
Published: December 2012

RATIONALENitrous oxide (N2O), a highly climate‐relevant trace gas, is mainly derived from microbial denitrification and nitrification processes in soils. Apportioning N2O to these source processes is a challenging task, but better understanding of the processes is required to improve mitigation strategies. The N2O site‐specific 15 N signatures from denitrification and nitrification have been shown to be clearly different, making this signature a potential tool for N2O source identification. We have applied for the first time quantum cascade laser absorption spectroscopy (QCLAS) for the continuous analysis of the intramolecular 15 N distribution of soil‐derived N2O and compared this with state‐of‐the‐art isotope ratio mass spectrometry (IRMS).METHODSSoil was amended with nitrate and sucrose and incubated in a laboratory setup. The N2O release was quantified by FTIR spectroscopy, while the N2O intramolecular 15 N distribution was continuously analyzed by online QCLAS at 1 Hz resolution. The QCLAS results on time‐integrating flask samples were compared with those from the IRMS analysis.RESULTSThe analytical precision (2σ) of QCLAS was around 0.3 ‰ for the δ15Nbulk and the 15 N site preference (SP) for 1‐min average values. Comparing the two techniques on flask samples, excellent agreement (R2 = 0.99; offset of 1.2 ‰) was observed for the δ15Nbulk values while for the SP values the correlation was less good (R2 = 0.76; offset of 0.9 ‰), presumably due to the lower precision of the IRMS SP measurements.CONCLUSIONSThese findings validate QCLAS as a viable alternative technique with even higher precision than state‐of‐the‐art IRMS. Thus, laser spectroscopy has the potential to contribute significantly to a better understanding of N turnover in soils, which is crucial for advancing strategies to mitigate emissions of this efficient greenhouse gas. Copyright © 2012 John Wiley & Sons, Ltd.
Comparison of the LTQ‐Orbitrap Velos and the Q‐Exactive for proteomic analysis of 1–1000 ng RAW 264.7 cell lysate digests
Authors: Sun Liangliang , Zhu Guijie , Dovichi Norman J. 
Published: December 2012

RATIONALEThere is interest in extending bottom‐up proteomics to the smallest possible sample size. We investigated the performance of two modern mass spectrometers for the analysis of samples ranging from 1 ng to 1 µg of RAW 264.7 cell lysate digests.METHODSAn ultra‐performance liquid chromatography (UPLC) system coupled with either an LTQ‐Orbitrap Velos or a Q‐Exactive mass spectrometer was used for peptide separation and identification.RESULTSFor 1–1000 ng RAW 264.7 cell lysate digests, the Q‐Exactive generated 10–83% more protein groups and 11–109% more peptides than the LTQ‐Orbitrap Velos (higher‐energy collisional dissociation, HCD) with MASCOT database searching, due to its faster scan rate and higher resolution. In addition, HCD and collision‐induced dissociation (CID) modes of the LTQ‐Orbitrap Velos were compared. HCD produced higher peptide and protein group IDs than CID for 1–1000 ng RAW 264.7 cell lysate digests with MASCOT database searching. Database searching results from SEQUEST and MASCOT were also compared and comparable protein group IDs were obtained from the two search engines.CONCLUSIONSThe Q‐Exactive outperformed the LTQ‐Orbitrap Velos for shotgun proteomics analysis of 1 to 1000 ng RAW 264.7 cell lysate digests in terms of obtained peptide and protein group IDs. Copyright © 2012 John Wiley & Sons, Ltd.
Analysis and quantification of vitamin D metabolites in serum by ultra‐performance liquid chromatography coupled to tandem mass spectrometry and high‐resolution mass spectrometry – a method comparison and validation
Authors: Bruce Stephen J. , Rochat Bertrand , Béguin Alexandre , Pesse Benoît , Guessous Idris , Boulat Olivier , Henry Hugues 
Published: December 2012

RATIONALEThe aim of the work was to develop and validate a method for the quantification of vitamin D metabolites in serum using ultra‐high‐pressure liquid chromatography coupled to mass spectrometry (LC/MS), and to validate a high‐resolution mass spectrometry (LC/HRMS) approach against a tandem mass spectrometry (LC/MS/MS) approach using a large clinical sample set.METHODSA fast, accurate and reliable method for the quantification of the vitamin D metabolites, 25‐hydroxyvitamin D2 (25OH‐D2) and 25‐hydroxyvitamin D3 (25OH‐D3), in human serum was developed and validated. The C3 epimer of 25OH‐D3 (3‐epi‐25OH‐D3) was also separated from 25OH‐D3. The samples were rapidly prepared via a protein precipitation step followed by solid‐phase extraction (SPE) using an HLB μelution plate. Quantification was performed using both LC/MS/MS and LC/HRMS systems.RESULTSRecovery, matrix effect, inter‐ and intra‐day reproducibility were assessed. Lower limits of quantification (LLOQs) were determined for both 25OH‐D2 and 25OH‐D3 for the LC/MS/MS approach (6.2 and 3.4 µg/L, respectively) and the LC/HRMS approach (2.1 and 1.7 µg/L, respectively). A Passing & Bablok fit was determined between both approaches for 25OH‐D3 on 662 clinical samples (1.11 + 1.06x). It was also shown that results can be affected by the inclusion of the isomer 3‐epi‐25OH‐D3.CONCLUSIONSQuantification of the relevant vitamin D metabolites was successfully developed and validated here. It was shown that LC/HRMS is an accurate, powerful and easy to use approach for quantification within clinical laboratories. Finally, the results here suggest that it is important to separate 3‐epi‐25OH‐D3 from 25OH‐D3. Copyright © 2012 John Wiley & Sons, Ltd.
Using dissociation energies to predict observability of b‐ and y‐peaks in mass spectra of short peptides. II. Results for hexapeptides with non‐polar side chains
Authors: Obolensky O. I. , Wu Wells W. , Shen Rong‐Fong , Yu Yi‐Kuo 
Published: December 2012

RATIONALEThe hypothesis that dissociation energies can serve as a predictor of observability of b‐ and y‐peaks is tested for seven hexapeptides. If the hypothesis holds true for large classes of peptides, one would be able to improve the scoring accuracy of peptide identification tools by excluding theoretical peaks that cannot be observed in practical product ion spectra due to various physical, chemical or thermodynamic considerations.METHODSProduct ion m/z spectra of hexapeptides AAAAAA, AAAFAA, AAAVAA, AAFAAA, AAVAAA, AAFFAA and AAVVAA have been acquired on a Finnigan LTQ XL mass spectrometer in the collision‐induced dissociation (CID) activation mode on a grid of activation times 0.05 to 100 ms and normalized collision energy 10 to 35%. Dissociation energies were calculated for all fragmentation channels leading to b‐ and y‐fragments at the TPSS/6‐31G(d,p) level of the density functional theory.RESULTSIt was demonstrated that the m/z peaks observed in the product ion spectra correspond to the fragmentation channels with dissociation energies below a certain threshold value. However, there is no direct correlation between the most intense m/z peaks and the lowest dissociation energies. Using the dissociation energies, it was predicted that out of 63 theoretically possible peaks in the b‐ and y‐series of the seven hexapeptides, 19 should not be observable in practical spectra. In the experiments, 24 peaks were not observed, including all 19 predicted.CONCLUSIONSDissociation energies alone are not sufficient for predicting ion intensity relationships in product ion m/z spectra. Nevertheless, the present data suggest that dissociation energies appear to be good predictors of observability of b‐ and y‐peaks and potentially very useful for filtering theoretical peaks of each candidate peptide in peptide identification tools. Published 2012. This article is a US Government work and is in the public domain in the USA.
Abundant naphthenic acids in oil sands process‐affected water: studies by synthesis, derivatisation and two‐dimensional gas chromatography/high‐resolution mass spectrometry
Authors: West Charles E. , Scarlett Alan G. , Pureveen Jos , Tegelaar Erik W. , Rowland Steven J. 
Published: December 2012

RATIONALEThe large volumes of 'supercomplex' mixtures of reputedly toxic organic compounds in acidic extracts of oil sands process‐affected waters (OSPW) represent a challenging goal for complete characterisation. To date, comprehensive two‐dimensional gas chromatography/time‐of‐flight mass spectrometry (GCxGC/TOFMS) has allowed the acquisition and interpretation of numerous electron ionisation mass spectra including many of those confirmed to be tricyclic and pentacyclic carboxylic acids by reference to the spectra and retention positions of authentic or synthetic compounds. This has allowed the toxicities of some of the identified acids to be determined and their environmental significance to be better assessed.METHODSSynthesis, derivatisation (methyl, trideuteriomethyl and trimethylsilyl esters) and GCxGC/TOFMS with nominal mass and higher mass accuracy (ca. 5 ppm) were used to study three abundant unknown acids present in OSPW samples from two different industrial suppliers.RESULTSGCxGC/TOFMS with nominal mass accuracy, of methyl, trideuteriomethyl and trimethylsilyl esters of three abundant acids in two OSPW samples, produced mass spectra consistent with their assignment as either C16 tetracyclic acids or as isobaric pentacyclic C15 hydroxy acids ('O3') or sulfur‐containing ('SO2') species. The synthesis of several isomeric pentacyclic C15 hydroxy acids and examination of the GCxGC retention times and mass spectra (nominal mass) of their derivatives suggested that the unknown OSPW acids were not hydroxy acids, and GCxGC/TOFMS with higher mass accuracy ruled out the possibility. The possibility that they were isobaric 'SO2' species could also be dismissed as this was inconsistent with accurate masses, the derivatisation reactions observed, the fragmentation patterns and the isotope distributions, which excluded the presence of sulphur.CONCLUSIONSThe data support the contention that the three abundant unknowns were indeed C16 tetracyclic acids. An equally rigorous approach will be necessary to characterise further acids in such mixtures. This is important so that chemistry can be used to guide the search for toxic modes of action. Copyright © 2012 John Wiley & Sons, Ltd.
Red‐Emitting Upconverting Nanoparticles for Photodynamic Therapy in Cancer Cells Under Near‐Infrared Excitation
Authors: Tian Gan , Ren Wenlu , Yan Liang , Jian Shan , Gu Zhanjun , Zhou Liangjun , Jin Shan , Yin Wenyan , Li Shoujian , Zhao Yuliang 
Published: December 2012

AbstractUpconverting nanoparticles (UCNPs) have attracted considerable attention as potential photosensitizer carriers for photodynamic therapy (PDT) in deep tissues. In this work, a new and efficient NIR photosensitizing nanoplatform for PDT based on red‐emitting UCNPs is designed. The red emission band matches well with the efficient absorption bands of the widely used commercially available photosensitizers (Ps), benefiting the fluorescence resonance energy transfer (FRET) from UCNPs to the attached photosensitizers and thus efficiently activating them to generate cytotoxic singlet oxygen. Three commonly used photosensitizers, including chlorine e6 (Ce6), zinc phthalocyanine (ZnPc) and methylene blue (MB), are loaded onto the alpha‐cyclodextrin‐modified UCNPs to form Ps@UCNPs complexes that efficiently produce singlet oxygen to kill cancer cells under 980 nm near‐infrared excitation. Moreover, two different kinds of drugs are co‐loaded onto these nanoparticles: chemotherapy drug doxorubicin and PDT agent Ce6. The combinational therapy based on doxorubicin (DOX)‐induced chemotherapy and Ce6‐triggered PDT exhibits higher therapeutic efficacy relative to the individual means for cancer therapy in vitro.
Poly(A) binding proteins: are they all created equal?
Authors: Goss Dixie J. , Kleiman Frida Esther 
Published: December 2012

AbstractThe PABP family of proteins were originally thought of as a simple shield for the mRNA poly(A) tail. Years of research have shown that PABPs interact not only with the poly(A) tail, but also with specific sequences in the mRNA, having a general and specific role on the metabolism of different mRNAs. The complexity of PABPs function is increased by the interactions of PABPs with factors involved in different cellular functions. PABPs participate in all the metabolic pathways of the mRNA: polyadenylation/deadenylation, mRNA export, mRNA surveillance, translation, mRNA degradation, microRNA‐associated regulation, and regulation of expression during development. In this review, we update information on the roles of PABPs and emerging data on the specific interactions of PABP homologs. Specific functions of individual members of PABPC family in development and viral infection are beginning to be elucidated. However, the interactions are complex and recent evidence for exchange of nuclear and cytoplasmic forms of the proteins, as well as post‐translational modifications, emphasize the possibilities for fine‐tuning the PABP metabolic network. WIREs RNA 2013, 4:167–179. doi: 10.1002/wrna.1151This article is categorized under:

RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications
Translation > Translation Regulation
RNA Processing > 3' End Processing
In situ Synthesis, Crystal Structures, and Characterization of Three Milrinone Tetrazolyl Complexes
Authors: Tang Yun‐Zhi , Huang Jun , Zhou Man , Wu Ji‐Si , Tan Yu‐Hui , Wen He‐Rui 
Published: December 2012

AbstractAbstract. In situ [2+3] cycloaddition reactions of milrinone [= 3‐cyano‐6‐methyl‐5‐(4‐pyridyl)‐2‐pyridone] with sodium azide in the presence of MnCl2·4H2O, FeSO4·7H2O, or CoCl2·6H2O as Lewis acids, gave three new complexes {[Mn(Mitz)2(H2O)2]·(H2O)} (1), {[Fe(Mitz)2(H2O)2]·(H2O)} (2), and {[Co(Mitz)2(H2O)2]·(H2O)} (3) [Mitz = 3‐tetrazole‐6‐methyl‐5‐(4‐pyridyl)‐2‐pyridone]. All the complexes were characterized by elemental analysis, IR spectroscopy, single‐crystal X‐ray diffraction analysis, X‐ray powder diffraction, and thermogravimetric analysis. X‐ray diffraction analyses show that complexes 1–3 have isomorphous structures. The central metal atoms in these complexes are hexacoordinated and connected by two water molecules, two nitrogen atoms from different tetrazolyl groups, and two oxygen atoms from carbonyl functions respectively. The fluorescent emission spectrum of 1 in the solid‐state at room temperature shows a maximal emission peak at 365 nm.
Paleoenvironmental reconstruction of the early Neolithic to middle Bronze Age Peña Larga rock shelter (Álava, Spain) from the small mammal record
Authors: Rofes Juan , Zuluaga Mari Cruz , Murelaga Xabier , Fernández-Eraso Javier , Bailon Salvador , Iriarte María José , Ortega Luis Ángel , Alonso-Olazabal Ainhoa 
Published: December 2012

AbstractThe Peña Larga site, a rock shelter on the southern slopes of the Cantabrian cordillera (north Spain), is an archeological deposit covering nearly 4000 years, from the early Neolithic to the middle Bronze Age (Atlantic/Subboreal chronozones). It was used both as a household and as a stable, with a hiatus in the Chalcolithic when it was used as a collective sepulcher. Nearly twenty-eight thousand small vertebrate elements were recovered from its seven stratigraphic units, of which 2553 items were identified to the genus and/or species levels. The assemblage is composed of mammals, birds, reptiles, and amphibians. Of these, small mammals were used for paleoenvironmental reconstruction since they are very sensitive to climatic conditions, the sample sizes are large, and their preservation is good. Their distributions over time, measured in terms of relative abundance, serve as reliable proxies of habitat and climate change. The reconstruction of Peña Larga's past environments based on small mammals roughly coincides with the pollen and the amphibian/reptile records on the local scale, and with that of an ice core from Central Greenland on the global scale. This makes it a valuable tool for comparative purposes both in the regional and continental scales.