bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of 4‐hydroxynonenal protein targets in rat, mouse and human liver microsomes by two‐dimensional liquid chromatography/tandem mass spectrometry
Authors: Golizeh Makan , Geib Timon , Sleno Lekha 
Published: June 2016

Rationale4‐Hydroxynonenal (HNE), endogenously generated through peroxidation and breakdown of polyunsaturated fatty acids, has been linked to a number of adverse biological effects through carbonylation of essential biomolecules. Covalent binding of HNE to proteins can alter their structure and functions, causing cell damage as well as adverse immune responses. The liver plays a predominant role in metabolic transformations and hepatic proteins are often targeted by reactive metabolites.MethodsRat, mouse and human liver microsomes were incubated with HNE, enzymatically digested, and subjected to strong cation‐exchange peptide fractionation prior to liquid chromatography/tandem mass spectrometry (LC/MS/MS) analysis coupled to electrospray ionization quadrupole time‐of‐flight (QqTOF) mass spectrometry. HNE‐modified peptides were detected by probability‐driven peptide spectral matching and comparative analysis between treated and control samples, and confirmed based on accurate mass and high‐resolution MS/MS spectra.ResultsA total of 99, 123 and 51 HNE‐modified peptides were identified in rat, mouse and human liver microsomes related to 76, 103 and 44 target proteins, respectively. Eight proteins were found to be adducted by HNE in all three species, including ATP synthase, carbamoyl phosphate synthase, cytochrome P450 1A2, glutamate dehydrogenase 1, protein ERGIC‐53, protein disulfide‐isomerase, and voltage‐dependent anion‐selective channel protein 1. These proteins play crucial roles in cellular processes and their covalent modification could potentially alter their function and lead to cytotoxicity.ConclusionsAn analytical approach was developed for the identification of in vitro HNE protein targets in rat, mouse and human liver microsomes using two‐dimensional (2D) LC/MS/MS. This approach can be applied to study HNE modification of proteins in vitro and in vivo, providing insight into the toxicology of HNE protein adduction. Copyright © 2016 John Wiley & Sons, Ltd.
Stable 18O‐labeling method for stercobilin and other bilins for metabolomics
Authors: Rudolph Heather L. , Sekera Emily R. , Wood Troy D. 
Published: June 2016

RationaleBilin tetrapyrroles including stercobilin are unique to mammalian waste; they have been used as markers of source water contamination and may have important diagnostic value in human health conditions. Unfortunately, commercial isotopomers for bilins are not available. Thus, there is a need for isotopomer standards of stercobilin and other bilins for quantification in environmental and clinical diagnostic applications.MethodsA procedure is described here using H218O to label the carboxylic acid groups of bilin tetrapyrroles. Reaction conditions as a function of temperature and reagent volume were found to produce a mixture of isotopomers, as assessed by electrospray ionization and Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). Stability as a function of storage time and temperature and in conjunction with solid‐phase extraction (SPE) was assessed.ResultsThe highest labeling efficiency was achieved at 70 °C for 8 h, while a stable ratio of the isotopmers could be produced at 60 °C for 4 h. The stability of the isotopic distribution was maintained under storage (room temperature or frozen) for 20 days. It was also stable throughout SPE. The high mass accuracy and resolving power of FTICRMS enables clear distinction between 18O‐labeled bilins from other unlabeled bilins present, avoiding a potential interference in quantitation.ConclusionsA procedure was developed to label bilins with 18O. The final ratio of the 18O‐labeled bilin isotopomers was reproducible and highly stable for at least 20 days under storage. This ratio was not changed in any statistically significant way even after SPE. Thus a reliable method for producing stable isotopomer ratios for bilins has been achieved. Copyright © 2016 John Wiley & Sons, Ltd.
Intraspecific carbon and nitrogen isotopic variability in foxtail millet (Setaria italica)
Authors: Lightfoot Emma , Przelomska Natalia , Craven Martha , O′Connell Tamsin C. , He Lu , Hunt Harriet V. , Jones Martin K. 
Published: June 2016

RationaleIsotopic palaeodietary studies generally focus on bone collagen from human and/or animal remains. While plant remains are rarely analysed, it is known that plant isotope values can vary as a result of numerous factors, including soil conditions, the environment and type of plant. The millets were important food crops in prehistoric Eurasia, yet little is known about the isotopic differences within millet species.MethodsHere we compare the stable isotope ratios within and between Setaria italica plants grown in a controlled environment chamber. Using homogenised samples, we compare carbon isotope ratios of leaves and grains, and nitrogen isotope ratios of grains, from 29 accessions of Setaria italica.ResultsWe find significant isotopic variability within single leaves and panicles, and between leaves and panicles within the same plant, which must be considered when undertaking plant isotope studies. We find that the leaves and grains from the different accessions have a ca 2‰ range in δ13C values, while the nitrogen isotope values in the grains have a ca 6‰ range. We also find an average offset of 0.9‰ between leaves and grains in their δ13C values.ConclusionsThe variation found is large enough to have archaeological implications and within‐ and between‐plant isotope variability should be considered in isotope studies. The range in δ15N values is particularly significant as it is larger than the typical values quoted for a trophic level enrichment, and as such may lead to erroneous interpretations of the amount of animal protein in human or animal diets. It is therefore necessary to account for the variability in plant stable isotope values during palaeodietary reconstructions. Copyright © 2016 John Wiley & Sons, Ltd.
Contamination risk of stable isotope samples during milling
Authors: Isaac‐Renton M. , Schneider L. , Treydte K. 
Published: June 2016

RationaleIsotope analysis of wood is an important tool in dendrochronology and ecophysiology. Prior to mass spectrometry analysis, wood must be homogenized, and a convenient method involves a ball mill capable of milling samples directly in sample tubes. However, sample‐tube plastic can contaminate wood during milling, which could lead to biological misinterpretations.MethodsWe tested possible contamination of whole wood and cellulose samples during ball‐mill homogenization for carbon and oxygen isotope measurements. We used a multi‐factorial design with two/three steel milling balls, two sample amounts (10 mg, 40 mg), and two milling times (5 min, 10 min). We further analyzed abrasion by milling empty tubes, and measured the isotope ratios of pure contaminants.ResultsA strong risk exists for carbon isotope bias through plastic contamination: the δ13C value of polypropylene deviated from the control by −6.77‰. Small fibers from PTFE filter bags used during cellulose extraction also present a risk as the δ13C value of this plastic deviated by −5.02‰. Low sample amounts (10 mg) showed highest contamination due to increased abrasion during milling (−1.34‰), which is further concentrated by cellulose extraction (−3.38‰). Oxygen isotope measurements were unaffected.ConclusionsA ball mill can be used to homogenize samples within test tubes prior to oxygen isotope analysis, but not prior to carbon or radiocarbon isotope analysis. There is still a need for a fast, simple and contamination‐free sample preparation procedure. Copyright © 2016 John Wiley & Sons, Ltd.
Automated simultaneous measurement of the δ13C and δ2H values of methane and the δ13C and δ18O values of carbon dioxide in flask air samples using a new multi cryo‐trap/gas chromatography/isotope ratio mass spectrometry system
Authors: Brand Willi A. , Rothe Michael , Sperlich Peter , Strube Martin , Wendeberg Magnus 
Published: June 2016

RationaleThe isotopic composition of greenhouse gases helps to constrain global budgets and to study sink and source processes. We present a new system for high‐precision stable isotope measurements of carbon, hydrogen and oxygen in atmospheric methane and carbon dioxide. The design is intended for analyzing flask air samples from existing sampling programs without the need for extra sample air for methane analysis.MethodsCO2 and CH4 isotopes are measured simultaneously using two isotope ratio mass spectrometers, one for the analysis of δ13C and δ18O values and the second one for δ2H values. The inlet carousel delivers air from 16 sample positions (glass flasks 1‐5 L and high‐pressure cylinders). Three 10‐port valves take aliquots from the sample stream. CH4 from 100‐mL air aliquots is preconcentrated in 0.8‐mL sample loops using a new cryo‐trap system. A precisely calibrated working reference air is used in parallel with the sample according to the Principle of Identical Treatment.ResultsIt takes about 36 hours for a fully calibrated analysis of a complete carousel including extractions of four working reference and one quality control reference air. Long‐term precision values, as obtained from the quality control reference gas since 2012, account for 0.04 ‰ (δ13C values of CO2), 0.07 ‰ (δ18O values of CO2), 0.11 ‰ (δ13C values of CH4) and 1.0 ‰ (δ2H values of CH4). Within a single day, the system exhibits a typical methane δ13C standard deviation (1σ) of 0.06 ‰ for 10 repeated measurements.ConclusionsThe system has been in routine operation at the MPI‐BGC since 2012. Consistency of the data and compatibility with results from other laboratories at a high precision level are of utmost importance. A high sample throughput and reliability of operation are important achievements of the presented system to cope with the large number of air samples to be analyzed. Copyright © 2016 John Wiley & Sons, Ltd.
A false positive finding in liquid chromatography/triple quadrupole mass spectrometry analysis by a non‐isobaric matrix component: the case of benzotriazole in urine for human biomonitoring
Authors: Schlittenbauer Linda , Seiwert Bettina , Reemtsma Thorsten 
Published: June 2016

RationaleMulti‐residual methods employing liquid chromatography coupled to triple quadrupole mass spectrometry (LC/MS/MS) with selected reaction monitoring (SRM) are attractive also for human biomonitoring (HBM). A new process is determined that can lead to false positive findings by matrix components that are not isobaric to the analyte of interest.MethodsBenzotriazole (1H‐BT) was false positively detected in 87 human urine samples analyzed by ultra‐high‐performance‐(UHP)‐LC/MS/MS. The quantifier/qualifier ratio (Q/q ratio) did not match. This was further confirmed by negative results with an optimized gradient. Investigations were performed by UHPLC/high‐resolution (HR)MS and model compounds to reveal the identity of the disturbing matrix compound and the way that it interfered with 1H‐BT detection.ResultsA formula of C7H5NO (m/z 120.0444) was found at the retention time of 1H‐BT (m/z 120.0556) belonging to an in‐source product ion of a heavier co‐eluting compound. Product ion spectra and Q/q ratios of model compounds indicated a benzene sub‐structure with a carbonyl and amine functional group in the ortho‐ or para‐position. Finally, folic acid was confirmed as the disturbing urine component, exhibiting an in‐source fragment with the nominal mass of 1H‐BT and the same product ions as used in the SRM mode for UHPLC/MS/MS monitoring.ConclusionsInterferences in SRM detection need not be due to co‐eluting isobaric matrix compounds, but can originate from in‐source fragmentation of heavier ions. Rigid quality control measures are recommended for LC/MS/MS analysis, especially for small molecules in complex sample matrices to overcome the selectivity limits of SRM. Copyright © 2016 John Wiley & Sons, Ltd.
Dissociation of doubly charged clusters of lithium acetate: Asymmetric fission and breakdown of the liquid drop model
Authors: Shukla Anil 
Published: June 2016

RationaleElectrospray ionization (ESI) results in the formation of multiply charged cluster ions which then fragment via two competing processes: fission (charge separation) via Coulomb repulsion, and evaporation of one or more neutrals from the fragmenting ion, as described by Rayleigh's liquid drop model. Unimolecular and collision‐induced dissociation (CID) of doubly charged lithium acetate clusters, (CH3COOLi)nLi22+, demonstrated that Coulomb fission via charge separation is the dominant dissociation process with no contribution from the neutral evaporation processes for all such ions from the critical limit to larger cluster ions, although the latter process was normally observed in most earlier studies of multiply charged clusters.MethodsDoubly and higher charged lithium acetate cluster ions were generated by ESI. Unimolecular and CID of mass selected doubly charged cluster ions above the critical limit were recorded at high resolution using an LTQ Velos Orbitrap mass spectrometer.ResultsUnimolecular and collision‐induced dissociation of doubly charged lithium acetate clusters proceed via symmetric fission processes and the intensity of the fragment ions decreases as the cluster size increases. Dissociations via neutral evaporation of a monomer or larger clusters are not observed.ConclusionsDoubly charged clusters of lithium acetate above the critical limit dissociate via symmetrical fission processes and not neutral evaporation. These results are clearly in disagreement with the Rayleigh liquid drop model that has been used previously to predict the critical size and explain the fragmentation behavior of multiply charged clusters. Copyright © 2016 John Wiley & Sons, Ltd.
Chemical characterization of α‐pinene secondary organic aerosol constituents using gas chromatography, liquid chromatography, and paper spray‐based mass spectrometry techniques
Authors: Rindelaub Joel D. , Wiley Joshua S. , Cooper Bruce R. , Shepson Paul B. 
Published: June 2016

RationaleDespite ample research into the atmospheric oxidation of α‐pinene, an important precursor to biogenic secondary organic aerosol formation, the identification of its reaction products, specifically organic nitrates, which impact atmospheric NOx concentrations, is still incomplete. This negatively impacts our understanding of α‐pinene oxidation chemistry and its relation to air quality.MethodsPhotochemical chamber experiments were conducted in conjunction with mass spectrometric techniques, including gas chromatography/mass spectrometry (GC/MS), high‐performance liquid chromatography/time‐of‐flight (HPLC/TOF), and paper spray ionization MS, to investigate products from the OH radical initiated oxidation of α‐pinene under high NOx conditions.ResultsOver 30 compounds were tentatively identified, including those newly detected from photochemical chamber studies of α‐pinene oxidation, pinocamphenol, fencholenic aldehyde, and α‐pinene‐derived nitrate isomers. α‐Pinene‐derived hydroxynitrate isomers were successfully detected using chromatographic methods, demonstrating, for the first time, the identification of individual first‐generation organic nitrate products derived from α‐pinene. The application of paper spray ionization to particle‐phase compounds collected on filters represents a novel method for the direct analysis of filter samples at ambient pressure and temperature.ConclusionsThe use of HPLC/TOF and paper spray ionization methods to identify previously unobserved α‐pinene‐derived products helps lower the uncertainty in α‐pinene oxidation chemistry and provides new platforms that can be used to identify and quantify important atmospheric compounds that relate to air quality in a complex sample matrix, such as ambient aerosol particles. Additionally, the use of paper spray ionization for direct filter analysis is a fast, relatively inexpensive sample preparation technique that can be used to reduce sample manipulation from solvent‐induced reactions. Copyright © 2016 John Wiley & Sons, Ltd.
Effect of Nitrogen Donor Disposition on Topology in Cobalt Isophthalate Coordination Polymers Containing Dipyridylamide Ligands
Authors: Sample Alexander D. , O'Donovan Megan E. , LaDuca Robert L. 
Published: June 2016

AbstractCobalt coordination complexes containing a substituted isophthalate ligand and hydrogen‐bonding capable dipyridylamide ligands were prepared hydrothermally and structurally characterized by single‐crystal X‐ray diffraction. {[Co(nip)(3‐pina)]n (1) (nip = 5‐nitroisophthalate, 3‐pina = 3‐pyridylisonicotinamide) displays [Co(nip)]n 1D ribbon motifs with embedded {Co2(OCO)2} dimeric units, linked by L‐shaped 3‐pina tethers into a 3D [Co(nip)(3‐pina)]n coordination polymer network with pcu topology. In contrast, {[Co(nip)(4‐pmina)(H2O)]·H2O}n (2) (4‐pmina = 4‐pyridylmethylisonicotinamide) manifests a twofold interpenetrated 66 topology diamondoid network. {[Co(meoip)(3‐pina)]n (3) (meoip = 5‐methoxyisophthalate) has a dimer‐based 3D pcu network as seen in 1. [Co(meoipH)2(4‐pmina)2(H2O)2] (4) contains neutral coordination complexes linked by hydrogen‐bonding into supramolecular ribbons. Thermal properties of these new solids were also investigated.
Self-adaptation and secure information flow in multiparty communications
Authors: Castellani Ilaria , Dezani-Ciancaglini Mariangiola , Pérez Jorge A. 
Published: June 2016

Abstract
We present a comprehensive model of structured communications in which self-adaptation and security concerns are jointly addressed. More specifically, we propose a model of multiparty, self-adaptive communications with access control and secure information flow guarantees. In our model, multiparty protocols (choreographies) are described as global types; security violations occur when process implementations of protocol participants attempt to read or write messages of inappropriate security levels within directed exchanges. Such violations trigger adaptation mechanisms that prevent the violations to occur and/or to propagate their effect in the choreography. Our model is equipped with local and global adaptation mechanisms for reacting to security violations of different gravity; type soundness results ensure that the overall multiparty protocol is still correctly executed while the system adapts itself to preserve the participants’ security.
Density‐dependent reproduction causes winter crashes in a common vole population
Authors: Pinot Adrien , Barraquand Frédéric , Tedesco Edoardo , Lecoustre Vincent , Bretagnolle Vincent , Gauffre Bertrand 
Published: June 2016

AbstractCommon voles in western France exhibit three‐year population cycles with winter crashes after large outbreaks. During the winter of 2011–2012, we monitored survival, reproduction, recruitment and population growth rate of common voles at different densities (from low to outbreak densities) in natura to better understand density dependence of demographic parameters. Between October and April, the number of animals decreased irrespective of initial density. However, the decline was more pronounced when October density was higher (loss of ≈54 % of individuals at low density and 95 % at high density). Using capture‐mark‐recapture models with Pradel's temporal symmetry approach, we found a negative effect of density on recruitment and reproduction. In contrast, density had a slightly positive effect on survival indicating that mortality did not drive the steeper declines in animal numbers at high density. We discuss these results in a population cycle framework, and suggest that crashes after outbreaks could reflect negative effects of density dependence on reproduction rather than changes in mortality rates.
Novelty design in gain flattening filter of ASE source based on fat ultra-long period fiber grating
Authors: Nafchi Fereshteh Mohammadi , Shahi Sharifeh , Shaffaatifar Mohammad Taha , Kanani Mohammad , Noormohammadi Hossein 
Published: June 2016

Abstract
A new type of gain flattening filter for amplified spontaneous emission (ASE) source based on erbium doped fiber (EDF) is proposed and demonstrated by fabricating and writing two series ultra-long period fiber grating (ULPFG) on single mode fiber (SMF-28). The novelty method in this research is based on writing the two ULPFGs as fat gratings. The LPG is written by a simple and available arc-discharge method. The pump power based on single-pass backward pump configuration is around 100 mW, and the average wavelength is near to 974 nm. The gain flattening profile is obtained by 3.4 (±1.7) dB ripple in the wavelength range between 1524 nm and 1565 nm with 41-nm band width.
Use of anti‐Müllerian hormone testing during ovarian reserve screening to identify women at risk of polycystic ovary syndrome
Authors: Safier Lauren Z. , Grossman Lisa C. , Chan Cariann W. , Sauer Mark V. , Lobo Rogerio A. , Douglas Nataki C. 
Published: June 2016

AbstractObjectiveTo assess the applicability of anti‐Müllerian hormone (AMH) testing in the identification of women at risk for polycystic ovary syndrome (PCOS) when AMH is used in ovarian reserve screening in the general population.MethodsA secondary analysis was undertaken of a large cross‐sectional study. Women aged 27–37 years, presently delaying childbearing but interested in future fertility, completed an online questionnaire to assess knowledge and attitudes about ovarian reserve testing, and underwent serum AMH testing between October 2014 and April 2015 in New York, NY, USA. For the secondary analysis, women considered to have elevated AMH levels (≥ 4.7 ng/mL) were invited for physical examination and transvaginal ultrasonography.ResultsAmong 97 women who underwent AMH testing, 32 (33.0%) had elevated AMH levels. Hyperandrogenism was reported by 8 (25.0%) women with elevated AMH and none with AMH concentrations lower than 4.7 ng/mL (P < 0.001). Irregular menstrual cycles before hormonal contraceptive use were reported by 16 (24.6%) of 65 women with AMH concentrations lower than 4.7 ng/mL and 11 (34.4%) with elevated AMH (P = 0.34). Of the 20 women with elevated AMH who returned for further evaluation, 16 (80.0%) had polycystic ovaries and 13 (65.0%) were diagnosed with PCOS (Rotterdam criteria).ConclusionWhen AMH levels are used as a screening test for fertility, elevated concentrations can identify women at risk for PCOS.
Big data to smart data in Alzheimer's disease: Real‐world examples of advanced modeling and simulation
Authors: Haas Magali , Stephenson Diane , Romero Klaus , Gordon Mark Forrest , Zach Neta , Geerts Hugo ,   Brain Health Modeling Initiative (BHMI)
Published: June 2016

AbstractMany disease‐modifying clinical development programs in Alzheimer's disease (AD) have failed to date, and development of new and advanced preclinical models that generate actionable knowledge is desperately needed. This review reports on computer‐based modeling and simulation approach as a powerful tool in AD research. Statistical data‐analysis techniques can identify associations between certain data and phenotypes, such as diagnosis or disease progression. Other approaches integrate domain expertise in a formalized mathematical way to understand how specific components of pathology integrate into complex brain networks. Private‐public partnerships focused on data sharing, causal inference and pathway‐based analysis, crowdsourcing, and mechanism‐based quantitative systems modeling represent successful real‐world modeling examples with substantial impact on CNS diseases. Similar to other disease indications, successful real‐world examples of advanced simulation can generate actionable support of drug discovery and development in AD, illustrating the value that can be generated for different stakeholders.