bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrashort echo time magnetization transfer (UTE‐MT) imaging and modeling: magic angle independent biomarkers of tissue properties
Authors: Ma Ya‐Jun , Shao Hongda , Du Jiang , Chang Eric Y. 
Published: September 2016

MRI biomarkers such as T2, T2* and T1rho have been widely used, but are confounded by the magic angle effect. The purpose of this study is to investigate the use of the two‐dimensional ultrashort echo time magnetization transfer (UTE‐MT) sequence for potential magic angle independent MR biomarkers. Magnetization transfer was investigated in cadaveric Achilles tendon samples using the UTE‐MT sequence at five MT powers and five frequency offsets ranging from 2 to 50 kHz. The protocol was applied at five sample orientations ranging from 0 to 90° relative to the B0 field. The results were analyzed with a two‐pool quantitative MT model. Multiple TE data were also acquired and mono‐exponential T2* was calculated for each orientation. Macromolecular proton fractions and exchange rates derived from UTE‐MT modeling did not appreciably change between the various orientations, whereas the T2* relaxation time demonstrated up to a sixfold increase from 0° to 55°. The UTE‐MT technique with two‐pool modeling shows promise as a clinically compatible technique that is resistant to the magic angle effect. This method provides information on the macromolecular proton pool that cannot be directly obtained by other methods, including regular UTE techniques.
Investigation of the pH‐dependence of dye‐doped protein–protein interactions
Authors: Nudelman Roman , Gloukhikh Ekaterina , Rekun Antonina , Richter Shachar 
Published: September 2016

AbstractProteins can dramatically change their conformation under environmental conditions such as temperature and pH. In this context, Glycoprotein's conformational determination is challenging. This is due to the variety of domains which contain rich chemical characters existing within this complex. Here we demonstrate a new, straightforward and efficient technique that uses the pH‐dependent properties of dyes‐doped Pig Gastric Mucin (PGM) for predicting and controlling protein–protein interaction and conformation. We utilize the PGM as natural host matrix which is capable of dynamically changing its conformational shape and adsorbing hydrophobic and hydrophilic dyes under different pH conditions and investigate and control the fluorescent properties of these composites in solution. It is shown at various pH conditions, a large variety of light emission from these complexes such as red, green and white is obtained. This phenomenon is explained by pH‐dependent protein folding and protein–protein interactions that induce different emission spectra which are mediated and controlled by means of dye–dye interactions and surrounding environment. This process is used to form the technologically challenging white light‐emitting liquid or solid coating for LED devices.
Effect of ultrasonic treatment on the defect structure of the Si‐SiO2 system
Authors: Kropman D. , Seeman V. , Dolgov S. , Medvids A. 
Published: September 2016

AbstractThe effect of ultrasonic treatment (UST) on the defect structure of the Si‐SiO2 system by means of electron spin resonance (ESR), metallography, MOS capacitance technique and secondary ions mass‐spectroscopy (SIMS) is presented. The non‐monotonous dependence of the defect densities on the US wave intensity has been observed. The influence of the UST frequency on the ESR signal intensity of the defect centres depended on the defects type and structure and may becaused by vibrational energy dissipation which are a functions of defect's centers type. The influence of the UST on the Si‐SiO2 interface properties depends on the oxide thickness and crystallographic orientation. The density of point defects and absorbed impurities at the Si–SiO2 interface can be reduced and its electrical parameters improved by an appropriate choice of the UST and oxidation conditions. (© 2016 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Detection of busulfan adducts on proteins
Authors: Acosta‐Martin Adelina E. , Antinori Paola , Uppugunduri Chakradhara Rao S. , Daali Youssef , Ansari Marc , Scherl Alexander , Müller Markus , Lescuyer Pierre 
Published: September 2016

RationaleBusulfan is a bifunctional alkyl sulfonate antineoplastic drug. This alkylating agent was described as forming covalent adducts on proteins. However, only limited data are available regarding the interaction of busulfan with proteins. Mass spectrometry and bioinformatics were used to identify busulfan adducts on human serum albumin and hemoglobin.MethodsAlbumin and hemoglobin were incubated with busulfan or control compounds, digested with trypsin and analyzed by liquid chromatography/tandem mass spectrometry (LC/MS/MS) on a Thermo Fisher LTQ Orbitrap Velos Pro. MS data were used to generate spectral libraries of non‐modified peptides and an open modification search was performed to identify potential adduct mass shifts and possible modification sites. Results were confirmed by a second database search including identified mass shifts and by visual inspection of annotated tandem mass spectra of adduct‐carrying peptides.ResultsFive structures of busulfan adducts were detected and a chemical structure could be attributed to four of them. Two were primary adducts corresponding to busulfan monoalkylation and alkylation of two amino acid residues by a single busulfan molecule. Two others corresponded to secondary adducts generated during sample processing. Adducts were mainly detected on Asp, Glu, and His residues. These findings were confirmed by subsequent database searches and experiments with synthetic peptides.ConclusionsThe combination of in vitro incubation of proteins with the drug of interest or control compounds, high‐resolution mass spectrometry, and open modification search allowed confirmation of the direct interaction of busulfan with proteins and characterization of the resulting adducts. Our results also showed that careful analysis of the data is required to detect experimental artifacts. Copyright © 2016 John Wiley & Sons, Ltd.
The gas‐phase ligand exchange of select magnesium and copper beta‐diketonate complexes
Authors: Fleming Kathleen M. , Pekar Jennifer C. , Leskiw Brian D. 
Published: September 2016

RationaleWhile much of the interest and application of beta‐diketonate complexes has focused predominately on the condensed phases, we report on the prevalence of gas‐phase ligand exchange reactions leading to the formation of novel species.MethodsGas‐phase ligand exchange reactions of Mg(eeac)2 and Mg(tftm)2 complexes with Cu(acac)2, Cu(tftm)2, Cu(dbm)2, and Cu(eeac)2 were investigated using a direct insertion electron impact triple quadrupole mass spectrometer. The collision cell of the triple quadrupole mass spectrometer was also employed to examine the gas‐phase reactions between mass‐selected ions and specific neutral target compounds.ResultsThe gas‐phase mixed ligand products of [Mg(acac)(eeac)]+, [Cu(acac)(eeac)]+, [Mg(eeac)(tftm)]+, [Cu(eeac)(tftm)]+, [Mg(acac)(tftm)]+, and [Mg(dbm)(tftm)]+ were formed following the co‐sublimation of hetero‐metal precursors and are reported herein for the first time. The corresponding fragmentation patterns of the precursor and mixed ligand species are also presented.ConclusionsSeveral gas‐phase ligand exchange reactions were observed leading to the formation of both mixed and complete ligand exchange products. Copyright © 2016 John Wiley & Sons, Ltd.
Bulk C, H, O, and fatty acid C stable isotope analyses for purity assessment of vegetable oils from the southern and northern hemispheres
Authors: Spangenberg Jorge E. 
Published: September 2016

RationaleThe carbon, hydrogen and oxygen stable isotope composition (δ13C, δ2H, and δ18O values) of plants and their products is linked to photosynthetic fractionation, environmental factors and agricultural practices. Therefore, they contribute to determining the purity of commercial vegetable oils and may provide information on their geographical origin.MethodsMaize, olive, sunflower, groundnut, soybean and rice oils differing in sites of growth in the southern and northern hemispheres were characterized by bulk oil stable isotope ratios (δ13Cbulk, δ2Hbulk, and δ18Obulk values), fatty acid (FA) concentrations and δ13CFA values using elemental analysis/isotope ratio mass spectrometry, gas chromatography/mass spectrometry, gas chromatography/flame ionization detection and gas chromatography/combustion/isotope ratio mass spectrometry. Principal component analysis was applied to examine the inherent structure of the data.ResultsThe δ13Cbulk values of maize oils (−18.4 to −14.9 ‰) are typical for C4 plants, and those of olive (−30.2 to −28.2 ‰), sunflower (−30.2 to −29.2 ‰), groundnut (−29.3 ‰), soybean (−30.6 ‰), and rice (−34.5 ‰) oils are typical for C3 plants. The δ2Hbulk values vary from −161 to −132 ‰ for maize oils and −171 to −109 ‰ for C3 oils. The δ18Obulk values of all oils vary between 15.2 and 38.9 ‰. The major δ13CFA differences (>5 ‰) within plant species render the inter‐C3‐species comparison difficult. These differences are explained in terms of variations in the lipid biosynthetic pathways and blend of vegetable oils of different FA composition and δ13CFA values. The samples from the southern hemisphere are generally enriched in 13C compared with those from the northern hemisphere. Differences between the southern and northern hemispheres were observed in δ2H (p < 0.001) and δ18Obulk (p = 0.129) values for all C3 oils, and in δ13C18:1 (p = 0.026) and δ18Obulk (p = 0.160) values for maize oils.ConclusionsThe results of this study show that combining bulk and molecular stable isotope ratios, FA compositions and their statistical analysis helps the characterization of the geographic origin of oils. This methodology can be used to detect and source impurities in valuable vegetable oils commercialized worldwide. Copyright © 2016 John Wiley & Sons, Ltd.
The compression chord capacity model for the shear design and assessment of reinforced and prestressed concrete beams
Authors: Cladera Antoni , Marí Antonio , Bairán Jesús Miguel , Ribas Carlos , Oller Eva , Duarte Noemí 
Published: September 2016

AbstractA simplified mechanical model is presented for the shear strength prediction of reinforced and prestressed concrete members with and without transverse reinforcement, with I, T or rectangular cross‐section. The model, derived with further simplifications from a previous one developed by the authors, incorporates the contributions of the concrete compression chord, the cracked web, the dowel action and the shear reinforcement in a compact formulation. The mechanical character of the model provides valuable information about the physics of the problem and incorporates the most relevant parameters governing the shear strength of structural concrete members. The predictions of the model fit very well the experimental results collected in the ACI‐DAfStb databases of shear tests on slender reinforced and prestressed concrete beams with and without stirrups. Due to this fact and the simplicity of the derived equations it may become a very useful tool for structural design and assessment in engineering practice.
Status and trends of dam removal research in the United States
Authors: Ryan Bellmore J. , Duda Jeffrey J. , Craig Laura S. , Greene Samantha L. , Torgersen Christian E. , Collins Mathias J. , Vittum Katherine 
Published: September 2016

Aging infrastructure coupled with growing interest in river restoration has driven a dramatic increase in the practice of dam removal. With this increase, there has been a proliferation of studies that assess the physical and ecological responses of rivers to these removals. As more dams are considered for removal, scientific information from these dam‐removal studies will increasingly be called upon to inform decisions about whether, and how best, to bring down dams. This raises a critical question: what is the current state of dam‐removal science in the United States? To explore the status, trends, and characteristics of dam‐removal research in the U.S., we searched the scientific literature and extracted basic information from studies on dam removal. Our literature review illustrates that although over 1200 dams have been removed in the U.S., fewer than 10% have been scientifically evaluated, and most of these studies were short in duration (<4 years) and had limited (1–2 years) or no pre‐removal monitoring. The majority of studies focused on hydrologic and geomorphic responses to removal rather than biological and water‐quality responses, and few studies were published on linkages between physical and ecological components. Our review illustrates the need for long‐term, multidisciplinary case studies, with robust study designs, in order to anticipate the effects of dam removal and inform future decision making. WIREs Water 2017, 4:e1164. doi: 10.1002/wat2.1164This article is categorized under:

Water and Life > Conservation, Management, and Awareness
Engineering Water > Sustainable Engineering of Water
Water and Life > Stresses and Pressures on Ecosystems
Osimertinib-induced interstitial lung disease after treatment with anti-PD1 antibody
Authors: Mamesaya Nobuaki , Kenmotsu Hirotsugu , Katsumata Mineo , Nakajima Takashi , Endo Masahiro , Takahashi Toshiaki 
Published: September 2016

SummaryWe report a case of a 38-year-old woman who was diagnosed with stage IV lung adenocarcinoma, harboring an epidermal growth factor receptor (EGFR) L858R mutation on exon 21 and a T790 M mutation on exon 20. The patient was treated with osimertinib, a third-generation EGFR tyrosine kinase inhibitor (EGFR-TKI) following treatment with nivolumab, an anti-Programmed Cell Death 1 (anti-PD1) antibody. After initiating osimertinib treatment, the patient began to complain of low-grade fever and shortness of breath without hypoxemia, and her chest radiograph and a CT scan revealed a remarkable antitumor response, although faint infiltrations were observed in the bilateral lung field. Bronchoalveolar lavage fluid mainly contained lymphocytes (CD4+/CD8+ ratio of 0.3), and a transbronchial lung biopsy specimen showed lymphocytic alveolitis with partial organization in several alveolar spaces. Therefore we diagnosed the patient with osimertinib-induced interstitial lung disease (ILD) after treatment with anti-PD1 antibody. We considered anti-PD1 therapies may be the risk factor of EGFR-TKI-induced ILD.
Stoichiometry of leaf nitrogen and phosphorus of grasslands of the Inner Mongolian and Qinghai‐Tibet Plateaus in relation to climatic variables and vegetation organization levels
Authors: Fan Jiangwen , Harris Warwick , Zhong Huaping 
Published: September 2016

AbstractNitrogen (N) and phosphorus (P) are most commonly the limiting essential elements that affect the functioning of plants and ecosystems. However, their stoichiometry in relation to climatic variables and vegetation organization levels has not been comprehensively characterized. N and P concentrations were measured for 329 leaf samples collected at 132 sites along the 5000 km long China Grassland Transect that traverses the Inner Mongolian and Qinghai‐Tibet Plateaus. The patterns of these measurements were analyzed with reference to climate factors, plant species, plant functional groups, grassland communities and grassland ecosystems. The aim was to explore whether geographical patterns of plant leaf elements are related to zonal climatic variables, and at which vegetation organization levels changes of plant leaf N and P stoichiometric characteristics and pattern occur. Results showed that interspecific differences of N and P concentrations were most significant for the three vegetation organization levels of species, community and ecosystem. Plant leaf N and P concentrations were higher, coefficients of variation of N and P lower, and N/P, C/N and C/P ratios were also lower for leaf samples from the cold high altitude Qinghai‐Tibet Plateau than for those from the relatively lower altitude and warmer Inner Mongolian Plateau. Correlation of N and P for Inner Mongolian grassland was higher than that for the Qinghai‐Tibet Plateau. The study indicates plant species are the most basic unit influencing plant stoichiometric geographic patterns, and that climatic variables affect leaf element concentrations mainly through their effect on changes of plant species composition of vegetation.
Effect of Sodium Carbonate on the Cloud Point in Alkyl Ether/Brine Systems: Apparent Relation with Dynamic Interfacial Tension Minimum
Authors: Hadji Moundher , Aoudia Mohamed , Al‐Rubkhi Adil , Al‐Maamari Rashid S. , Hadj‐Ziane‐Zafour Amel 
Published: September 2016

AbstractThe effect of Na2CO3 on the cloud point in Na2CO3/surfactant/brine was investigated using two series of nonionic surfactants, C13EOx and C17EOx. The cloud point, Tcp, was found to decrease linearly with increasing Na2CO3 concentration. This was attributed to Na+ and particularly to CO32−salting‐out effect. The slope a = dTcp/d[Na2CO3] became more and more negative as the degree of ethoxylation is increased, suggesting that the higher the number of ethylene oxide (EO) groups the stronger is the cloud point depression for a given increment in Na+and CO32−ions in solution. This was also illustrated by the linear variation of ΔTcp = Tcp,0 − Tcp,[Na2CO3] with the surfactant degree of ethoxylation.
ATRA mechanically reprograms pancreatic stellate cells to suppress matrix remodelling and inhibit cancer cell invasion
Authors: Chronopoulos Antonios , Robinson Benjamin , Sarper Muge , Cortes Ernesto , Auernheimer Vera , Lachowski Dariusz , Attwood Simon , García Rebeca , Ghassemi Saba , Fabry Ben , del Río Hernández Armando 
Published: September 2016

AbstractPancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy with a dismal survival rate. Persistent activation of pancreatic stellate cells (PSCs) can perturb the biomechanical homoeostasis of the tumour microenvironment to favour cancer cell invasion. Here we report that ATRA, an active metabolite of vitamin A, restores mechanical quiescence in PSCs via a mechanism involving a retinoic acid receptor beta (RAR-β)-dependent downregulation of actomyosin (MLC-2) contractility. We show that ATRA reduces the ability of PSCs to generate high traction forces and adapt to extracellular mechanical cues (mechanosensing), as well as suppresses force-mediated extracellular matrix remodelling to inhibit local cancer cell invasion in 3D organotypic models. Our findings implicate a RAR-β/MLC-2 pathway in peritumoural stromal remodelling and mechanosensory-driven activation of PSCs, and further suggest that mechanical reprogramming of PSCs with retinoic acid derivatives might be a viable alternative to stromal ablation strategies for the treatment of PDAC.
Accelerated Echo Planer J-resolved Spectroscopic Imaging of Putamen and Thalamus in Obstructive Sleep Apnea
Authors: Sarma Manoj K. , Macey Paul M. , Nagarajan Rajakumar , Aysola Ravi , Harper Ronald M. , Thomas M. Albert 
Published: September 2016

AbstractObstructive sleep apnea syndrome (OSAS) leads to neurocognitive and autonomic deficits that are partially mediated by thalamic and putamen pathology. We examined the underlying neurochemistry of those structures using compressed sensing-based 4D echo-planar J-resolved spectroscopic imaging (JRESI), and quantified values with prior knowledge fitting. Bilaterally increased thalamic mI/Cr, putamen Glx/Cr, and Glu/Cr, and bilaterally decreased thalamic and putamen tCho/Cr and GABA/Cr occurred in OSAS vs healthy subjects (p < 0.05). Increased right thalamic Glx/Cr, Glu/Cr, Gln/Cr, Asc/Cr, and decreased GPC/Cr and decreased left thalamic tNAA/Cr, NAA/Cr were detected. The right putamen showed increased mI/Cr and decreased tCho/Cr, and the left, decreased PE/Cr ratio. ROC curve analyses demonstrated 60–100% sensitivity and specificity for the metabolite ratios in differentiating OSAS vs. controls. Positive correlations were found between: left thalamus mI/Cr and baseline oxygen saturation (SaO2); right putamen tCho/Cr and apnea hypopnea index; right putamen GABA/Cr and baseline SaO2; left putamen PE/Cr and baseline SaO2; and left putamen NAA/Cr and SaO2 nadir (all p < 0.05). Negative correlations were found between left putamen PE/Cr and SaO2 nadir. These findings suggest underlying inflammation or glial activation, with greater alterations accompanying lower oxygen saturation. These metabolite levels may provide biomarkers for future neurochemical interventions by pharmacologic or other means.
Combining Statistical Tools and Ecological Assessments in the Study of Biodeterioration Patterns of Stone Temples in Angkor (Cambodia)
Authors: Caneva G. , Bartoli F. , Savo V. , Futagami Y. , Strona G. 
Published: September 2016

AbstractBiodeterioration is a major problem for the conservation of cultural heritage materials. We provide a new and original approach to analyzing changes in patterns of colonization (Biodeterioration patterns, BPs) by biological agents responsible for the deterioration of outdoor stone materials. Here we analyzed BPs of four Khmer temples in Angkor (Cambodia) exposed to variable environmental conditions, using qualitative ecological assessments and statistical approaches. The statistical analyses supported the findings obtained with the qualitative approach. Both approaches provided additional information not otherwise available using one single method. Our results indicate that studies on biodeterioration can benefit from integrating diverse methods so that conservation efforts might become more precise and effective.
Quantum correlation dynamics subjected to critical spin environment with short-range anisotropic interaction
Authors: Guo J. L. , Zhang X. Z. 
Published: September 2016

AbstractShort-range interaction among the spins can not only results in the rich phase diagram but also brings about fascinating phenomenon both in the contexts of quantum computing and information. In this paper, we investigate the quantum correlation of the system coupled to a surrounding environment with short-range anisotropic interaction. It is shown that the decay of quantum correlation of the central spins measured by pairwise entanglement and quantum discord can serve as a signature of quantum phase transition. In addition, we study the decoherence factor of the system when the environment is in the vicinity of the phase transition point. In the strong coupling regime, the decay of the decoherence factor exhibits Gaussian envelop in the time domain. However, in weak coupling limit, the quantum correlation of the system is robust against the disturbance of the magnetic field through optimal control of the anisotropic short-range interaction strength. Based on this, the effects of the short-range anisotropic interaction on the sudden transition from classical to quantum decoherence are also presented.