bluuebunny/crossref_metadata_2025_split huggingface dataset:
A sensitivity analysis of key natural factors in the modeled global acetone budget
Authors: Brewer J. F. , Bishop M. , Kelp M. , Keller C. A. , Ravishankara A. R. , Fischer E. V. 
Published: January 2017

AbstractAcetone is one of the most abundant carbonyl compounds in the atmosphere, and it serves as an important source of HOx (OH + HO2) radicals in the upper troposphere and a precursor for peroxyacetyl nitrate. We present a global sensitivity analysis targeted at several major natural source and sink terms in the global acetone budget to find the input factor or factors to which the simulated acetone mixing ratio was most sensitive. The ranges of input factors were taken from literature. We calculated the influence of these factors in terms of their elementary effects on model output. Of the six factors tested here, the four factors with the highest contribution to total global annual model sensitivity are direct emissions of acetone from the terrestrial biosphere, acetone loss to photolysis, the concentration of acetone in the ocean mixed layer, and the dry deposition of acetone to ice‐free land. The direct emissions of acetone from the terrestrial biosphere are globally important in determining acetone mixing ratios, but their importance varies seasonally outside the tropics. Photolysis is most influential in the upper troposphere. Additionally, the influence of the oceanic mixed layer concentrations are relatively invariant between seasons, compared to the other factors tested. Monoterpene oxidation in the troposphere, despite the significant uncertainties in acetone yield in this process, is responsible for only a small amount of model uncertainty in the budget analysis.
Crystal structure and luminescence properties of the blue‐green‐emitting Ba9(Lu, Y)2Si6O24:Ce3+ phosphor
Authors: Xu Huawei , Zhou Zhi , Liu Yongfu , Liu Qunxing , He Zhiyuan , Wang Shen , Huang Linyi , Zhu Hongbo 
Published: January 2017

AbstractSamples of the Ba9(Lu2‐xYx)Si6O24:Ce3+ (x = 0–2) blue‐green phosphors were synthesized by solid‐state reactions. All the samples exhibited a rhombohedral crystal structure. As the Y3+ concentration increased, the diffraction peaks shifted to the small angle region and the lattice parameters increased due to the larger ionic radius of Y3+ (r = 0.900 Å) compared with that of Lu3+ (r = 0.861 Å). Under 400 nm excitation, samples exhibited strong blue‐green emissions around 490 nm. The emission bands had a slight blue shift that resulted from weak crystal‐field splitting with increasing Y3+ concentration. Luminescence intensity and quantum efficiency (QE) decreased with increasing Y3+ concentration. The internal QE decreased from 74 to 50% and the external QE decreased from 50 to 34% as x increased from 0 to 2. The thermal stability of the Lu series was better than that of the Y‐series. The excitation band peak around 400 nm matched well with the emission light from the efficient near‐ultraviolet (NUV) chip. These results indicate promising applications for these NUV‐based white light‐emitting diodes.
A combination of NADHP and hispidin is not essential for bioluminescence in luminous fungal living gills of Mycena chlorophos
Authors: Teranishi Katsunori 
Published: January 2017

AbstractThe chemical mechanisms underlying visible bioluminescence in the fungus Mycena chlorophos are not clear. A combination of dihydronicotinamide adenine dinucleotide phosphate (NADPH) and hispidin, which has been reported to increase the intensity of in vitro luminescence in crude cold‐water extracts prepared from the bioluminescent fruiting bodies of M. chlorophos, exhibited potential bioluminescence activation in the early bioluminescence stages, in which the bioluminescence was ultra‐weak, for living gills and luminescence activation for non‐bioluminescent gills, which was collapsed by freezing and subsequent thawing, at all bioluminescence stages. These abilities were not evident in considerably bioluminescent gills. These abilities were blocked by trans‐4‐hydroxycinnamic acid and trans‐3,4‐dihydroxycinnamic acid, which were identified as in vivo bioluminescence‐activating components. Original bioluminescence and bioluminescence produced from the addition of trans‐4‐hydroxycinnamic acid and trans‐3,4‐dihydroxycinnamic acid in living gills were almost completely inhibited by 10 mM NaN3, whereas the luminescence produced form the combination of NADPH and hispidin in thawed non‐bioluminescent and living gills at the early weak bioluminescence stages was not inhibited by 10 mM NaN3. Thus, the combination of NADPH and hispidin plays different roles in luminescence systems compared with essential bioluminescence systems, and the combination of NADPH and hispidin was not essential for visible bioluminescence in living gills.
Computational de novo design of antibodies binding to a peptide with high affinity
Authors: Poosarla Venkata Giridhar , Li Tong , Goh Boon Chong , Schulten Klaus , Wood Thomas K. , Maranas Costas D. 
Published: January 2017

ABSTRACTAntibody drugs play a critical role in infectious diseases, cancer, autoimmune diseases, and inflammation. However, experimental methods for the generation of therapeutic antibodies such as using immunized mice or directed evolution remain time consuming and cannot target a specific antigen epitope. Here, we describe the application of a computational framework called OptMAVEn combined with molecular dynamics to de novo design antibodies. Our reference system is antibody 2D10, a single‐chain antibody (scFv) that recognizes the dodecapeptide DVFYPYPYASGS, a peptide mimic of mannose‐containing carbohydrates. Five de novo designed scFvs sharing less than 75% sequence similarity to all existing natural antibody sequences were generated using OptMAVEn and their binding to the dodecapeptide was experimentally characterized by biolayer interferometry and isothermal titration calorimetry. Among them, three scFvs show binding affinity to the dodecapeptide at the nM level. Critically, these de novo designed scFvs exhibit considerably diverse modeled binding modes with the dodecapeptide. The results demonstrate the potential of OptMAVEn for the de novo design of thermally and conformationally stable antibodies with high binding affinity to antigens and encourage the targeting of other antigen targets in the future. Biotechnol. Bioeng. 2017;114: 1331–1342. © 2017 Wiley Periodicals, Inc.
D‐Optimal mixture design optimization of an HPLC method for simultaneous determination of commonly used antihistaminic parent molecules and their active metabolites in human serum and urine
Authors: Kanthiah Selvakumar , Kannappan Valliappan 
Published: January 2017

AbstractThis study describes a specific, precise, sensitive and accurate method for simultaneous determination of hydroxyzine, loratadine, terfenadine, rupatadine and their main active metabolites cetirizine, desloratadine and fexofenadine, in serum and urine using meclizine as an internal standard. Solid‐phase extraction method for sample clean‐up and preconcentration of analytes was carried out using Phenomenex Strata‐X‐C and Strata X polymeric cartridges. Chromatographic analysis was performed on a Phenomenex cyano (150 × 4.6 mm i.d., 5 μm) analytical column. A D‐optimal mixture design methodology was used to evaluate the effect of changes in mobile phase compositions on dependent variables and optimization of the response of interest. The mixture design experiments were performed and results were analyzed. The region of ideal mobile phase composition consisting of acetonitrile–methanol–ammonium acetate buffer (40 mm; pH 3.8 adjusted with acetic acid): 18:36:46% v/v/v was identified by a graphical optimization technique using an overlay plot. While using this optimized condition all analytes were baseline resolved in <10 min. Solvent mixtures were delivered at 1.5 mL/min flow rate and analytes peaks were detected at 222 nm. The proposed bioanalytical method was validated according to US Food and Drug Administration guidelines. The proposed method was sensitive with detection limits of 0.06–0.15 μg/mL in serum and urine samples. Relative standard deviation for inter‐ and intra‐day precision data was found to be <7%. The proposed method may find application in the determination of selected antihistaminic drugs in biological fluids.
Determining the Composition of Active Cholesterol in the Plasma Membrane of Single Cells by using Electrochemiluminescence
Authors: Zuo Huanzhen , Wang Rui , Jiang Dechen , Fang Danjun 
Published: January 2017

AbstractActive and inactive cholesterol in the plasma membrane of one cell were co‐measured by using luminol electrochemiluminescence, so that the composition of active membrane cholesterol was determined at single cells. The cellular plasma membrane remained intact after the removal of active membrane cholesterol and, thus, inactive cholesterol was activated for reaction with cholesterol oxidase. By utilizing the reactions of active and inactive cholesterol with oxidase in series, both of them generated hydrogen peroxide, inducing the corresponding electrochemiluminescence for the respective quantitation of these two states of membrane cholesterol. The successful determination of active and inactive membrane cholesterol at one cell provides information about the composition of active membrane cholesterol, which is significant for the study of cellular cholesterol trafficking.
Supercritical water oxidation of lactose
Authors: Ferreira‐Pinto Leandro , Tavares Celia Regina Grahen , de Souza Thiago Leandro , Feihrmann Andresa Carla , Coimbra Jane , Vedoy Diógenes R. L. , Cardozo‐Filho Lúcio 
Published: January 2017

AbstractNew data on total organic carbon (TOC) reduction and H2 production were obtained by using supercritical water oxidation of lactose with and without oxidant agents (H2O2 and t‐BHP) in a continuous Inconel 625 flow reactor. The oxidation reactions were carried out at 550 and 700 °C, 22.5 MPa, 0.025 g/g (2.5 wt%) lactose concentration, feed flow rate of 5 g · min−1, and a total reaction time of 90 min. The average production of H2 yielded 4.5 mol/mol lactose with TOC reduction of ∼99 %. The results obtained in this study with supercritical water oxidation (SCWO) may be used to generate energy via production of H2 from dairy industry effluents.
Plant chemical defense indirectly mediates aphid performance via interactions with tending ants
Authors: Züst Tobias , Agrawal Anurag A. 
Published: January 2017

AbstractThe benefits of mutualistic interactions are often highly context dependent. We studied the interaction between the milkweed aphid Aphis asclepiadis and a tending ant, Formica podzolica. Although this interaction is generally considered beneficial, variation in plant genotype may alter it from mutualistic to antagonistic. Here we link the shift in strength and relative benefit of the ant‐aphid interaction to plant genotypic variation in the production of cardenolides, a class of toxic defensive chemicals. In a field experiment with highly variable genotypes of the common milkweed (Asclepias syriaca), we show that plant cardenolides, especially polar forms, are ingested by aphids and excreted in honeydew proportionally to plant concentrations without directly affecting aphid performance. Ants consume honeydew, and aphids that excreted high amounts of cardenolides received fewer ant visits, which in turn reduced aphid survival. On at least some plant genotypes, aphid numbers per plant were reduced in the presence of ants to levels lower than in corresponding ant‐exclusion treatments, suggesting antagonistic ant behavior. Although cardenolides appear ineffective as direct plant defenses against aphids, the multi‐trophic context reveals an ant‐mediated negative indirect effect on aphid performance and population dynamics.
Evaluation of the phototoxicity of unsubstituted and alkylated polycyclic aromatic hydrocarbons to mysid shrimp (Americamysis bahia): Validation of predictive models
Authors: Finch Bryson E. , Marzooghi Solmaz , Di Toro Dominic M. , Stubblefield William A. 
Published: January 2017

Abstract

Crude oils are composed of an assortment of hydrocarbons, some of which are polycyclic aromatic hydrocarbons (PAHs). Polycyclic aromatic hydrocarbons are of particular interest due to their narcotic and potential phototoxic effects. Several studies have examined the phototoxicity of individual PAHs and fresh and weathered crude oils, and several models have been developed to predict PAH toxicity. Fingerprint analyses of oils have shown that PAHs in crude oils are predominantly alkylated. However, current models for estimating PAH phototoxicity assume toxic equivalence between unsubstituted (i.e., parent) and alkyl-substituted compounds. This approach may be incorrect if substantial differences in toxic potency exist between unsubstituted and substituted PAHs. The objective of the present study was to examine the narcotic and photo-enhanced toxicity of commercially available unsubstituted and alkylated PAHs to mysid shrimp (Americamysis bahia). Data were used to validate predictive models of phototoxicity based on the highest occupied molecular orbital–lowest unoccupied molecular orbital (HOMO-LUMO) gap approach and to develop relative effect potencies. Results demonstrated that photo-enhanced toxicity increased with increasing methylation and that phototoxic PAH potencies vary significantly among unsubstituted compounds. Overall, predictive models based on the HOMO-LUMO gap were relatively accurate in predicting phototoxicity for unsubstituted PAHs but are limited to qualitative assessments. Environ Toxicol Chem 2017;36:2043–2049. © 2017 SETAC
Prognostic impact of specific molecular profiles in pediatric acute megakaryoblastic leukemia in non‐Down syndrome
Authors: Hara Yusuke , Shiba Norio , Ohki Kentaro , Tabuchi Ken , Yamato Genki , Park Myoung‐ja , Tomizawa Daisuke , Kinoshita Akitoshi , Shimada Akira , Arakawa Hirokazu , Saito Akiko M. , Kiyokawa Nobutaka , Tawa Akio , Horibe Keizo , Taga Takashi , Adachi Souichi , Taki Tomohiko , Hayashi Yasuhide 
Published: January 2017

AbstractPediatric acute megakaryoblastic leukemia in non‐Down syndrome (AMKL) is a unique subtype of acute myeloid leukemia (AML). Novel CBFA2T3‐GLIS2 and NUP98‐KDM5A fusions recurrently found in AMKL were recently reported as poor prognostic factors. However, their detailed clinical and molecular characteristics in patients treated with recent improved therapies remain uncertain. We analyzed molecular features of 44 AMKL patients treated on two recent Japanese AML protocols, the AML99 and AML‐05 trials. We identified CBFA2T3‐GLIS2, NUP98‐KDM5A, RBM15‐MKL1, and KMT2A rearrangements in 12 (27%), 4 (9%), 2 (5%), and 3 (7%) patients, respectively. Among 459 other AML patients, NUP98‐KDM5A was identified in 3 patients, whereas CBFA2T3‐GLIS2 and RBM15‐MKL1 were only present in AMKL. GATA1 mutations were found in 5 patients (11%). Four‐year overall survival (OS) and event‐free survival (EFS) rates of CBFA2T3‐GLIS2‐positive patients in AMKL were 41.7% and 16.7%, respectively. Three‐year cumulative incidence of relapse in CBFA2T3‐GLIS2‐positive patients was significantly higher than that of CBFA2T3‐GLIS2‐negative patients (75.0% vs. 35.7%, P = 0.024). In multivariate analyses, CBFA2T3‐GLIS2 was an independent poor prognostic factor for OS (HR, 4.34; 95% CI, 1.31–14.38) and EFS (HR, 2.95; 95% CI, 1.20–7.23). Furthermore, seven (54%) of 13 infant AMKL patients were CBFA2T3‐GLIS2‐positive. Notably, out of 7 CBFA2T3‐GLIS2‐positive infants, six (86%) relapsed and five (71%) died. Moreover, all of CBFA2T3‐GLIS2‐positive patients who experienced induction failure (n = 3) were infants, indicating worse prognosis of CBFA2T3‐GLIS2‐positive infants. These findings indicated the significance of CBFA2T3‐GLIS2 as a poor prognostic factor in AMKL patients, particularly in infants.
Assessment of river flow with significant lateral inflow through reverse routing modeling
Authors: Spada Eleonora , Sinagra Marco , Tucciarelli Tullio , Barbetta Silvia , Moramarco Tommaso , Corato Giovanni 
Published: January 2017

AbstractThe discharge hydrograph estimation in rivers based on reverse routing modeling and using only water level data at two gauged sections is here extended to the most general case of significant lateral flow contribution, without needing to deploy rainfall–runoff procedures. The proposed methodology solves the Saint‐Venant equations in diffusive form also involving the lateral contribution using a “head‐driven” modeling approach where lateral inflow is assumed to be function of the water level at the tributary junction. The procedure allows to assess the discharge hydrograph at ends of a selected river reach with significant lateral inflow, starting from the stage recorded there and without needing rainfall data.Specifically, the MAST 1D hydraulic model is applied to solve the diffusive wave equation using the observed stage hydrograph at the upstream section as upstream boundary condition. The other required data are (a) the observed stage hydrograph at the downstream section, as benchmark for the parameter calibration, and (b) the bathymetry of the river reach, from the upstream section to a short distance after the downstream gauged section. The method is validated with different flood events observed in two river reaches with a significant intermediate basin, where reliable rating curves were available, selected along the Tiber River, in central Italy, and the Alzette River, in Luxembourg. Very good performance indices are found for the computed discharge hydrographs at both the channel ends and along the tributaries. The mean Nash‐Sutcliffe value (NSq) at the channel ends of two rivers is found equal to 0.99 and 0.86 for the upstream and downstream sites, respectively. The procedure is also validated on a longer stretch of the Tiber River including three tributaries for which appreciable results are obtained in terms of NSq for the computed discharge hydrographs at both the channel ends for three investigated flood events.
Long Non‐Coding RNA MALAT1 Interacts With miR‐204 to Modulate Human Hilar Cholangiocarcinoma Proliferation, Migration, and Invasion by Targeting CXCR4
Authors: Tan Xinyu , Huang Zhiguo , Li Xiaogang 
Published: January 2017

ABSTRACTMetastasis‐associated lung adenocarcinoma transcript 1 (MALAT1) is involved in the development and progression of many types of tumors. An aberrant expression of MALAT1 was observed in many kinds of cancers. However, the exact effects and molecular mechanisms of MALAT1 in human hilar cholangiocarcinoma (HCCA) progression are still unknown. Here, we investigated the role of MALAT1 in human HCCA cell lines and clinical tumor samples in order to determine the function of this lncRNA. In our research, lncRNA‐MALAT1 was specifically upregulated in HCCA tissues and cell lines, and was associated with pathological T stage, a larger tumor size, and perineural invasion. Knockdown of MALAT1 inhibited the proliferation, migration, and invasion of human HCCA cell. In addition, chemokine receptor‐4 (CXCR4) was involved in MALAT1 induced human HCCA growth, migration, and invasion. By using online tools and a series of mechanistic analysis, we also demonstrated that miR‐204‐dependent CXCR4 regulation was required in MALAT1 modulating HCCA cell growth, migration and invasion. Taken together, our data indicated that MALAT1 might play an oncogenic role in HCCA through miR‐204‐dependent CXCR4 regulation, and could be regarded as a therapeutic target in HCCA. J. Cell. Biochem. 118: 3643–3653, 2017. © 2017 Wiley Periodicals, Inc.
MutY DNA Glycosylase Protects Cells From Tumor Necrosis Factor Alpha‐Induced Necroptosis
Authors: Tran An Hue Vy , Han Se Hee , Kim Joon , Grasso Francesca , Kim In San , Han Ye Sun 
Published: January 2017

ABSTRACTNumerous studies have implied that mutY DNA glycosylase (MYH) is involved in the repair of post‐replicative mispairs and plays a critical role in the base excision repair pathway. Recent in vitro studies have shown that MYH interacts with tumor necrosis factor receptor type 1‐associated death domain (TRADD), a key effector protein of tumor necrosis factor receptor‐1 (TNFR1) signaling. The association between MYH and TRADD is reversed during tumor necrosis factor alpha (TNF‐α)‐ and camptothecin (CPT)‐induced apoptosis, and enhanced during TNF‐α‐induced survival. After investigating the role of MYH interacts with various proteins following TNF‐α stimulation, here, we focus on MYH and TRADD interaction functions in necroptosis and its effects to related proteins. We report that the level of the MYH and TRADD complex was also reduced during necroptosis induced by TNF‐α and zVAD‐fmk. In particular, we also found that MYH is a biologically important necrosis suppressor. Under combined TNF‐α and zVAD‐fmk treatment, MYH‐deficient cells were induced to enter the necroptosis pathway but primary mouse embryonic fibroblasts (MEFs) were not. Necroptosis in the absence of MYH proceeds via the inactivation of caspase‐8, followed by an increase in the formation of the kinase receptor‐ interacting protein 1 (RIP1)‐RIP3 complex. Our results suggested that MYH, which interacts with TRADD, inhibits TNF‐α necroptotic signaling. Therefore, MYH inactivation is essential for necroptosis via the downregulation of caspase‐8. J. Cell. Biochem. 118: 1827–1838, 2017. © 2017 Wiley Periodicals, Inc.
Use of partially purified peroxidase of agricultural by‐product rice bran in deoxynivalenol reduction
Authors: Gautério Gabrielle Victoria , Malta Danielle Specht , Reginatto Laís , Feltrin Ana Carla Penteado , Garda‐Buffon Jaqueline , Kalil Susana Juliano 
Published: January 2017

AbstractBACKGROUNDOnce peroxidase purification can improve substrate degradation capacity, peroxidase from rice bran was purified by expanded bed adsorption (EBA) coupled to diafiltration/ultrafiltration (DF/UF) and applied for deoxynivalenol (DON) reduction.RESULTSThe DF/UF step was optimized according to membrane molecular weight cutoff (MWCO), DF cycles number, operation temperature and CaCl2
addition to the DF buffer. DON reduction tests were carried out with both clarified and purified peroxidase. The use of MWCO of 10 kDa, 10 °C, six DF cycles and adding 4 mmol L−1 CaCl2
to DF buffer promoted enzyme purification of 4.4‐fold and enzymatic recovery of 79.4%. The global purification process combining two techniques resulted in enzyme purification of 75.1‐fold with an enzymatic recovery of 22.8%. Peroxidase purified by EBA combined with DF/UF resulted in DON reduction of 81.7% in a model system.CONCLUSIONPeroxidase purification was achieved by scale‐up integrated strategies. The use of purified peroxidase from agricultural by‐products could be a promising alternative for enzymatic DON levels reduction. © 2017 Society of Chemical Industry