bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Denoising Method Based on Kernel Principal Component Analysis for Airborne Time‐Domain Electromagnetic Data
Authors: Bin CHEN , Cong‐De LU , Guang‐Ding LIU 
Published: April 2014

AbstractAirborne time‐domain electromagnetic (ATEM) data usually contain natural and cultural noise, which can lower data quality, influence inversion accuracy or even lead to incorrect interpretation if it is not removed from data using an appropriate filter. To solve this problem, this work suggests a denosing method based on kernel principal component analysis. Firstly, it extracts the principal component from stacked decay curves. Then the useful signals, which are associated with subsurface media, and noise are separated using the energy ratio. Finally, these signals are used to perform reconstruction. This method can not only remove natural noise such as spikes or oscillation caused by sferies, but also effectively suppress cultural noise. Using this method and the AeroTEM software, the real ATEM data from a helicopter survey is processed separately. Comparison of the results shows that the denoising effect of the method suggested by this paper is superior to that of the AeroTEM software.
Nonlinear Dimensionality Reduction for Visualizing Toxicity Data: Distance‐Based Versus Topology‐Based Approaches
Authors: Kireeva Natalia V. , Ovchinnikova Svetlana I. , Tetko Igor V. , Asiri Abdullah M. , Balakin Konstantin V. , Tsivadze Aslan Yu. 
Published: April 2014

AbstractOver the years, a number of dimensionality reduction techniques have been proposed and used in chemoinformatics to perform nonlinear mappings. In this study, four representatives of nonlinear dimensionality reduction methods related to two different families were analyzed: distance‐based approaches (Isomap and Diffusion Maps) and topology‐based approaches (Generative Topographic Mapping (GTM) and Laplacian Eigenmaps). The considered methods were applied for the visualization of three toxicity datasets by using four sets of descriptors. Two methods, GTM and Diffusion Maps, were identified as the best approaches, which thus made it impossible to prioritize a single family of the considered dimensionality reduction methods. The intrinsic dimensionality assessment of data was performed by using the Maximum Likelihood Estimation. It was observed that descriptor sets with a higher intrinsic dimensionality contributed maps of lower quality. A new statistical coefficient, which combines two previously known ones, was proposed to automatically rank the maps. Instead of relying on one of the best methods, we propose to automatically generate maps with different parameter values for different descriptor sets. By following this procedure, the maps with the highest values of the introduced statistical coefficient can be automatically selected and used as a starting point for visual inspection by the user.
The Discovery of Potent Nonstructural Protein 5A (NS5A) Inhibitors with a Unique Resistance Profile—Part 2
Authors: Wakenhut Florian , Tran Thien Duc , Pickford Chris , Shaw Stephen , Westby Mike , Smith‐Burchnell Caroline , Watson Lesa , Paradowski Michael , Milbank Jared , Stonehouse David , Cheung Kathy , Wybrow Robert , Daverio Felice , Crook Samuel , Statham Keith , Leese David , Stead Darren , Adam Fiona , Hay Duncan , Roberts Lee R. , Chiva Jean‐Yves , Nichols Carly , Blakemore David C. , Goetz Gilles H. , Che Ye , Gardner Iain , Dayal Satish , Pike Andrew , Webster Rob , Pryde David C. 
Published: April 2014

AbstractIn ongoing studies towards novel hepatitis C virus (HCV) therapeutics, inhibitors of nonstructural protein 5A (NS5A) were evaluated. Specifically, starting from previously reported lead compounds, peripheral substitution patterns of a series of biaryl‐linked pyrrolidine NS5A replication complex inhibitors were probed and structure–activity relationships were elucidated. Using molecular modelling and a supercritical fluid chromatographic (SFC) technique, intramolecular H‐bonding and peripheral functional group topology were evaluated as key determinants of activity and membrane permeability. The novel compounds exhibited retained potency as compared with the lead compounds, and also showed promising results against a panel of resistance viruses. Together, the results of the study take us a step closer towards understanding the potency of daclatasvir, a clinical candidate upon which the compounds were based, and to designing improved analogues as second‐generation antiviral agents targeting NS5A.
Location and Conformation of Amyloid β(25–35) Peptide and its Sequence‐Shuffled Peptides within Membranes: Implications for Aggregation and Toxicity in PC12 Cells
Authors: Tsai Hui‐Hsu Gavin , Lee Jian‐Bin , Shih Yuan‐Ci , Wan Lei , Shieh Fa‐Kuen , Chen Chin‐Yu 
Published: April 2014

AbstractExtracellular deposits of amyloid β (Aβ) aggregates in the brain is the hallmark of Alzheimer’s disease. We present the configurations (location and conformation) and the interfacial folding and membrane insertion mechanisms of Aβ fragments, wild‐type Aβ(25–35), Aβ(35–25), and a sequence‐shuffled peptide [Aβ(25–35)‐shuffled] from Aβ(25–35) within membranes by replica‐exchange molecular dynamics simulations. Although these peptides have the same amino acid composition, simulations show they have distinct locations and conformations within membranes. Moreover, our in vitro experiments show that these peptides have distinct neurotoxicities. We rationalize the distinct neurotoxicities of these peptides in terms of their simulated locations and conformations in membranes. This work provides another view that complements the general hydrophobicity–toxicity views, to better explain the neurotoxicity of Aβ peptides.
Inhibition of Cathepsin Activity in a Cell‐Based Assay by a Light‐Activated Ruthenium Compound
Authors: Respondek Tomasz , Sharma Rajgopal , Herroon Mackenzie K. , Garner Robert N. , Knoll Jessica D. , Cueny Eric , Turro Claudia , Podgorski Izabela , Kodanko Jeremy J. 
Published: April 2014

AbstractLight‐activated inhibition of cathepsin activity was demonstrated in a cell‐based assay. Inhibitors of cathepsin K, Cbz‐Leu‐NHCH2CN (2) and Cbz‐Leu‐Ser(OBn)‐CN (3), were caged within the complexes cis‐[Ru(bpy)2(2)2]Cl2 (4) and cis‐[Ru(bpy)2(3)2](BF4)2 (5) (bpy=2,2′‐bipyridine) as 1:1 mixtures of Δ and Λ stereoisomers. Complexes 4 and 5 were characterized by 1H NMR, IR, and UV/Vis spectroscopies and electrospray mass spectrometry. Photochemical experiments confirm that 4 releases two molecules of 2 upon exposure to visible light for 15 min, whereas release of 3 by 5 requires longer irradiation times. IC50 determinations against purified cathepsin K under light and dark conditions with 4 and 5 confirm that inhibition is enhanced from 35‐ to 88‐fold, respectively, upon irradiation with visible light. No apparent toxicity was observed for 4 in the absence or presence of irradiation in bone marrow macrophage (BMM) or PC3 cells, as determined by MTT assays, at concentrations up to 10 μM. Compound 5 is well tolerated at lower concentrations (<1 μM), but does show growth‐inhibitory effects at higher concentrations. Confocal microscopy experiments show that 4 decreases intracellular cathepsin activity in osteoclasts with light activation. These results support the further development of caged nitrile‐based inhibitors as chemical tools for investigating spatial aspects of proteolysis within living systems.
Caulerpenyne and Related Bis‐enol Esters Are Novel‐Type Inhibitors of Human 5‐Lipoxygenase
Authors: Richter Phillipp , Schubert Gregor , Schaible Anja Maria , Cavas Levent , Werz Oliver , Pohnert Georg 
Published: April 2014

AbstractCaulerpenyne (CYN) is a sesquiterpene from green algae with known inhibitory properties against soybean lipoxygenase. Here we introduce a detailed structure–activity study elucidating the inhibitory effects of CYN and a library of six synthetic CYN analogues on isolated human 5‐lipoxygenase (5‐LO) and cellular 5‐LO in polymorphonuclear leukocytes. Essential structural elements are identified and a structurally simplified inhibitor is introduced. The modes of 5‐LO inhibition by CYN and the synthetic inhibitors cannot be assigned to any of the known categories of lipoxygenase inhibitors. These compounds clearly interfere directly with 5‐LO and represent rather small and flexible molecules, with unique structures among 5‐LO inhibitors identified thus far.
OB‐IMA: out‐of‐the‐box integrity measurement approach for guest virtual machines
Authors: Xing Bin , Han Zhen , Chang Xiaolin , Liu Jiqiang 
Published: April 2014

SummaryInfrastructure as a Service cloud provides elasticity and scalable virtual machines (VMs) as computing service to multiple tenants, but the tenants lose the full control of their data. Measuring the integrity of critical files of the VMs and providing the integrity attestation to the tenants on the basis of TCG trusted computing techniques is an effective way to alleviate their anxiety. This paper considers how to measure the integrity of the processes run in guest VMs and files opened in guest VMs. We propose an out‐of‐the‐box integrity measurement approach to measure the integrity of critical files through system call (syscall) interception without any modification of the guest VMs. Out‐of‐the‐box integrity measurement approach can not only measure the integrity of all files that have been considered by existing approaches but also measure the integrity of the system configuration files, program loaders, and script interpreters, which affect the system behaviors and integrity. The ability of supporting both system and manual measurement policies makes our approach flexible. We implement this approach in Xen hypervisor with little modification of the existing syscall interception method, and this approach can be ported to other virtualization platform easily. Copyright © 2014 John Wiley & Sons, Ltd.
A Metallocene Molecular Complex as Visible‐Light Absorber for High‐Voltage Organic–Inorganic Hybrid Photovoltaic Cells
Authors: Ishii Ayumi , Miyasaka Tsutomu 
Published: April 2014

AbstractA thin solid‐state dye‐sensitized photovoltaic cell is fabricated by composing organic and inorganic heterojunctions in which the visible‐light sensitizers are cyclopentadiene derivatives (Cp*) coordinated to a metal oxide, typically TiO2. The coordination bonds of the metallocene molecular complex (Ti–Cp*) create a new LMCT (ligand‐to‐metal charge transfer) absorption band and induce a rectified charge transfer from the organic ligands to TiO2, leading to photocurrent generation. Photovoltaic junctions are completed by coating crystalline organic molecules (perylene) as a hole‐transport layer on the Cp*‐coordinated TiO2 surface by using the vapor deposition method. The molecular plane of Cp* on the TiO2 surfaces seems to help the hole‐transport layer to form ordered structures, which effectively improve carrier conductivities and minimize interfacial resistance. The organic–inorganic hybrid thin‐film photocell with metallocene molecular complexes is capable of generating high open‐circuit voltages exceeding 1.2 V.
From Molecular Structures of Ionic Liquids to Predicted Retention of Fatty Acid Methyl Esters in Comprehensive Two‐Dimensional Gas Chromatography
Authors: Kulsing Chadin , Nolvachai Yada , Zeng Annie Xu , Chin Sung‐Tong , Mitrevski Blagoj , Marriott Philip J. 
Published: April 2014

AbstractIonic liquids (ILs) are attractive stationary phases to broaden selectivity in gas chromatography (GC). The rational design, selection and application of ILs in comprehensive two‐dimensional GC is a desirable goal. In this study, methods to predict two‐dimensional chromatograms of fatty acid methyl esters (FAMEs) starting from given structures of IL stationary phases and their interactions with FAME solutes are described. Molecular parameters of the dipole moment, lowest unoccupied molecular orbital energy and molar volume of different ILs were calculated by using Gaussian 09. With established correlations between molecular simulation and linear solvation energy relationships, molecular parameters were converted to s, e and l values for stationary phase descriptors. This allowed reliable prediction of the equivalent chain length of FAMEs on each IL column (with the correlation R2=0.98). Isovolatility curves in GC×GC space of reference saturated FAMEs were then determined for each IL column to take into account the dependence of retention time on temperature in temperature‐programmed separation. The resulting predicted GC×GC chromatograms were compared with previously reported experimental results. Correlations with R2 values of 0.99 and 0.98 were achieved for the first‐ and second‐dimension retention times, respectively.
Characterization of Scrape‐Off Layer Turbulence Changes Induced by a Non‐Axisymmetric Magnetic Perturbation in an ASDEX Upgrade Low Density L‐Mode
Authors: Müller H. W. , Carralero D. , Birkenmeier G. , Conway G. D. , Fischer R. , Happel T. , Manz P. , Suttrop W. , Wolfrum E. , ASDEX Upgrade Team  
Published: April 2014

AbstractIn the tokamak ASDEX Upgrade the influence of a non‐axisymmetric n = 2 error field on the turbulence in the far scrape‐off layer of a low density L‐mode discharge has been studied. There is no density pump‐out with the non‐axisymmetric perturbation but an increase of the scrape‐off layer density at the outer midplane. While the relative ion saturation current fluctuation level in the far scrape‐off layer is decreasing, the skewness rises and especially the excess kurtosis grows by a factor of 1.5–3. The frequency of intermittent events (blobs) is increasing by 50 %. Also the poloidal velocity grows with the magnetic perturbation while the typical turbulent structure size becomes smaller by a factor 5–10 about 20–25 mm outside the separatrix. The local spectral density has been calculated from a two‐point measurement of the ion saturation current. It is used to derive a dispersion relation. Two poloidal propagation velocities depending on the wave number have been found. One is an upper limit for the bulk E × B velocity and the second one the lower limit of the phase velocity. There is a significant contribution of the phase velocity to the propagation speed in the far scrape‐off layer. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Developmental and contextual considerations for adrenal and gonadal hormone functioning during adolescence: Implications for adolescent mental health
Authors: Marceau Kristine , Ruttle Paula L. , Shirtcliff Elizabeth A. , Essex Marilyn J. , Susman Elizabeth J. 
Published: April 2014

ABSTRACTSubstantial research has implicated the hypothalamic‐pituitary‐adrenal (HPA) and hypothalamic‐pituitary‐gonadal (HPG) axes independently in adolescent mental health problems, though this literature remains largely inconclusive. Given the cross‐talk between the HPA and HPG axes and their increased activation in adolescence, a dual‐axis approach that examines both axes simultaneously is proposed to predict the emergence and persistence of adolescent mental health problems. After briefly orienting readers to HPA and HPG axis functioning, we review the literature examining associations between hormone levels and changes with behavior during adolescence. Then, we provide a review of the literature supporting examination of both axes simultaneously and present the limited research that has taken a dual‐axis approach. We propose future directions including consideration of between‐person and within‐person approaches to address questions of correlated changes in HPA and HPG hormones. Potential moderators are considered to increase understanding of the nuanced hormone–behavior associations during key developmental transitions. © 2014 Wiley Periodicals, Inc. Dev Psychobiol 57: 742–768, 2015.
Cardio‐adipose tissue cross‐talk: relationship between adiponectin, plasma pro brain natriuretic peptide and incident heart failure
Authors: Lindberg Søren , Jensen Jan Skov , Bjerre Mette , Pedersen Sune H. , Frystyk Jan , Flyvbjerg Allan , Mogelvang Rasmus 
Published: April 2014

AimsThere is increasing evidence of cross‐talk between the heart, body metabolism, and adipose tissue, but the precise mechanisms are poorly understood. Natriuretic peptides (NPs) have recently emerged as the prime candidate for a mediator. In patients with heart failure (HF), infusion of NPs increases adiponectin secretion, indicating that NPs may improve adipose tissue function and in this way function as a cardio‐protective agent in HF. Accordingly we investigated the interplay between plasma adiponectin, plasma proBNP, and development of HF.Methods and resultsWe prospectively followed 5574 randomly selected men and women from the community without ischaemic heart disease or HF. Plasma adiponectin and proBNP were measured at study entry. Median follow‐up time was 8.5 years (interquartile range 8.0–9.1 years). During follow‐up 271 participants developed symptomatic HF. Plasma adiponectin and proBNP were strongly associated (P < 0.001). Participants with increasing adiponectin had increased risk of incident HF (P < 0.001). After adjustment for confounding risk factors (including age, gender, smoking status, body mass ratio, waist–hip ratio, glucose, glycated haemoglobin, systolic and diastolic blood pressure, lipid profile, high sensitivity C‐reactive protein, estimated glomerular filtration rate, and physical activity) by Cox regression analysis, adiponectin remained an independent predictor of HF: the hazard ratio (HR) per 1 standard deviation (SD) increase in adiponectin was 1.20 [95% confidence interval (CI) 1.06–1.30; P = 0.003]. However, the association vanished when plasma proBNP was included in the analysis, HR 1.08 (95% CI 0.95–1.23; P = 0.26).ConclusionsIn conclusion, plasma adiponectin and proBNP are strongly associated. Increasing plasma adiponectin is associated with increased risk of HF. However, concomitantly elevated proBNP levels appear to explain the positive association between adiponectin and risk of HF.
Differential presentation of endogenous and exogenous hepatitis B surface antigens influences priming of CD8+ T cells in an epitope‐specific manner
Authors: Riedl Petra , Reiser Michael , Stifter Katja , Krieger Jana , Schirmbeck Reinhold 
Published: April 2014

Little is known about whether presentation of endogenous and exogenous hepatitis B virus (HBV) surface antigens on APCs targeted by vaccination and/or virus‐harboring hepatocytes influences de novo priming of CD8+ T cells. We showed that surface antigen‐expressing transfectants exclusively display a Kb/S190 epitope, whereas cells pulsed with recombinant surface particles (rSPs) exclusively present a Kb/S208 epitope to CD8+ T cells. The differential presentation of these epitopes largely reflects the selective, but not exclusive, priming of Kb/S190‐ and Kb/S208‐specific T cells in C57BL/6 mice by endogenous/DNA‐ or exogenous/protein‐based vaccines, respectively. Silencing the Kb/S190 epitope (Kb/S190V194F) in antigen‐expressing vectors rescued the presentation of the Kb/S208 epitope in stable transfectants and significantly enhanced priming of Kb/S208‐specific T cells in C57BL/6 mice. A Kb/S190‐mediated immunodominance operating in surface antigen‐expressing cells, but not in rSP‐pulsed cells, led to an efficient suppression in the presentation of the Kb/S208 epitope and a consequent decrease in the priming of Kb/S208‐specific T cells. This Kb/S190‐mediated immunodominance also operated in 1.4HBV‐Smut transgenic (tg) hepatocytes selectively expressing endogenous surface antigens and allowed priming of Kb/S208‐ but not Kb/S190‐specific T cells in 1.4HBV‐Smut tg mice. However, IFN‐γ+ Kb/S208‐specific T cells could not inhibit HBV replication in the liver of 1.4HBV‐Smut tg mice. These results have practical implications for the design of T‐cell‐stimulating therapeutic vaccines.
Stimulation through very late antigen‐4 and ‐5 improves the multifunctionality and memory formation of CD8+ T cells
Authors: Hosoi Hayato , Ikeda Hiroaki , Imai Naoko , Amaike Chisaki , Wang Linan , Orito Yuki , Yamane Makiko , Ueno Hiroaki , Ideno Mitsuko , Nukaya Ikuei , Enoki Tatsuji , Mineno Junichi , Takesako Kazutoh , Hirano Satoshi , Shiku Hiroshi 
Published: April 2014

T cells express multiple integrin molecules. The significance of signaling through these molecules on acquisition of T‐cell effector functions and memory formation capacity remains largely unknown. Moreover, the impact of stimulation through these signals on the generation of T cells for adoptive immunotherapy has not been elucidated. In this study, using a recombinant fragment of fibronectin, CH‐296, we demonstrated that stimulation via very late Ag (VLA)‐4 and VLA‐5 in human and BALB/c mouse CD8+ T cells, in combination with TCR stimulation, enhances effector multifunctionality and in vivo memory formation. Using TCR‐transgenic mouse‐derived CD8+ T cells expressing TCR specific for the syngeneic CMS5 fibrosarcoma‐derived tumor Ag, we showed that stimulation by CH‐296 improved the ability of tumor‐specific CD8+ T cells to inhibit CMS5 tumor growth when adoptively transferred into hosts with progressing tumors. Improved antitumor effects were associated with decreased infiltration of Foxp3+CD4+ Treg cells in tumors. These results suggest that stimulation via VLA‐4 and VLA‐5 modulates the qualities of effector T cells and could potentially increase the efficacy of adoptive therapy against cancer.
Relative Kinetic Reactivities of Boronic Acids and Boronate Ions toward 1,2‐Diols
Authors: Okamoto Takuya , Tanaka Asumi , Watanabe Eisuke , Miyazaki Takehiro , Sugaya Tomoaki , Iwatsuki Satoshi , Inamo Masahiko , Takagi Hideo D. , Odani Akira , Ishihara Koji 
Published: April 2014

AbstractThe following reaction systems, with and without proton ambiguity, were set up for direct measurements of the rate constants of borate and boronate ions: boric acid [B(OH)3] and 4,5‐dihydroxy‐1,3‐benzenedisulfonic acid disodium salt (Tiron); 3‐nitrophenylboronic acid [3‐NO2PhB(OH)2] and Tiron; phenylboronic acid [PhB(OH)2] and 4‐nitrocatechol; boric acid and 4‐nitrocatechol. Each rate constant for boric or boronic acid is larger than that for the conjugate borate or boronate ion for the reaction systems without proton ambiguity. These results explicitly indicate that the widespread belief that the rate constants of boronate ions are several orders of magnitude larger than those of the conjugate boronic acids is erroneous. The relative kinetic reactivities of RB(OH)2 and RB(OH)3– were investigated in relation to the linear free energy relationships between the rate constants and acidities of the boronic acids and diols.
Domino Recombinant γ‐Isomerization and Reverse Wacker Oxidation of γ‐Vinyl‐γ‐butyrolactone: Synthesis of (+)‐trans‐, (–)‐ and (+)‐Disparlures
Authors: Bethi Venkati , Kattanguru Pullaiah , Fernandes Rodney A. 
Published: April 2014

AbstractA domino palladium‐catalyzed recombinant γ‐isomerization and reverse Wacker oxidation of γ‐vinyl‐γ‐butyrolactone has been explored. The strategy has been used in the stereoselective synthesis of (+)‐trans‐, (–)‐ and (+)‐disparlures. The synthesis was achieved in seven to eight steps from D‐glucono‐δ‐lactone with overall yields of 19.3, 20.7 and 22.6 %, respectively.