Open Access. Powered by Scholars. Published by Universities.®
- Keyword
-
- Articles (4)
- Carbonyl derivative (2)
- Protein stability (2)
- Alternative stable states (1)
- Amino acids (1)
-
- Approximation bounds (1)
- Aqueous acids (1)
- Bacterial phosphotransferase system (1)
- Basic conditions (1)
- Beamforming (1)
- Benzoxaborole (1)
- Biosensors (1)
- Boronic acid derivative (1)
- CH4 flux (1)
- Cardinality constrained quadratic program (1)
- Chains (1)
- Chemical structure (1)
- Chemistry (1)
- Chromatographic retention factors (1)
- Common carp (1)
- Computational approach (1)
- Computational complexity (1)
- Conformational stabilities (1)
- Crystal structure (1)
- Cyprinus carpio (1)
- Decomposition (1)
- Dipole interactions (1)
- Disease diagnostics (1)
- Disturbance (1)
- Donor and acceptor (1)
Articles 1 - 19 of 19
Full-Text Articles in Entire DC Network
The North American Carbon Program Multi-Scale Synthesis And Terrestrial Model Intercomparison Project – Part 1: Overview And Experimental Design, D. N. Huntzinger, C. Schwalm, A, M, Michalak, K. Schaefer, A. W. King, Y. Wei, A. Jacobson, S. Liu, R. B. Cook, W. M. Post, G. Berthier, D Hayes, M. Huang, A. Ito, H. Lei, Chaoqun (Crystal) Lu, J. Mao, C. H. Peng, S. Peng, B. Poulter, D. Ricciuto, X. Shi, Hanqin Tian, W. Wang, N. Zeng, F. Zhao, Q. Zhu
The North American Carbon Program Multi-Scale Synthesis And Terrestrial Model Intercomparison Project – Part 1: Overview And Experimental Design, D. N. Huntzinger, C. Schwalm, A, M, Michalak, K. Schaefer, A. W. King, Y. Wei, A. Jacobson, S. Liu, R. B. Cook, W. M. Post, G. Berthier, D Hayes, M. Huang, A. Ito, H. Lei, Chaoqun (Crystal) Lu, J. Mao, C. H. Peng, S. Peng, B. Poulter, D. Ricciuto, X. Shi, Hanqin Tian, W. Wang, N. Zeng, F. Zhao, Q. Zhu
Chaoqun (Crystal) Lu
Terrestrial biosphere models (TBMs) have become an integral tool for extrapolating local observations and understanding of land–atmosphere carbon exchange to larger regions. The North American Carbon Program (NACP) Multi-scale synthesis and Terrestrial Model Intercomparison Project (MsTMIP) is a formal model intercomparison and evaluation effort focused on improving the diagnosis and attribution of carbon exchange at regional and global scales. MsTMIP builds upon current and past synthesis activities, and has a unique framework designed to isolate, interpret, and inform understanding of how model structural differences impact estimates of carbon uptake and release. Here we provide an overview of the MsTMIP effort …
Interplay Of Hydrogen Bonds And N→Π* Interactions In Proteins, Gail J. Bartlett, Robert W. Newberry, Brett Vanveller, Ronald T. Raines, Derek N. Woolfson
Interplay Of Hydrogen Bonds And N→Π* Interactions In Proteins, Gail J. Bartlett, Robert W. Newberry, Brett Vanveller, Ronald T. Raines, Derek N. Woolfson
Brett VanVeller
Protein structures are stabilized by multiple weak interactions, including the hydrophobic effect, hydrogen bonds, electrostatic effects, and van der Waals interactions. Among these interactions, the hydrogen bond is distinct in having its origins in electron delocalization. Recently, another type of electron delocalization, the n→π* interaction between carbonyl groups, has been shown to play a role in stabilizing protein structure. Here we examine the interplay between hydrogen bonding and n→π* interactions. To address this issue, we used data available from high-resolution protein crystal structures to interrogate asparagine side-chain oxygen atoms that are both acceptors of a hydrogen bond and donors of …
Ionic Liquids In Analytical Chemistry: Fundamentals, Advances, And Perspectives, Tien D. Ho, Cheng Zhang, Leandro W. Hantao, Jared L. Anderson
Ionic Liquids In Analytical Chemistry: Fundamentals, Advances, And Perspectives, Tien D. Ho, Cheng Zhang, Leandro W. Hantao, Jared L. Anderson
Jared L. Anderson
Since their initial discovery in 1914, ionic liquids (ILs) have been widely studied in multiple chemistry disciplines. Applications of ILs in analytical chemistry have enjoyed much success and contributed to the rapid evolution of the ionic liquid field. ILs are collectively known as organic salts which possess melting points at or below 100 °C. In most cases, ILs are composed of an organic cation and an organic or inorganic anion. It has been estimated there can be up to 1018 possible combinations of ILs, due to the ability to interchange their corresponding cationic/anionic moieties.
Defining The Value Of Injection Current And Effective Electrical Contact Area For Egain-Based Molecular Tunneling Junctions, Felice C. Simeone, Hyo Jae Yoon, Martin M. Thuo, Jabulani R. Barber, Barbara Smith, George M. Whitesides
Defining The Value Of Injection Current And Effective Electrical Contact Area For Egain-Based Molecular Tunneling Junctions, Felice C. Simeone, Hyo Jae Yoon, Martin M. Thuo, Jabulani R. Barber, Barbara Smith, George M. Whitesides
Martin M. Thuo
Analysis of rates of tunneling across self-assembled monolayers (SAMs) of n-alkanethiolates SCn (with n = number of carbon atoms) incorporated in junctions having structure AgTS-SAM//Ga2O3/EGaIn leads to a value for the injection tunnel current density J0 (i.e., the current flowing through an ideal junction with n = 0) of 103.6±0.3 A·cm–2 (V = +0.5 V). This estimation of J0 does not involve an extrapolation in length, because it was possible to measure current densities across SAMs over the range of lengths n = 1–18. This value of J0 is estimated under the assumption that values of the geometrical contact area …
A Microfluidic Paper-Based Electrochemical Biosensor Array For Multiplexed Detection Of Metabolic Biomarkers, Chen Zhao, Martin M. Thuo, Xinyu Liu
A Microfluidic Paper-Based Electrochemical Biosensor Array For Multiplexed Detection Of Metabolic Biomarkers, Chen Zhao, Martin M. Thuo, Xinyu Liu
Martin M. Thuo
Paper-based microfluidic devices have emerged as simple yet powerful platforms for performing low-cost analytical tests. This paper reports a microfluidic paper-based electrochemical biosensor array for multiplexed detection of physiologically relevant metabolic biomarkers. Different from existing paper-based electrochemical devices, our device includes an array of eight electrochemical sensors and utilizes a handheld custom-made electrochemical reader (potentiostat) for signal readout. The biosensor array can detect several analytes in a sample solution and produce multiple measurements for each analyte from a single run. Using the device, we demonstrate simultaneous detection of glucose, lactate and uric acid in urine, with analytical performance comparable to …
Detection Of Boronic Acids Through Excited-State Intramolecular Proton-Transfer Fluorescence, Matthew R. Aronoff, Brett Vanveller, Ronald T. Raines
Detection Of Boronic Acids Through Excited-State Intramolecular Proton-Transfer Fluorescence, Matthew R. Aronoff, Brett Vanveller, Ronald T. Raines
Brett VanVeller
Boronic acids are versatile reagents for the chemical synthesis of organic molecules. They and other boron-containing compounds can be detected readily by the interruption of the excited-state intramolecular proton transfer (ESIPT) of 10-hydroxybenzo[h]quinolone. This method is highly sensitive and selective, and useful for monitoring synthetic reactions and detecting boron-containing compounds on a solid support.
Joint User Grouping And Linear Virtual Beamforming: Complexity, Algorithms And Approximation Bounds, Mingyi Hong, Zi Xu, Meisam Razaviyayn, Zhi-Quan Luo
Joint User Grouping And Linear Virtual Beamforming: Complexity, Algorithms And Approximation Bounds, Mingyi Hong, Zi Xu, Meisam Razaviyayn, Zhi-Quan Luo
Mingyi Hong
In a wireless system with a large number of distributed nodes, the quality of communication can be greatly improved by pooling the nodes to perform joint transmission/reception. In this paper, we consider the problem of optimally selecting a subset of nodes from potentially a large number of candidates to form a virtual multi-antenna system, while at the same time designing their joint linear transmission strategies. We focus on two specific application scenarios: 1) multiple single antenna transmitters cooperatively transmit to a receiver; 2) a single transmitter transmits to a receiver with the help of a number of cooperative relays. We …
A Divalent Protecting Group For Benzoxaboroles, Brett Vanveller, Matthew R. Aronoff, Ronald T. Raines
A Divalent Protecting Group For Benzoxaboroles, Brett Vanveller, Matthew R. Aronoff, Ronald T. Raines
Brett VanVeller
1-Dimethylamino-8-methylaminonaphthalene is put forth as a protecting group for benzoxaboroles. The ensuing complex is fluorescent, charge-neutral, highly stable under basic conditions, stable to anhydrous acid, and readily cleavable in aqueous acid to return the free benzoxaborole.
The Genome And Developmental Transcriptome Of The Strongylid Nematode Haemonchus Contortus, Erich M. Schwarz, Pasi K. Korhonen, Bronwyn E. Campbell, Neil D. Young, Aaron R. Jex, Abdul Jabbar, Ross S. Hall, Alinda Mondal, Adina C. Howe, Jason Pell, Andreas Hofmann, Peter R. Boag, Xing-Quan Zhu, T. Ryan Gregory, Alex Loukas, Brian A. Williams, Igor Antoshechkin, C. Titus Brown, Paul W. Sternberg, Robin B. Gasser
The Genome And Developmental Transcriptome Of The Strongylid Nematode Haemonchus Contortus, Erich M. Schwarz, Pasi K. Korhonen, Bronwyn E. Campbell, Neil D. Young, Aaron R. Jex, Abdul Jabbar, Ross S. Hall, Alinda Mondal, Adina C. Howe, Jason Pell, Andreas Hofmann, Peter R. Boag, Xing-Quan Zhu, T. Ryan Gregory, Alex Loukas, Brian A. Williams, Igor Antoshechkin, C. Titus Brown, Paul W. Sternberg, Robin B. Gasser
Adina Howe
Background The barber's pole worm, Haemonchus contortus, is one of the most economically important parasites of small ruminants worldwide. Although this parasite can be controlled using anthelmintic drugs, resistance against most drugs in common use has become a widespread problem. We provide a draft of the genome and the transcriptomes of all key developmental stages of H. contortus to support biological and biotechnological research areas of this and related parasites. Results The draft genome of H. contortus is 320 Mb in size and encodes 23,610 protein-coding genes. On a fundamental level, we elucidate transcriptional alterations taking place throughout the life …
Paramagnetic Ionic Liquids For Measurements Of Density Using Magnetic Levitation, David K. Bwambok, Martin M. Thuo, Manza B.J. Atkinson, Katherine A. Mirica, Nathan D. Shapiro, George M. Whitesides
Paramagnetic Ionic Liquids For Measurements Of Density Using Magnetic Levitation, David K. Bwambok, Martin M. Thuo, Manza B.J. Atkinson, Katherine A. Mirica, Nathan D. Shapiro, George M. Whitesides
Martin M. Thuo
Paramagnetic ionic liquids (PILs) provide new capabilities to measurements of density using magnetic levitation (MagLev). In a typical measurement, a diamagnetic object of unknown density is placed in a container containing a PIL. The container is placed between two magnets (typically NdFeB, oriented with like poles facing). The density of the diamagnetic object can be determined by measuring its position in the magnetic field along the vertical axis (levitation height, h), either as an absolute value or relative to internal standards of known density. For density measurements by MagLev, PILs have three advantages over solutions of paramagnetic salts in aqueous …
Effect Of Continued Nitrogen Enrichment On Greenhouse Gas Emissions From A Wetland Ecosystem In The Sanjiang Plain, Northeast China: A 5 Year Nitrogen Addition Experiment, Changchun Song, Lili Wang, Hanqin Tian, Deyan Liu, Chaoqun (Crystal) Lu, Xiaofeng Xu, Lihua Zhang, Guisheng Yang, Zhongmei Wan
Effect Of Continued Nitrogen Enrichment On Greenhouse Gas Emissions From A Wetland Ecosystem In The Sanjiang Plain, Northeast China: A 5 Year Nitrogen Addition Experiment, Changchun Song, Lili Wang, Hanqin Tian, Deyan Liu, Chaoqun (Crystal) Lu, Xiaofeng Xu, Lihua Zhang, Guisheng Yang, Zhongmei Wan
Chaoqun (Crystal) Lu
Mounting evidence supports that wetland ecosystems, one of the largest carbon pools on the earth, are exposed to ample nitrogen (N) additions due to atmospheric deposition or N loading from upstream agricultural fertilizer application. However, our understanding of how N enrichment affects the fluxes of greenhouse gases (GHGs) in wetlands is weak. A 5 year N addition experiment was conducted to examine the responses of CH4 and N2O fluxes as well as ecosystem respiration from wetlands in the Sanjiang Plain, Northeast China, through 2005 to 2009. Four levels of N addition (control, 0 kg N ha−1 yr−1; low-level, 60 kg …
N→Π* Interactions Of Amides And Thioamides: Implications For Protein Stability, Robert W. Newberry, Brett Vanveller, Ilia A. Guzei, Ronald T. Raines
N→Π* Interactions Of Amides And Thioamides: Implications For Protein Stability, Robert W. Newberry, Brett Vanveller, Ilia A. Guzei, Ronald T. Raines
Brett VanVeller
Carbonyl–carbonyl interactions between adjacent backbone amides have been implicated in the conformational stability of proteins. By combining experimental and computational approaches, we show that relevant amidic carbonyl groups associate through an n→π* donor–acceptor interaction with an energy of at least 0.27 kcal/mol. The n→π* interaction between two thioamides is 3-fold stronger than between two oxoamides due to increased overlap and reduced energy difference between the donor and acceptor orbitals. This result suggests that backbone thioamide incorporation could stabilize protein structures. Finally, we demonstrate that intimate carbonyl interactions are described more completely as donor–acceptor orbital interactions rather than dipole–dipole interactions.
Continuous, Pulsed And Disrupted Nutrient Subsidy Effects On Ecosystem Productivity, Stability, And Energy Flow, Michael J. Weber, Michael L. Brown
Continuous, Pulsed And Disrupted Nutrient Subsidy Effects On Ecosystem Productivity, Stability, And Energy Flow, Michael J. Weber, Michael L. Brown
Michael J Weber Dr
Resource pulses and subsidies can supply ecosystems with an important source of nutrients that supports additional productivity at multiple trophic levels. Common carp Cyprinus carpio provide ecosystems with a continuous nutrient subsidy through bioturbation and excretion but may also initiate a nutrient pulse through carcass decomposition. We examined how continuous (common carp foraging and excretion), pulsed (carcass decomposition) and disrupted (carp introduced and then removed) nutrient subsidies differed in their ability to alter nutrient availability, ecosystem productivity and stability and energy flow. Nitrogen and phosphorus availability and primary production were highest in pulsed, intermediate in continuous and lowest for disrupted …
Derivative Estimation With Local Polynomial Fitting, Kris De Brabanter, Jos De Brabanter, Bart De Moor, Irene Gijbels
Derivative Estimation With Local Polynomial Fitting, Kris De Brabanter, Jos De Brabanter, Bart De Moor, Irene Gijbels
Kris De Brabanter
We present a fully automated framework to estimate derivatives nonparametrically without estimating the regression function. Derivative estimation plays an important role in the exploration of structures in curves (jump detection and discontinuities), comparison of regression curves, analysis of human growth data, etc. Hence, the study of estimating derivatives is equally important as regression estimation itself. Via empirical derivatives we approximate the qth order derivative and create a new data set which can be smoothed by any nonparametric regression estimator. We derive L1 and L2 rates and establish consistency of the estimator. The new data sets created by this technique are …
Predicting Modes Of Toxic Action From Chemical Structure, Steven P. Bradbury, Christine L. Russom, Steven J. Broderius, Dean J. Hammermeister, Robert A. Drummond, Gilman D. Veith
Predicting Modes Of Toxic Action From Chemical Structure, Steven P. Bradbury, Christine L. Russom, Steven J. Broderius, Dean J. Hammermeister, Robert A. Drummond, Gilman D. Veith
Steven P. Bradbury
Like many of the papers in the Environmental Toxicology and Chemistry “Top 100” list, the development of the fathead minnow database [1] and the assignment of modes of action to the 617 chemicals therein resulted from a comprehensive research effort by a multidisciplinary team of researchers with expertise in quantitative structure–activity relationship (QSAR) modeling, chemistry, toxicokinetics, joint toxicity of chemical mixtures, and behavioral and aquatic toxicology. The fathead minnow database was the culmination of the US Environmental Protection Agency’s (USEPA) QSAR research program, which spanned nearly 20 yr, a rare program because many research planning efforts typically run within a …
Structural Basis For Enzyme I Inhibition By Α-Ketoglutarate, Vincenzo Venditti, Rodolfo Ghirlando, G. Marius Clore
Structural Basis For Enzyme I Inhibition By Α-Ketoglutarate, Vincenzo Venditti, Rodolfo Ghirlando, G. Marius Clore
Vincenzo Venditti
Creating new bacterial strains in which carbon and nitrogen metabolism are uncoupled is potentially very useful for optimizing yields of microbial produced chemicals from renewable carbon sources. However, the mechanisms that balance carbon and nitrogen consumption in bacteria are poorly understood. Recently, α-ketoglutarate (αKG), the carbon substrate for ammonia assimilation, has been observed to inhibit Escherichia coli enzyme I (EI), the first component of the bacterial phosphotransferase system (PTS), thereby providing a direct biochemical link between central carbon and nitrogen metabolism. Here we investigate the EI-αKG interaction by NMR and enzymatic assays. We show that αKG binds with a KD …
Structure, Dynamics And Biophysics Of The Cytoplasmic Protein–Protein Complexes Of The Bacterial Phosphoenolpyruvate: Sugar Phosphotransferase System, Vincenzo Venditti
Structure, Dynamics And Biophysics Of The Cytoplasmic Protein–Protein Complexes Of The Bacterial Phosphoenolpyruvate: Sugar Phosphotransferase System, Vincenzo Venditti
Vincenzo Venditti
The bacterial phosphotransferase system (PTS) couples phosphoryl transfer, via a series of bimolecular protein–protein interactions, to sugar transport across the membrane. The multitude of complexes in the PTS provides a paradigm for studying protein interactions, and for understanding how the same binding surface can specifically recognize a diverse array of targets. Fifteen years of work aimed at solving the solution structures of all soluble protein–protein complexes of the PTS has served as a test bed for developing NMR and integrated hybrid approaches to study larger complexes in solution and to probe transient, spectroscopically invisible states, including encounter complexes. We review …
Abraham Model Correlations For Predicting Gas-To-Liquid Partition Coefficients And Activity Coefficients Of Organic Solutes Dissolved In 1-(2-Methoxyethyl)-1- Methylpyrrolidinium Tris(Pentafluoroethyl)Trifluorophosphate, Rui Jiang, Jared L. Anderson, Timothy W. Stephens, William E. Acree Jr., Micael H. Abraham
Abraham Model Correlations For Predicting Gas-To-Liquid Partition Coefficients And Activity Coefficients Of Organic Solutes Dissolved In 1-(2-Methoxyethyl)-1- Methylpyrrolidinium Tris(Pentafluoroethyl)Trifluorophosphate, Rui Jiang, Jared L. Anderson, Timothy W. Stephens, William E. Acree Jr., Micael H. Abraham
Jared L. Anderson
Chromatographic retention factors were measured for 45 different organic solutes of varying polarity and hydrogen-bonding capability on an anhydrous 1-(2-methoxyethyl)-1-methylpyrrolidinium tris(pentafluoroethyl)trifluorophosphate, ([MeoeMPyrr]+ [FAP]– ), stationary phase at both 323 K and 353 K. The experimental retention factor data were combined with recently published thermodynamic data for solutes dissolved in ([MeoeMPyrr]+ [FAP]– ) to give the corresponding gas-to-liquid partition coefficients (log K). The water-to-anhydrous ([MeoeMPyrr]+ [FAP]– ) partition coefficients (log P) were also calculated using published gas-to-water partition coefficient data for the solutes studied. The derived partition coefficients were analyzed in accordance with the Abraham model. The Abraham model expressions that …
New Generation Of Ensemble-Decision Aliquot Ranking Based On Simplified Microfluidic Components For Large-Capacity Trapping Of Circulating Tumor Cells, Mengxia Zhao, Wyatt C. Nelson, Bingchuan Wei, Perry G. Schiro, Bejan M. Hakimi, Eleanor S. Johnson, Robbyn K. Anand, Grace S. Gyurkey, Lisa M. White, Samuel H. Whiting, Andrew L. Coveler, Daniel T. Chiu
New Generation Of Ensemble-Decision Aliquot Ranking Based On Simplified Microfluidic Components For Large-Capacity Trapping Of Circulating Tumor Cells, Mengxia Zhao, Wyatt C. Nelson, Bingchuan Wei, Perry G. Schiro, Bejan M. Hakimi, Eleanor S. Johnson, Robbyn K. Anand, Grace S. Gyurkey, Lisa M. White, Samuel H. Whiting, Andrew L. Coveler, Daniel T. Chiu
Robbyn Anand
Ensemble-decision aliquot ranking (eDAR) is a sensitive and high-throughput method to analyze circulating tumor cells (CTCs) from peripheral blood. Here, we report the next generation of eDAR, where we designed and optimized a new hydrodynamic switching scheme for the active sorting step in eDAR, which provided fast cell sorting with an improved reproducibility and stability. The microfluidic chip was also simplified by incorporating a functional area for subsequent purification using microslits fabricated by standard lithography method. Using the reported second generation of eDAR, we were able to analyze 1 mL of whole-blood samples in 12.5 min, with a 95% recovery …