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Articles 144841 - 144870 of 302419

Full-Text Articles in Physical Sciences and Mathematics

A Pan-Arctic Synthesis Of Ch4 And Co2 Production From Anoxic Soil Incubations, Claire C. Treat, Susan M. Natali, Jessica G. Ernakovich, Colleen M. Iversen, Massimo Lupascu, Anthony David Mcguire, Richard J. Norby, Taniya Roy Chowdhury, Andreas Richter, Hana Santruckova, Christina Schadel, Edward A. G. Schuur, Victoria L. Sloan, Merritt R. Turestsky, Mark P. Waldrop Jan 2015

A Pan-Arctic Synthesis Of Ch4 And Co2 Production From Anoxic Soil Incubations, Claire C. Treat, Susan M. Natali, Jessica G. Ernakovich, Colleen M. Iversen, Massimo Lupascu, Anthony David Mcguire, Richard J. Norby, Taniya Roy Chowdhury, Andreas Richter, Hana Santruckova, Christina Schadel, Edward A. G. Schuur, Victoria L. Sloan, Merritt R. Turestsky, Mark P. Waldrop

Faculty Publications

Permafrost thaw can alter the soil environment through changes in soil moisture, frequently resulting in soil saturation, a shift to anaerobic decomposition, and changes in the plant community. These changes, along with thawing of previously frozen organic material, can alter the form and magnitude of greenhouse gas production from permafrost ecosystems. We synthesized existing methane (CH4) and carbon dioxide (CO2) production measurements from anaerobic incubations of boreal and tundra soils from the geographic permafrost region to evaluate large-scale controls of anaerobic CO2 and CH4 production and compare the relative importance of landscape-level factors (e.g., vegetation type and landscape position), soil …

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Structural Basis And Distal Effects Of Gag Substrate Coevolution In Drug Resistance To Hiv-1 Protease, Aysegul Ozen, Kuan-Hung Lin, Nese Yilmaz, Celia Schiffer Jan 2015

Structural Basis And Distal Effects Of Gag Substrate Coevolution In Drug Resistance To Hiv-1 Protease, Aysegul Ozen, Kuan-Hung Lin, Nese Yilmaz, Celia Schiffer

Celia A. Schiffer

Drug resistance mutations in response to HIV-1 protease inhibitors are selected not only in the drug target but elsewhere in the viral genome, especially at the protease cleavage sites in the precursor protein Gag. To understand the molecular basis of this protease-substrate coevolution, we solved the crystal structures of drug resistant I50V/A71V HIV-1 protease with p1-p6 substrates bearing coevolved mutations. Analyses of the protease-substrate interactions reveal that compensatory coevolved mutations in the substrate do not restore interactions lost due to protease mutations, but instead establish other interactions that are not restricted to the site of mutation. Mutation of a substrate …

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Structural Analysis Of Asunaprevir Resistance In Hcv Ns3/4a Protease, Djade Soumana, Akbar Ali, Celia Schiffer Jan 2015

Structural Analysis Of Asunaprevir Resistance In Hcv Ns3/4a Protease, Djade Soumana, Akbar Ali, Celia Schiffer

Celia A. Schiffer

Asunaprevir (ASV), an isoquinoline-based competitive inhibitor targeting the hepatitis C virus (HCV) NS3/4A protease, is very potent in vivo. However, the potency is significantly compromised by the drug resistance mutations R155K and D168A. In this study three crystal structures of ASV and an analogue were determined to analyze the structural basis of drug resistance susceptibility. These structures revealed that ASV makes extensive contacts with Arg155 outside the substrate envelope. Arg155 in turn is stabilized by Asp168, and thus when either residue is mutated, the enzyme's interaction with ASV's P2* isoquinoline is disrupted. Adding a P1-P3 macrocycle to ASV enhances the …

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Improving The Resistance Profile Of Hepatitis C Ns3/4a Inhibitors: Dynamic Substrate Envelope Guided Design, Aysegul Ozen, Woody Sherman, Celia Schiffer Jan 2015

Improving The Resistance Profile Of Hepatitis C Ns3/4a Inhibitors: Dynamic Substrate Envelope Guided Design, Aysegul Ozen, Woody Sherman, Celia Schiffer

Celia A. Schiffer

Drug resistance is a principal concern in the treatment of quickly evolving diseases. The viral protease NS3/4A is a primary drug target for the hepatitis C virus (HCV) and is known to evolve resistance mutations in response to drug therapy. At the molecular level, drug resistance reflects a subtle change in the balance of molecular recognition by NS3/4A; the drug resistant protease variants are no longer effectively inhibited by the competitive active site inhibitors but can still process the natural substrates with enough efficiency for viral survival. In previous works we have developed the "substrate envelope" hypothesis, which posits that …

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Efficient Computation Of Small-Molecule Configurational Binding Entropy And Free Energy Changes By Ensemble Enumeration, Nathaniel Silver, Bracken King, Madhavi Nalam, Hong Cao, Akbar Ali, G. S. Kiran Kumar Reddy, Tariq Rana, Celia Schiffer, Bruce Tidor Jan 2015

Efficient Computation Of Small-Molecule Configurational Binding Entropy And Free Energy Changes By Ensemble Enumeration, Nathaniel Silver, Bracken King, Madhavi Nalam, Hong Cao, Akbar Ali, G. S. Kiran Kumar Reddy, Tariq Rana, Celia Schiffer, Bruce Tidor

Celia A. Schiffer

Here we present a novel, end-point method using the dead-end-elimination and A* algorithms to efficiently and accurately calculate the change in free energy, enthalpy, and configurational entropy of binding for ligand-receptor association reactions. We apply the new approach to the binding of a series of human immunodeficiency virus (HIV-1) protease inhibitors to examine the effect ensemble reranking has on relative accuracy as well as to evaluate the role of the absolute and relative ligand configurational entropy losses upon binding in affinity differences for structurally related inhibitors. Our results suggest that most thermodynamic parameters can be estimated using only a small …

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Drug Resistance Conferred By Mutations Outside The Active Site Through Alterations In The Dynamic And Structural Ensemble Of Hiv-1 Protease, Debra Ragland, Ellen Nalivaika, Madhavi Nalam, Kristina Prachanronarong, Hong Cao, Rajintha Bandaranayake, Yufeng Cai, Nese Yilmaz, Celia Schiffer Jan 2015

Drug Resistance Conferred By Mutations Outside The Active Site Through Alterations In The Dynamic And Structural Ensemble Of Hiv-1 Protease, Debra Ragland, Ellen Nalivaika, Madhavi Nalam, Kristina Prachanronarong, Hong Cao, Rajintha Bandaranayake, Yufeng Cai, Nese Yilmaz, Celia Schiffer

Celia A. Schiffer

HIV-1 protease inhibitors are part of the highly active antiretroviral therapy effectively used in the treatment of HIV infection and AIDS. Darunavir (DRV) is the most potent of these inhibitors, soliciting drug resistance only when a complex combination of mutations occur both inside and outside the protease active site. With few exceptions, the role of mutations outside the active site in conferring resistance remains largely elusive. Through a series of DRV-protease complex crystal structures, inhibition assays, and molecular dynamics simulations, we find that single and double site mutations outside the active site often associated with DRV resistance alter the structure …

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Testing The Substrate-Envelope Hypothesis With Designed Pairs Of Compounds, Yang Shen, Michael Altman, Akbar Ali, Madhavi Nalam, Hong Cao, Tariq Rana, Celia Schiffer, Bruce Tidor Jan 2015

Testing The Substrate-Envelope Hypothesis With Designed Pairs Of Compounds, Yang Shen, Michael Altman, Akbar Ali, Madhavi Nalam, Hong Cao, Tariq Rana, Celia Schiffer, Bruce Tidor

Celia A. Schiffer

Acquired resistance to therapeutic agents is a significant barrier to the development of clinically effective treatments for diseases in which evolution occurs on clinical time scales, frequently arising from target mutations. We previously reported a general strategy to design effective inhibitors for rapidly mutating enzyme targets, which we demonstrated for HIV-1 protease inhibition [Altman et al. J. Am. Chem. Soc. 2008, 130, 6099-6113]. Specifically, we developed a computational inverse design procedure with the added constraint that designed inhibitors bind entirely inside the substrate envelope, a consensus volume occupied by natural substrates. The rationale for the substrate-envelope constraint is that it …

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Development Of A Novel Screening Strategy Designed To Discover A New Class Of Hiv Drugs, Nancy Cheng, Sook-Kyung Lee, P. Donover, Mel Reichman, Celia Schiffer, Emily Hull-Ryde, Ronald Swanstrom, William Janzen Jan 2015

Development Of A Novel Screening Strategy Designed To Discover A New Class Of Hiv Drugs, Nancy Cheng, Sook-Kyung Lee, P. Donover, Mel Reichman, Celia Schiffer, Emily Hull-Ryde, Ronald Swanstrom, William Janzen

Celia A. Schiffer

Current antiretroviral treatments target multiple pathways important for human immunodeficiency virus (HIV) multiplication, including viral entry, synthesis and integration of the DNA provirus, and the processing of viral polyprotein precursors. However, HIV is becoming increasingly resistant to these "combination therapies." Recent findings show that inhibition of HIV Gag protein cleavage into its two structural proteins, matrix (MA) and capsid (CA), has a devastating effect on viral production, revealing a potential new target class for HIV treatment. Unlike the widely used HIV protease inhibitors, this new class of inhibitor would target the substrate, not the protease enzyme itself. This approach offers …

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Crystal Structures Of Human Ctbp In Complex With Substrate Mtob Reveal Active Site Features Useful For Inhibitor Design, Brendan Hilbert, Steven Grossman, Celia Schiffer, William Royer Jan 2015

Crystal Structures Of Human Ctbp In Complex With Substrate Mtob Reveal Active Site Features Useful For Inhibitor Design, Brendan Hilbert, Steven Grossman, Celia Schiffer, William Royer

Celia A. Schiffer

The oncogenic corepressors C-terminal Binding Protein (CtBP) 1 and 2 harbor regulatory d-isomer specific 2-hydroxyacid dehydrogenase (d2-HDH) domains. 4-Methylthio 2-oxobutyric acid (MTOB) exhibits substrate inhibition and can interfere with CtBP oncogenic activity in cell culture and mice. Crystal structures of human CtBP1 and CtBP2 in complex with MTOB and NAD(+) revealed two key features: a conserved tryptophan that likely contributes to substrate specificity and a hydrophilic cavity that links MTOB with an NAD(+) phosphate. Neither feature is present in other d2-HDH enzymes. These structures thus offer key opportunities for the development of highly selective anti-neoplastic CtBP inhibitors. Elsevier B.V. All …

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Drug Resistance Mutations Alter Dynamics Of Inhibitor-Bound Hiv-1 Protease, Yufeng Cai, Wazo Myint, Janet Paulsen, Celia Schiffer, Rieko Ishima, Nese Yilmaz Jan 2015

Drug Resistance Mutations Alter Dynamics Of Inhibitor-Bound Hiv-1 Protease, Yufeng Cai, Wazo Myint, Janet Paulsen, Celia Schiffer, Rieko Ishima, Nese Yilmaz

Celia A. Schiffer

Under the selective pressure of therapy, HIV-1 protease mutants resistant to inhibitors evolve to confer drug resistance. Such mutations can impact both the dynamics and structures of the bound and unbound forms of the enzyme. Flap+ is a multidrug-resistant variant of HIV-1 protease with a combination of primary and secondary resistance mutations (L10I, G48V, I54V, V82A) and a strikingly altered thermodynamic profile for darunavir (DRV) binding relative to the wild-type protease. We elucidated the impact of these mutations on protein dynamics in the DRV-bound state using molecular dynamics simulations and NMR relaxation experiments. Both methods concur in that the conformational …

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Negative Binomial Regerssion, 2nd Ed, 2nd Print, Errata And Comments, Joseph Hilbe Jan 2015

Negative Binomial Regerssion, 2nd Ed, 2nd Print, Errata And Comments, Joseph Hilbe

Joseph M Hilbe

Errata and Comments for 2nd printing of NBR2, 2nd edition. Previous errata from first printing all corrected. Some added and new text as well.

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Characterization Of Biomass Burning Emissions From Cooking Fires, Peat, Crop Residue, And Other Fuels With High-Resolution Proton-Transfer-Reaction Time-Of-Flight Mass Spectrometry, C. Stockwell, P. Veres, J. Williams Jan 2015

Characterization Of Biomass Burning Emissions From Cooking Fires, Peat, Crop Residue, And Other Fuels With High-Resolution Proton-Transfer-Reaction Time-Of-Flight Mass Spectrometry, C. Stockwell, P. Veres, J. Williams

Chemistry and Biochemistry Faculty Publications

We deployed a high-resolution proton-transferreaction time-of-flight mass spectrometer (PTR-TOF-MS) to measure biomass-burning emissions from peat, crop residue, cooking fires, and many other fire types during the fourth Fire Lab at Missoula Experiment (FLAME-4) laboratory campaign. A combination of gas standard calibrations and composition sensitive, mass-dependent calibration curves was applied to quantify gas-phase non-methane organic compounds (NMOCs) observed in the complex mixture of fire emissions. We used several approaches to assign the best identities to most major “exact masses”, including many high molecular mass species. Using these methods, approximately 80–96% of the total NMOC mass detected by the PTR-TOFMS and Fourier …

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Storm Surge And Street-Level Inundation Modeling In New York City During Hurricane Sandy, Harry V. Wang, Derek Loftis, Zhou Liu, Jay Titlow, David Forrest, Joseph Zhang Jan 2015

Storm Surge And Street-Level Inundation Modeling In New York City During Hurricane Sandy, Harry V. Wang, Derek Loftis, Zhou Liu, Jay Titlow, David Forrest, Joseph Zhang

January 23, 2015: Storm Surge Modeling Tools for Planning and Response

No abstract provided.

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Introduction To Storm Surge Modeling, Rick Luettich Jan 2015

Introduction To Storm Surge Modeling, Rick Luettich

January 23, 2015: Storm Surge Modeling Tools for Planning and Response

No abstract provided.

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Panel - Real World Applications: Overview Of Virginia Beach Center For Gis' Geoprocessing Of Storm Surge Models, Dave Arnold Jan 2015

Panel - Real World Applications: Overview Of Virginia Beach Center For Gis' Geoprocessing Of Storm Surge Models, Dave Arnold

January 23, 2015: Storm Surge Modeling Tools for Planning and Response

No abstract provided.

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The Storm Surge Hazard, Jeff Orrock Jan 2015

The Storm Surge Hazard, Jeff Orrock

January 23, 2015: Storm Surge Modeling Tools for Planning and Response

No abstract provided.

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Applications Of The Adcirc Storm Surge, Tide, And Wind-Wave Model, Rick Luettich, Brian Blanton Jan 2015

Applications Of The Adcirc Storm Surge, Tide, And Wind-Wave Model, Rick Luettich, Brian Blanton

January 23, 2015: Storm Surge Modeling Tools for Planning and Response

No abstract provided.

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Agenda, Hr Adaptation Forum Jan 2015

Agenda, Hr Adaptation Forum

January 23, 2015: Storm Surge Modeling Tools for Planning and Response

No abstract provided.

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Maximally Entangled States Of Four Nnonbinary Particles, Mario Gaeta, Andrei Klimov, Jay Lawrence Jan 2015

Maximally Entangled States Of Four Nnonbinary Particles, Mario Gaeta, Andrei Klimov, Jay Lawrence

Dartmouth Scholarship

Systems of four nonbinary particles, with each particle having d≥3 internal states, exhibit maximally entangled states that are inaccessible to four qubits. This breaks the pattern of two- and three-particle systems, in which the existing graph states are equally accessible to binary and nonbinary systems alike. We compare the entanglement properties of these special states (called P states) with those of the more familiar Greenberger-Horne-Zeilinger (GHZ) and cluster states accessible to qubits. The comparison includes familiar entanglement measures, the “steering” of states by projective measurements, and the probability that two such measurements, chosen at random, leave the remaining particles in …

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Exchanging Demands: Weaknesses In Ssl Implemenations For Mobile Platforms, Peter Hannay, Clinton Carpene, Craig Valli, Andrew Woodward, Mike Johnstone Jan 2015

Exchanging Demands: Weaknesses In Ssl Implemenations For Mobile Platforms, Peter Hannay, Clinton Carpene, Craig Valli, Andrew Woodward, Mike Johnstone

Clinton Carpene

The ActiveSync protocol’s implementation on some embedded devices leaves clients vulnerable to unauthorised remote policy enforcement. This paper discusses a proof of concept attack against the implementation of ActiveSync in common Smart phones including Android devices and iOS devices. A two‐phase approach to exploiting the ActiveSync protocol is introduced. Phase 1 details the usage of a man‐in‐the‐middle attack to gain a vantage point over the client device, whilst Phase 2 involves spoofing the server‐side ActiveSync responses to initiate the unauthorised policy enforcement. These vulnerabilities are demonstrated by experiment, highlighting how the system can be exploited to perform a remote factory …

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Exposing Potential Privacy Issues With Ipv6 Address Construction, Clinton Carpene, Andrew Woodward Jan 2015

Exposing Potential Privacy Issues With Ipv6 Address Construction, Clinton Carpene, Andrew Woodward

Clinton Carpene

The usage of 128 bit addresses with hexadecimal representation in IPv6 poses significant potential privacy issues. This paper discusses the means of allocating IPv6 addresses, along with the implications each method may have upon privacy in different usage scenarios. The division of address space amongst the global registries in a hierarchal fashion can provide geographical information about the location of an address, and its originating device. Many IPv6 address configuration methods are available, including DHCPv6, SLAAC (with or without privacy extensions), and Manual assignment. These assignment techniques are dissected to expose the identifying characteristics of each technique. It is seen …

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Eavesdropping On The Smart Grid, Craig Valli, Andrew Woodward, Clinton Carpene, Peter Hannay, Murray Brand, Reino Karvinen, Christopher Holme Jan 2015

Eavesdropping On The Smart Grid, Craig Valli, Andrew Woodward, Clinton Carpene, Peter Hannay, Murray Brand, Reino Karvinen, Christopher Holme

Clinton Carpene

An in-situ deployment of smart grid technology, from meters through to access points and wider grid connectivity, was examined. The aim of the research was to determine what vulnerabilities were inherent in this deployment, and what other consideration issues may have led to further vulnerability in the system. It was determined that there were numerous vulnerabilities embedded in both hardware and software and that configuration issues further compounded these vulnerabilities. The cyber threat against critical infrastructure has been public knowledge for several years, and with increasing awareness, attention and resource being devoted to protecting critical in the structure, it is …

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Looking To Iphone Backup Files For Evidence Extraction, Clinton Carpene Jan 2015

Looking To Iphone Backup Files For Evidence Extraction, Clinton Carpene

Clinton Carpene

iPhone logical backup files can provide forensic examiners with almost the entire contents of its host phone up until the point that the backup took place. This paper serves to provide an overview of the information attainable via the analysis of an iPhone backup, making references to the applicability of such analysis in the digital forensics field. The paper introduces the backup directories for various common operating systems, and exposes the contents. Information about the property lists (plist files) containing information about the backed-up device and its contents are detailed, along with the mbdb/mbdx database files, and finally the extension-less …

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Nonlinear Optical Conductivity Of Two-Dimensional Semiconductors With Rashba Spin-Orbit Coupling In Terahertz Regime, Yee Sin Ang, J C. Cao, Chao Zhang Jan 2015

Nonlinear Optical Conductivity Of Two-Dimensional Semiconductors With Rashba Spin-Orbit Coupling In Terahertz Regime, Yee Sin Ang, J C. Cao, Chao Zhang

Yee Sin Ang

We reveal that two-dimensional semiconductors with Rashba spin-orbit interaction (R2DG) exhibit exceptionally strong nonlinear optical response (NOR) in the terahertz frequency regime. The spin-split of the parabolic energy band in R2DG allows strong multiple-photon process to occur via inter-subband mechanism. We show sharp multiple photon edges in the nonlinear conductivity. The edges correspond to the cut-off effect produced by the multiple-photon process. For Rashba coupling parameter of λ R ≈ 10−10 eV m, electric field strength in the order of only 102 V/cm is required for the NOR to dominate over the linear response. Furthermore, the roles of the parabolic …

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Wonder-Worlds Of Words, Sandra A. Yocum Jan 2015

Wonder-Worlds Of Words, Sandra A. Yocum

Sandra A. Yocum

An essay on the impact of the works in the Imprints and Impressions: Milestones in Human Progress, an exhibition of rare books from the collection of Stuart Rose. Exhibition was held Sept. 29-Nov. 9, 2014, at the University of Dayton.

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Exhibition Catalogue — Imprints And Impressions: Milestones In Human Progress, Paul H. Benson, Sandra A. Yocum, Mark Masthay, Donald J. Polzella Jan 2015

Exhibition Catalogue — Imprints And Impressions: Milestones In Human Progress, Paul H. Benson, Sandra A. Yocum, Mark Masthay, Donald J. Polzella

Sandra A. Yocum

Exhibition catalogue for Imprints and Impressions: Milestones in Human Progress — Highlights from the Rose Rare Book Collection. Includes an introduction by Kathleen M. Webb, dean of University Libraries; essays about the impact of the exhibition's books on modern inquiry, the humanities, the sciences, and the social sciences; and photographs of the works in the exhibit.

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Collaborative Proposal: Cameo: Using Interdecadal Comparisons To Understand Trade-Offs Between Abundance And Condition In Fishery Ecosystems, Andrew J. Pershing, Jeffrey A. Runge Jan 2015

Collaborative Proposal: Cameo: Using Interdecadal Comparisons To Understand Trade-Offs Between Abundance And Condition In Fishery Ecosystems, Andrew J. Pershing, Jeffrey A. Runge

University of Maine Office of Research Administration: Grant Reports

The investigators will conduct a model-based investigation of the dynamics of a productive pelagic ecosystems in the Gulf of Maine. The middle trophic levels in highly productive marine ecosystems are typically dominated by a few species of pelagic fish, such as sardines and anchovies in upwelling environments or herring and/or capelin in temperate and subpolar regions. These species act as important conduits for energy to higher trophic levels, including larger fish, seabirds, and cetaceans. When abundant, small pelagics can exert significant pressure on their prey, typically large mesozooplankton. Small pelagic fish exhibit complex dynamics and managing these species under an …

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Repressive Mutations Restore Function-Loss Caused By The Disruption Of Trimerization In Escherichia Coli Multidrug Transporter Acrb, Zhaoshuai Wang, Meng Zhong, Wei Lu, Qian Chai, Yinan Wei Jan 2015

Repressive Mutations Restore Function-Loss Caused By The Disruption Of Trimerization In Escherichia Coli Multidrug Transporter Acrb, Zhaoshuai Wang, Meng Zhong, Wei Lu, Qian Chai, Yinan Wei

Chemistry Faculty Publications

AcrAB-TolC and their homologs are major multidrug efflux systems in Gram-negative bacteria. The inner membrane component AcrB functions as a trimer. Replacement of Pro223 by Gly in AcrB decreases the trimer stability and drastically reduces the drug efflux activity. The goal of this study is to identify suppressor mutations that restore function to mutant AcrBP223G and explore the mechanism of function recovery. Two methods were used to introduce random mutations into the plasmid of AcrBP223G. Mutants with elevated drug efflux activity were identified, purified, and characterized to examine their expression level, trimer stability, interaction with AcrA, and …

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Hidden Formaldehyde In E-Cigarette Aerosols, R. Paul Jensen, Wentai Luo, James F. Pankow, Robert M. Strongin, David H. Peyton Jan 2015

Hidden Formaldehyde In E-Cigarette Aerosols, R. Paul Jensen, Wentai Luo, James F. Pankow, Robert M. Strongin, David H. Peyton

Chemistry Faculty Publications and Presentations

This letter reports a chemical analysis of vapor from electronic cigarettes that shows high levels of formaldehyde, a known carcinogen. The authors project that the associated incremental lifetime risk of cancer could be higher than that from long-term smoking.

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The Influence Of Long-Term Gamma-Radiation And Initially Dissolved Chemicals On Aqueous Kinetics And Interfacial Processes, Pamela A. Yakabuskie Jan 2015

The Influence Of Long-Term Gamma-Radiation And Initially Dissolved Chemicals On Aqueous Kinetics And Interfacial Processes, Pamela A. Yakabuskie

Electronic Thesis and Dissertation Repository

This thesis presents work focusing on the long-term effect of gamma-radiation on aqueous solution kinetics. Ionizing radiation drives the decomposition of water to form both oxidizing (•OH, O2, H2O2) and reducing (•eaq−, •O2−, •H, H2) chemical species. Over time, these radiolysis products can react with dissolved solutes and participate in interfacial reactions. This can lead to significant changes in the eventual solution redox condition, and gas phase composition, and in certain cases result in the formation of solid species. Understanding the long-term solution kinetics for radiolysis …

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