gebhart/patrepeval huggingface dataset:
Antifungal amphiphilic aminoglycosides (2014)

The attachment of alkyl and other hydrophobic groups to traditional antibacterial kanamycins and neomycins creates amphiphilic aminoglycosides with altered antimicrobial properties. In this review, we summarize the discovery of amphiphilic kanamycins that are antifungal, but not antibacterial, and that inhibit the growth of fungi by perturbation of plasma membrane functions. With low toxicities against plant and mammalian cells, they appear to specifically target the fungal plasma membrane. These new antifungal agents offer new options for fighting fungal pathogens and are examples of reviving old drugs to confront new therapeutic challenges.
ChemInform Abstract: Protein Engineering by in vivo Incorporation of Non‐natural Amino Acids: Control of Incorporation of Methionine Analogues by Methionyl‐tRNA Synthetase. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Liquid crystal interactions with nanostructure and applications to diagnostics and medical research (2005)

Liquid crystals are rigid organic molecules that exhibit orientational behavior on surfaces. The orientation of liquid crystals can be controlled by the design of surfaces with regular nanoscale features and/or defined chemistries. The orientation of liquid crystals on such surfaces can be exploited to sensitively report the binding of proteins to the surface [1-6]. Liquid crystal based detection of proteins can be the basis for a new generation of diagnostics and research tools. The use of liquid crystals to detect proteins enables the development of label free, rapid, sensitive and multiplexed assays.
Use of multiple-discrete-frequency microwave radiation to enhance the performances of traditional B-minimum electron cyclotron resonance ion sources (1998)

The performances of electron cyclotron resonance (ECR) ion sources, in terms of high-charge-state yields and intensities within a particular charge-state, can be enhanced by increasing the physical sizes of the ECR zones in relation to the sizes of their plasma volumes. The ECR plasma “volumes” of traditional B-minimum ECR sources can be increased by injecting broadband microwave radiation (multiple-discrete frequency, variable frequency, or broad-bandwidth frequency microwave radiation) derived from standard klystron, gyrotron, or traveling-wave-tube (TWT) technologies (frequency domain). In this work, comparisons were made of the charge-state distributions of Arq+ and Xeq+ extracted from the ORNL Caprice ECR ion source, when excited with single frequency and multiple-discrete-frequency microwave radiation, derived from standard klystron and/or TWT technologies. The charge-state populations for Arq+ and Xeq+ move toward higher values when excited with modest power from two and three discrete frequency, microwave radiation compared to those generated with power from single-frequency radiation. For three-frequency plasma excitation, the most probable charge state for Xe is increased by one charge-state unit while the beam intensities for charge-states higher than the most probable are increased by factors of ∼3 over those for the single frequency plasma case. The results of these measurements along with details on the modifications to the injection system required to couple the microwave radiation into the plasma volume of the Caprice source will be presented in this article.
Transfer of Pre-Assembled Block Copolymer Thin Film to Nanopattern Unconventional Substrates (2014)

In this work, we demonstrate that a preassembled block copolymer (BCP) thin film can be floated, transferred, and utilized to effectively nanopattern unconventional substrates. As target substrates, we chose Cu foil and graphene/Cu foil since they cannot be nanopatterned via conventional processes due to the high surface roughness and susceptibility to harsh processing chemicals and etchants. Perpendicular hexagonal PMMA cylinder arrays in diblock copolymer poly(styrene-block-methyl methacrylate) [P(S-b-MMA)] thin films were preassembled on sacrificial SiO2/Si substrates. The BCP thin film was floated at the air/water interface off of a SiO2/Si substrate and then collected with the target substrate, leading to well-defined nanoporous PS templates on these uneven surfaces. We further show that the nanoporous template can be used for a subtractive process to fabricate nanoperforated graphene on Cu foil in sub-20 nm dimension, and for an additive process to create aluminum oxide nanodot arrays without any polymeric residues or use of harsh chemicals and etchants.
A Prokaryotic Voltage-Gated Sodium Channel (2001)

The pore-forming subunits of canonical voltage-gated sodium and calcium channels are encoded by four repeated domains of six-transmembrane (6TM) segments. We expressed and characterized a bacterial ion channel (NaChBac) from Bacillus halodurans that is encoded by one 6TM segment. The sequence, especially in the pore region, is similar to that of voltage-gated calcium channels. The expressed channel was activated by voltage and was blocked by calcium channel blockers. However, the channel was selective for sodium. The identification of NaChBac as a functionally expressed bacterial voltage-sensitive ion-selective channel provides insight into both voltage-dependent activation and divalent cation selectivity.
Robust loop-free on-demand routing in ad hoc networks (2006)

In this thesis, we explore new techniques for robust, efficient, loop-free on-demand routing in Mobile Ad hoc Networks (MANETs) using the same information (i.e., topology information, sequence numbers, etc.,) used in prior on-demand routing protocol proposals. 
We provide new insights into the robustness of protocols based on destination-sequence numbers when operating with node failures and loss of routing information, and present a new destination-sequence number framework that works correctly even with failure conditions. We also show how destination-sequence numbers can be manipulated as routing labels for improving performance, rather than being strictly treated as time-stamps. 
We present two different routing approaches that exploit the topology information that can be collected on-demand during the route request flood search. The first approach translates topology information into labels that are then stored at nodes in strict lexicographic ordering along any successor path to a destination. Loop-freedom is maintained by allowing nodes to only pick smaller labels. The second approach maintains a list of topology information that should not be trusted in-addition to the known path to a destination. Using the notion of trusted topology, nodes can always make routing decisions only with the correct topology information, which ensures loop-freedom. 
We conclude our research with a new on-demand routing technique that exploits the route request flood search process, which is an integral part of any on-demand routing protocol. Without requiring any additional mechanisms or information, we use the uniqueness of route requests to realize a on-demand routing framework. We, then, present extensions to the basic framework to improve performance using more information that can be collected during the flood search process. 
Through extensive simulations, we show that all our new proposed approaches perform better than the current state-of-the-art MANET protocols prescribed by the IETF working group.
Demulsification of Water-in-Crude Oil Emulsions Using Ionic Liquids and Microwave Irradiation (2010)

The main objective of this work is to investigate the role of two types of ionic liquids, omimBF4 and omimPF6, upon the microwave demulsification process. A series of batch demulsification runs were carried out to evaluate the final emulsified water content of emulsion samples after the exposure to microwaves at distinct ionic liquid concentrations. Tests were performed in a commercial microwave reactor system, using high stable water-in-crude oil emulsion samples containing different salt and water contents. Similar separation tests conducted under conventional heating were investigated for comparisons. Results showed that increasing the concentration of each ionic liquid yields improved demulsification results in both microwave and conventional heating processes. However, the microwave process was always much faster and more efficient than the conventional case. Blank tests without ionic liquid have not produced water separation, which indicates the high stability of the investigated emulsions. In particular, the joint use of omimPF6 (even at low concentrations) and microwave irradiation allows for system demulsification with high efficiency at short time, with some cases even reaching water contents in the range of 1−2% in the final emulsion.
Curcumin Scaffold as a Multifunctional Tool for Alzheimer’s Disease Research (2022)

Alzheimer's disease (AD) is one of the most common neurodegenerative disorders, which is caused by multi-factors and characterized by two histopathological hallmarks: amyloid-β (Aβ) plaques and neurofibrillary tangles of Tau proteins. Thus, researchers have been devoting tremendous efforts to developing and designing new molecules for the early diagnosis of AD and curative purposes. Curcumin and its scaffold have fluorescent and photochemical properties. Mounting evidence showed that curcumin scaffold had neuroprotective effects on AD such as anti-amyloidogenic, anti-inflammatory, anti-oxidative and metal chelating. In this review, we summarized different curcumin derivatives and analyzed the in vitro and in vivo results in order to exhibit the applications in AD diagnosis, therapeutic monitoring and therapy. The analysis results showed that, although curcumin and its analogues have some disadvantages such as short wavelength and low bioavailability, these shortcomings can be conquered by modifying the structures. Curcumin scaffold still has the potential to be a multifunctional tool for AD research, including AD diagnosis and therapy.
Constrained data-driven parallelism (2013)

In data-driven parallelism, changes to data spawn new tasks, which may change more data, spawning yet more tasks. Computation propagates until no further changes occur. Benefits include increasing opportunities for fine-grained parallelism, avoiding redundant work, and supporting incremental computations on large data sets. Nonetheless, data-driven parallelism can be problematic. For example, convergence times of data-driven singlesource shortest paths algorithms can vary by two orders of magnitude depending on task execution order. We propose constrained data-driven parallelism, in which programmers can impose ordering constraints on tasks. In particular, we propose new abstractions for defining groups of tasks and constraining the execution order of tasks within each group. We sketch an initial implementation and present experimental results demonstrating that our approach enables new efficient data-driven implementations of a variety of graph algorithms.
Antibody responses to recombinant and plasma derived hepatitis B vaccines. (1986)

The antibody response to hepatitis B surface antigen (anti-HBs) induced in 25 recipients of a recombinant hepatitis B vaccine derived from yeast was compared with that induced in 25 recipients of a vaccine prepared from hepatitis B surface antigen (HBsAg) derived from plasma. Anti-HBs affinity and specificity were compared using assays of antibody affinity with two different antigens, a complex of the major polypeptide of HBsAg (p25; molecular weight 25 000 daltons) covalently linked to its glycosylated form (gp30) prepared from native purified HBsAg, and a cyclical synthetic peptide representing amino acid residues 139-147 of the major polypeptide of HBsAg and known to represent a major part of an a determinant. There was no difference in anti-HBs affinity or molar antigen binding sites of the antibody measured with either antigen between the two groups. All subjects in both groups produced antibody that bound to the gp30/p25 complex antigen, whereas 22 of the recipients of the plasma derived vaccine compared with 24 of those receiving the yeast derived vaccine produced antibodies that bound to the cyclical synthetic peptide 139-147. These results support the finding of similar levels of anti-HBs, measured by commercial solid phase radioimmunoassay, in the two vaccine groups after three doses of vaccine. These results show no significant difference in the quantity, quality, or specificity of the anti-HBs response induced by the recombinant hepatitis B vaccine and the plasma derived hepatitis B vaccine.
Collisionally Activated Dissociation and Electron Capture Dissociation of Several Mass Spectrometry-Identifiable Chemical Cross-Linkers (2006)

One of the challenges in protein interaction studies with chemical cross-linking stems from the complexity of intra-, inter-, and dead-end cross-linked peptide mixtures. We have developed new cross-linkers to study protein-protein interactions with mass spectrometry to improve the ability to deal with this complexity. Even the accurate mass capabilities of FTICR-MS alone cannot unambiguously identify cross-linked peptides from cell-labeling experiments due to the complexity of these mixtures resultant from the enormous number of possible cross-linked species. We have developed novel cross-linkers that have unique fragmentation features in the gas phase. The characteristics of these cross-linkers combined with the accurate mass capability of FTICR-MS can help distinguish cross-linking reaction products and assign protein identities. These cross-linkers that we call protein interaction reporters (PIRs) have been constructed with two reactive groups attached through two bonds that can be preferentially cleaved by low-energy CID of the respective protonated precursor ions. After cleavage of the labile bonds, the middle part of the linker serves as a reporter ion to aid identification of cross-linked peptides. This report highlights three new PIRs with new features that have been developed to improve the efficiency of release of reporter ions. The new cross-linkers reported here were tuned with the addition of an affinity tag, a hydrophilic group, a photocleavable group, and new low-energy MS/MS cleavable bonds. This report presents our investigation of the MSMS fragmentation behavior of selected protonated ions of the new compounds. The comprehensive fragmentation of these PIRs and PIR-labeled cross-linked peptides with low-energy collisions and an example of electron capture dissociation in FTICR-MS is presented. These new cross-linkers will contribute to current systems biology research by allowing acquisition of global or large-scale data on protein-protein interactions.
Electronically rotated and translated field‐free line generation for open bore magnetic particle imaging (2017)

Purpose We propose a coil arrangement for open bore field‐free line ( FFL ) magnetic particle imaging ( MPI ) system, which is suitable for accessing the subject from the sides. The purpose of this study is twofold, to show that the FFL can be rotated and translated electronically in a volume of interest with this arrangement and to analyze the current, voltage and power requirements for a 1 T/m gradient human sized scanner for a 200 mm diameter × 200 mm height cylindrical field of view ( FOV ). Methods We used split coils side by side with alternating current directions to generate a field‐free line. Employing two of these coil groups, one of which is rotated 90 degrees with respect to the other, a rotating FFL was generated. We conducted numerical simulations to show the feasibility of this arrangement for three‐dimensional (3D) electronical scan of the FFL . Using simulations, we obtained images of a two‐dimensional (2D) in silico dot phantom for a human size scanner with system matrix‐based reconstruction. Results Simulations showed that the FFL can be generated and rotated in one plane and can be translated in two axes, allowing for 3D imaging of a large subject with the proposed arrangement. Human sized scanner required 63–215 kW power for the selection field coils to scan the focus inside the FOV. Conclusions The proposed setup is suitable for FFL MPI imaging with an open bore configuration without the need for mechanical rotation, which is preferable for clinical usage in terms of imaging time and patient access. Further studies are necessary to determine the limitations imposed by peripheral nerve stimulation, and to optimize the system parameters and the sequence design.
Effect of Ru Additions on the TCP-Phase Formation and Creep Strength of a Ni-base Single Crystal Superalloy (2004)

In the ‘High Temperature Materials 21’ project, fourth generation single crystal (SC) superalloys have been developed adding Ru as a phase stabilizing element. A relationship between the amount of TCP-phase and the creep strength has been investigated for a series of Ni-base SC superalloys with 2 to 5 mass% Ru; these alloys were designed using an SC superalloy containing 5 mass% Re as a base alloy. The amount of TCP-phase decreased with increased Ru content from 2 to 5 mass%. and the amount of γ′ envelope, which normally forms on the TCP plate, decrease also with increase in Ru content. The creep strength increase with these structual changes but the main reason was considered to be the decrease in volume fraction of the γ′ envelope rather than the decrease in the amount of TCP-phase.
Seismic Response Control of Bridges by Variable Dampers (1994)

This paper discusses a variable damper proposed to control bridge response against an earthquake. The variable damper changes its damping coefficient depending on the structural response so that it functions as a passive energy dissipator, a damper stopper at small deck displacements, and a stopper with shock absorber for excessive deck displacements. The effectiveness of variable dampers is studied first by analytical simulations. It is demonstrated that the peak deck displacement and acceleration are reduced to 26% and 44%, respectively, of the bridge response without control. A prototype variable damper with a maximum damping force of 200 kN is developed, and its effectiveness is studied by a series of dynamic loading tests. A series of shake‐table tests is also performed using a model bridge with a deck weight of 390 kN. It is found that providing the prototype variable damper reduces the deck response acceleration and displacement from 376 cm/s2 and 9.2 cm to 203 cm/s2 and 1.3 cm, respectively. Analytical simulation of the experimental results is made. The predicted deck responses are quite close to the measured ones.
Type-II superlattice unipolar barrier infrared detectors (2016)

Recent material and device architecture development have led to significant advances in III-V semiconductor infrared detectors and focal plane arrays. We provide an overview of high-performance type-II superlattice based unipolar barrier infrared detectors.
FACET: Future ATM Concepts Evaluation Tool (2000)

FACET (Future ATM Concepts Evaluation Tool) is an Air Traffic Management research tool being developed at the NASA Ames Research Center. This paper describes the design, architecture and functionalities of FACET. The purpose of FACET is to provide E simulation environment for exploration, development and evaluation of advanced ATM concepts. Examples of these concepts include new ATM paradigms such as Distributed Air-Ground Traffic Management, airspace redesign and new Decision Support Tools (DSTs) for controllers working within the operational procedures of the existing air traffic control system. FACET is currently capable of modeling system-wide en route airspace operations over the contiguous United States. Airspace models (e.g., Center/sector boundaries, airways, locations of navigation aids and airports) are available from databases. A core capability of FACET is the modeling of aircraft trajectories. Using round-earth kinematic equations, aircraft can be flown along flight plan routes or great circle routes as they climb, cruise and descend according to their individual aircraft-type performance models. Performance parameters (e.g., climb/descent rates and speeds, cruise speeds) are obtained from data table lookups. Heading, airspeed and altitude-rate dynamics are also modeled. Additional functionalities will be added as necessary for specific applications. FACET software is written in Java and C programming languages. It is platform-independent, and can be run on a variety of computers. FACET has been designed with a modular software architecture to enable rapid integration of research prototype implementations of new ATM concepts. There are several advanced ATM concepts that are currently being implemented in FACET airborne separation assurance, dynamic density predictions, airspace redesign (re-sectorization), benefits of a controller DST for direct-routing, and the integration of commercial space transportation system operations into the U.S. National Airspace System (NAS).
In-band OSNR monitoring using a pair of Michelson fiber interferometers (2010)

Two polarization-independent Michelson fiber interferometers with different optical delays were used to measure the in-band OSNR of an optical signal from 5 to 30 dB within an accuracy of 0.5 dB. Using an expansion of the amplitude autocorrelation function of the signal around zero delay, it was possible to perform measurements without any prior knowledge of the signal. The system is shown to be immune to the effects of modulation frequency (up to 10G), partially and fully polarized noise, chromatic dispersion and poorly biased modulators.
Liquid deposition photolithography for the fabrication of gradient index (GRIN) micro-optics (2014)

One photon diffusive photopolymers enable self-developing three dimensional (3D) refractive index patterning of up to cm thick solid volumes for the fabrication of micro-optics. However, one photon absorption in solid, thick materials does not yield complete control of the 3D refractive index distribution due to diffraction and the excessive development time for index features measuring 100’s of microns in diameter or larger. We present a fabrication method and photopolymer formulation that can efficiently create mm<sup>3</sup> optical devices with programmable, gradient index of refraction with arbitrary feature size and shape. Index contrast of 0.1 is demonstrated, which is 20 times larger than commercial holographic photopolymers. Devices are fabricated by repetitive micro-fluidic layering of a self-developing photopolymer structured by projection lithography. The process has the unusual property that total fabrication time for a fixed thickness decreases as the number of layers is increased, reducing the fabrication time for high axial resolution micro-optics. We demonstrate the process by fabricating thick waveguide arrays and gradient index lenses.
Nanoparticles from Chitosan (2005)

Abstract Novel biodegradable nanoparticles were synthesized by chemical modification of the chitosan linear chain. A natural dicarboxylic acid (malic acid) was used as a crosslinking agent for intramolecular covalent condensation reaction to obtain hydrophilic nanoparticles based on chitosan. A variety of methods including, solubility studies, laser light scattering (DLS), transmission electron microscopy (TEM) and nuclear magnetic resonance (NMR) was used to characterize the crosslinked macromolecules. The prepared biodegradable chitosan nanoparticles, soluble in aqueous media, might be useful for various biomedical applications, like injectable drug‐ or gene‐delivery systems.