gebhart/patrepeval huggingface dataset:
Robust design and optimization of retroaldol enzymes (2012)

Enzyme catalysts of a retroaldol reaction have been generated by computational design using a motif that combines a lysine in a nonpolar environment with water-mediated stabilization of the carbinolamine hydroxyl and β-hydroxyl groups. Here, we show that the design process is robust and repeatable, with 33 new active designs constructed on 13 different protein scaffold backbones. The initial activities are not high but are increased through site-directed mutagenesis and laboratory evolution. Mutational data highlight areas for improvement in design. Different designed catalysts give different borohydride-reduced reaction intermediates, suggesting a distribution of properties of the designed enzymes that may be further explored and exploited.
Ion Acoustic Waves in an Electron Cyclotron Resonance Plasma (1964)

Ion acoustic waves have been generated in an electron cyclotron resonance plasma. The plasma was produced in a long microwave cavity at the heating frequency of 3.025 Gc/sec. When the resonance condition ${{\ensuremath{\omega}}_{p}}^{2}=2\ensuremath{\omega}(\ensuremath{\omega}\ensuremath{-}{\ensuremath{\omega}}_{b})$ is approached, the plasma constricts, corresponding to present theory. The waves appeared when the magnetic field was increased slightly above the value necessary to achieve the resonance condition. The waves were observed by means of a photomultiplier, a Langmuir probe, and a shift in frequency of a higher order cavity mode. Harmonics of the waves up to and including the 4th have been seen.
CandidTree: Visualizing Structural Uncertainty in Similar Hierarchies (2007)

Most visualization systems fail to convey uncertainty within data. To provide a way to show uncertainty in similar hierarchies, we interpreted the differences between two tree structures as uncertainty. We developed a new interactive visualization system called CandidTree that merges two trees into one and visualizes two types of structural uncertainty: location and sub-tree structure uncertainty. Since CandidTree can visualize the differences between two tree structures, we conducted a series of user studies with tree-comparison tasks. First a usability study was conducted to identify major usability issues and evaluate how our system works. Another qualitative user study was conducted to see if biologists, who regularly work with hierarchically organized names, are able to use CandidTree, and to assess the ‘uncertainty’ metric we used. A controlled experiment with software engineers was conducted to compare CandidTree with WinDiff, a traditional files and folders comparison tool. The results showed that users performed better with CandidTree. Furthermore, CandidTree received better satisfaction ratings and all users preferred CandidTree to WinDiff.
The Critical Role of βPdZn Alloy in Pd/ZnO Catalysts for the Hydrogenation of Carbon Dioxide to Methanol (2022)

The rise in atmospheric CO<sub>2</sub> concentration and the concomitant rise in global surface temperature have prompted massive research effort in designing catalytic routes to utilize CO<sub>2</sub> as a feedstock. Prime among these is the hydrogenation of CO<sub>2</sub> to make methanol, which is a key commodity chemical intermediate, a hydrogen storage molecule, and a possible future fuel for transport sectors that cannot be electrified. Pd/ZnO has been identified as an effective candidate as a catalyst for this reaction, yet there has been no attempt to gain a fundamental understanding of how this catalyst works and more importantly to establish specific design criteria for CO<sub>2</sub> hydrogenation catalysts. Here, we show that Pd/ZnO catalysts have the same metal particle composition, irrespective of the different synthesis procedures and types of ZnO used here. We demonstrate that all of these Pd/ZnO catalysts exhibit the same activity trend. In all cases, the β-PdZn 1:1 alloy is produced and dictates the catalysis. This conclusion is further supported by the relationship between conversion and selectivity and their small variation with ZnO surface area in the range 6-80 m<sup>2</sup>g<sup>-1</sup>. Without alloying with Zn, Pd is a reverse water-gas shift catalyst and when supported on alumina and silica is much less active for CO<sub>2</sub> conversion to methanol than on ZnO. Our approach is applicable to the discovery and design of improved catalysts for CO<sub>2</sub> hydrogenation and will aid future catalyst discovery.
Single-molecule nanopore dielectrophoretic trapping of α-Synuclein with lipid membranes (2022)

ABSTRACT The lipid-α-Synuclein (α-Syn) interaction plays a crucial role in the pathogenesis of Parkinson’s disease. Here, we trap α-Syn at a conjunction of an α-hemolysin (αHL) single nanopore-lipid to investigate the folding and unfolding kinetics of α-Syn in a lipidic environment. The hybridized α-Syn is generated through a reaction between a 5’-thiol-modified nucleotide oligo (dC30) and the α-Syn mutant (A140C). Owing to an applied voltage, single-molecule hybridized α-Syn can be trapped at the single nanopore. The trapping events are associated with dielectrophoretic force. The folding and unfolding events of α-Syn can be observed at the pore-membrane junction through interpretation of blockade current amplitudes and dwell time. This can be related to the protein quaternary structure influenced by the α-Syn-membrane interaction, allowing further analysis of α-Syn conformational dynamics. We studied how disease associated metal ions (Cu 2+ , Zn 2+ ) modulate folding and unfolding of α-Syn at the interface of the membranes and pore, and how α-helical peptidomimetics stabilize the helical conformation of α-Syn in the presence of a membrane. These studies aid our understanding of the complexity of the interaction of α-Syn, lipid membranes and metal ions, and in using peptidomimetics, a new strategy against α-Syn toxicity and aggregation is advanced.
ChemInform Abstract: Synthesis of Prenyl Diazoacetate (VII) and Its Intramolecular Catalytic Dediazoniation to 6,6‐Dimethyl‐3‐oxabicyclo(3.1.0)hexan‐2‐one (VIII). (1991)

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.
Relationship between storage media and blue photoluminescence for oxidized porous silicon (1997)

Blue photoluminescence is observed, with nanosecond decay time, from rapid thermally oxidized porous silicon as a result of accelerated aging in plastic containers. Photoluminescence measurements, combined with chemical analyses of the “aged” porous silicon, indicate that the emission is a consequence of the incorporation of trace organic (hydrocarbon) contamination from the plastic containers as they outgas at a mildly elevated temperature (80 °C) and, albeit at a reduced rate, at room temperature. Such carbonaceous contaminants can subsequently be removed by high-temperature annealing, a process which also quenches the blue photoluminescence. Consequently, it is important to take into consideration the storage medium used when making comparative luminescent and compositional studies of porous silicon and, perhaps, porous materials in general.
Inertial Electrostatic Confinement3He Breeder for D-3He Satellite Systems (1998)

Fusion fuel of D-3He combines a high-energy yield per fusion reaction with a relatively high fusion cross section. Moreover, its nuclear reaction (D + 3He → p + α, 18.3 MeV) minimizes neutrons and maximizes charged fusion products, enabling increased energy recovery efficiency by direct conversion. However, scarce 3He terrestrial resources have deterred research and development on this alternative. Production of 3He through inertial electrostatic confinement breeders, which supply 3He to field-reversed-configuration reactors (called satellites in reference to their dependence on the breeder) is explored. The breeder-satellite system is analyzed in terms of both energy balance and economics. The energy balance takes the net energy gain of the global system as the key parameter. The economic study determines the competitiveness of breeding with respect to 3He lunar mining, which was already shown to be an ultimately attractive route for commercial development.
Modeling key agreement in multi-hop ad hoc networks (2006)

Securing multicast communications in ad hoc networks has become one of the most challenging research directions in the areas of wireless networking and security. This is especially true as ad hoc networks are emerging as the desired environment for an increasing number of civilian, commercial and military applications, also addressing an increasingly large number of users. In this paper we study a very basic security question for Ad Hoc Networks: Key Agreement against passive adversaries. Despite being a widely studied area in wired networks, the problem becomes significantly more challenging for ad hoc networks, and even more for sensor networks, due to lack of trusted entities, infrastructures, full connectivity, routing structures, and due to severe limitations on the resources and capabilities of network nodes. In this paper we perform a comprehensive investigation of Key Agreement over resource constrained ad hoc networks. First, we formally model the key agreement problem over multi-hop ad hop networks, and we directly extend known key agreement protocols for wired networks, and evaluate the efficiency of such approaches. We then go beyond natural extensions of such protocols, by proposing non-trivial extensions based on efficient topology-driven simulations of logical networks over an arbitrary physical network, in order to optimize the most significant metrics of interest for such networks: i.e. bandwidth, latency, processing cost. Indeed, the resulting protocols are significantly more efficient in some or all of the above metrics, as our analytical results indicate.
Effect of Vericiguat on Left Ventricular Structure and Function in Patients with Heart Failure with Reduced Ejection Fraction: The VICTORIA Echocardiographic Substudy (2023)

In this pre-specified echocardiographic study, significant improvements in LV structure and function occurred over 8 months in both vericiguat and placebo in a high-risk HFrEF population with recent worsening HF. Further studies are warranted to define the mechanisms of vericiguat's benefit in HFrEF.
The Law of the Iterated Logarithm and Upper-Lower Class Tests for Partial Sums of Stationary Gaussian Sequences (1978)

Herein, laws of the iterated logarithm and various upper-lower class refinements are established for partial sums of stationary Gaussian random variables. These stationary Gaussian random variables are not necessarily in any sense weakly dependent. For example, if the random variables are nonnegatively correlated, then the upper half of the law of the iterated logarithm holds. Under more restrictive, but still quite general hypotheses, an upper-lower class test which classifies all monotone sequences $\{\phi(n)\}$ is established.
Tight control of light beams in photonic crystals with spatially-variant lattice orientation (2014)

Spatially-variant photonic crystals (SVPCs), in which the orientation of the unit cell changes as a function of position, are shown to be capable of abruptly controlling light beams using just low index materials and can be made to have high polarization selectivity. Multi-photon direct laser writing in the photo-polymer SU-8 was used to fabricate three-dimensional SVPCs that direct the flow of light around a 90 degree bend. The lattice spacing and fill factor were maintained nearly constant throughout the structure. The SVPCs were characterized at a wavelength of 2.94 μm by scanning the faces with optical fibers and the results were compared to electromagnetic simulations. The lattices were shown to direct infrared light of one polarization through sharp bends while the other polarization propagated straight through the SVPC. This work introduces a new scheme for controlling light that should be useful for integrated photonics.
Activation of ER stress and mTORC1 suppresses hepatic sortilin-1 levels in obese mice (2012)

Recent GWAS have identified SNPs at a human chromosom1 locus associated with coronary artery disease risk and LDL cholesterol levels. The SNPs are also associated with altered expression of hepatic sortilin-1 (SORT1), which encodes a protein thought to be involved in apoB trafficking and degradation. Here, we investigated the regulation of Sort1 expression in mouse models of obesity. Sort1 expression was markedly repressed in both genetic (ob/ob) and high-fat diet models of obesity; restoration of hepatic sortilin-1 levels resulted in reduced triglyceride and apoB secretion. Mouse models of obesity also exhibit increased hepatic activity of mammalian target of rapamycin complex 1 (mTORC1) and ER stress, and we found that administration of the mTOR inhibitor rapamycin to ob/ob mice reduced ER stress and increased hepatic sortilin-1 levels. Conversely, genetically increased hepatic mTORC1 activity was associated with repressed Sort1 and increased apoB secretion. Treating WT mice with the ER stressor tunicamycin led to marked repression of hepatic sortilin-1 expression, while administration of the chemical chaperone PBA to ob/ob mice led to amelioration of ER stress, increased sortilin-1 expression, and reduced apoB and triglyceride secretion. Moreover, the ER stress target Atf3 acted at the SORT1 promoter region as a transcriptional repressor, whereas knockdown of Atf3 mRNA in ob/ob mice led to increased hepatic sortilin-1 levels and decreased apoB and triglyceride secretion. Thus, in mouse models of obesity, induction of mTORC1 and ER stress led to repression of hepatic Sort1 and increased VLDL secretion via Atf3. This pathway may contribute to dyslipidemia in metabolic disease.
On Color Texture Normalization for Active Appearance Models (2009)

The extension of the standard grayscale active appearance model (AAM) techniques to color images is investigated. Prior work in this field has mainly focused on RGB color models which did not demonstrate noticeable benefits over grayscale models from the point of view of convergence accuracy. We improve on previous work by normalizing the color texture vector separately for intensity and chromaticity components. Where an appropriate color space is chosen, we demonstrate improvements in convergence accuracy as well as image synthesization quality for AAMs. Optimal results are achieved when a color space in which the image channels are strongly decorrelated is chosen. Our best results are achieved using the I1I2I3 color space, originally proposed by Ohta.
Discovery and Development of the Covalent Hydrates of Trifluoromethylated Pyrazoles as Riboflavin Synthase Inhibitors with Antibiotic Activity Against Mycobacterium tuberculosis (2009)

A high-throughput screening (HTS) hit compound displayed moderate inhibition of Mycobacterium tuberculosis and Escherichia coli riboflavin synthases. The structure of the hit compound provided by the commercial vendor was reassigned as [3-(4-chlorophenyl)-5-hydroxy-5-(trifluoromethyl)-4,5-dihydro-1H-pyrazol-1-yl](o-tolyl)methanone (18). The hit compound had a k(is) of 8.7 microM vs. M. tuberculosis riboflavin synthase and moderate antibiotic activity against both M. tuberculosis replicating phenotype and nonreplicating persistent phenotype. Molecular modeling studies suggest that two inhibitor molecules bind in the active site of the enzyme, and that the binding is stabilized by stacking between the benzene rings of two adjacent ligands. The most potent antibiotic in the series proved to be [5-(4-chlorophenyl)-5-hydroxy-3-(trifluoromethyl)-4,5-dihydro-1H-pyrazol-1-yl](m-tolyl)methanone (16), which displayed a minimum inhibitory concentration (MIC) of 36.6 microM vs. M. tuberculosis replicating phenotype and 48.9 microM vs. M. tuberculosis nonreplicating phenotype. The HTS hit compound and its analogues provide the first examples of riboflavin synthase inhibitors with antibiotic activity.
Ontology-guided Semantic Composition for Zero-Shot Learning (2020)

Zero-shot learning (ZSL) is a popular research problem that aims at predicting for those classes that have never appeared in the training stage by utilizing the inter-class relationship with some side information. In this study, we propose to model the compositional and expressive semantics of class labels by an OWL (Web Ontology Language) ontology, and further develop a new ZSL framework with ontology embedding. The effectiveness has been verified by some primary experiments on animal image classification and visual question answering.
Isotope Ratio Mass Spectrometry (IRMS) (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Helping system engineers bridge the peaks (2014)

In our experience at NASA, system engineers generally follow the Twin Peaks approach when developing safety-critical systems. However, iterations between the peaks require considerable manual, and in some cases duplicate, effort. A significant part of the manual effort stems from the fact that requirements are written in English natural language rather than a formal notation. In this work, we propose an approach that enables system engineers to leverage formal requirements and automated test generation to streamline iterations, effectively "bridging the peaks". The key to the approach is a formal language notation that a) system engineers are comfortable with, b) is supported by a family of automated V&V tools, and c) is semantically rich enough to describe the requirements of interest. We believe the combination of formalizing requirements and providing tool support to automate the iterations will lead to a more efficient Twin Peaks implementation at NASA.
Gamut Mapping: An Overview of the Problem. (1999)

Preeclampsia (PE) is a gestational disorder and genetic and epigenetic alterations can affect its pathogenesis. Some evidences showed that the altered expression of miRNAs in the placentas complicated by PE. The blood samples from 219 PE and 242 normotensive pregnant women and placental tissue samples from 111 PE and 119 normotensive women were collected. MiR-146a and miR-149 polymorphisms were genotyped in blood samples and placentas using PCR-RFLP method. The frequencies of maternal miR-146a rs2910164 GC and CC genotypes did not differ between PE and control groups. However, the miR-146a rs2910164 G/C polymorphism was associated with an increased risk of PE in dominant (OR 1.5, 95% CI 1-2.1; P = 0.04) and allelic (OR 1.4, 95% CI 1-1.9; P = 0.04) but not recessive models. Moreover, the maternal GC and CC genotypes were associated with a 1.9- and 3.4-fold increased risk of severe PE (OR 1.9, 95% CI 1.1-3.2; P = 0.02 and OR 3.4, 95% CI 1.3-9; P = 0.01, respectively) and miR-146a rs2910164 polymorphism could increase risk of severe PE in dominant and recessive models (OR 2.1, 95% CI 1.3-3.4; P = 0.004 and OR 2.6, 95% CI 1-6.7; P = 0.04). The placental miR-146a rs2910164 polymorphism was associated with PE susceptibility in dominant (OR 1.8, 95% CI 1.1-3; P = 0.03) and allelic models (OR 1.7, 95% CI 1.1-2.5; P = 0.02). The frequencies of maternal and placental miR-149 rs2292832 genotypes were not different between two groups and these genotypes were not associated with PE or severe PE risk. In conclusion, according to logistic regression analysis the maternal/placental miR-146a rs2910164 G/C polymorphism was associated with PE and/or severe PE risk.
Silicon cylinder spiral coil for nuclear magnetic resonance spectroscopy of nanoliter samples (2009)

Abstract This contribution presents a new high sensitivity microdetector designed for high resolution proton NMR at 750 MHz (17.6 T) of sample volumes ranging from 5 to 40 nl. The desired volume of fluid is placed in a sealed 330/200 μm outer/inner diameter glass capillary and is then situated in the center of the detection coil. The high quality factor detection coils are fabricated using silicon microtechnology. The materials from which the device is constructed are specially shaped to improve the homogeneity of the static magnetic field within the sample. Adverse effects of the finite, nonspherical sample geometry on the spectral resolution are mitigated by employing sample rotation up to 2.5 kHz at the magic angle. The new detector exhibits linewidths of smaller than 3.0 Hz (0.004 ppm) and a signal‐to‐noise ratio in the spectral domain of higher than 4,000 per μmol of water. Results with respect to sensitivity, spectral resolution, and total sample volume are given and put into context with already published microprobes. © 2009 Wiley Periodicals, Inc. Concepts Magn Reson Part B (Magn Reson Engineering) 35B: 11–22, 2009
Hybrid Closed‐Loop and Open‐Loop Methods (2003)

This chapter contains sections titled: A Comparison of Open-loop and Closed-loop Systems Transceiver Concepts Performance Space–Time Retransmission Adaptive Space–Time Modulation Arrangements Summary
SECURE WEB BROWSING OVER LONG-DELAY BROADBAND NETWORKS - Recommendations for Web Browsers (2004)

Current browser implementations provide less than desirable secure web page response time over geosynchronous satellite and other long delay broadband networks (e.g., intercontinental access across the Internet). This document defines the issues and recommends a set of enhancements that improve response time without compromising security. These enhancements are shown, by analysis, to provide more than a 50% response time reduction for a typical secure web page.
Supplementary Figure S1 from A Human Genome-Wide RNAi Screen Reveals Diverse Modulators that Mediate IRE1α–XBP1 Activation (2023)

&lt;p&gt;Data analysis for genome-wide RNAi screen.&lt;/p&gt;