gebhart/patrepeval huggingface dataset:
Visualizing the robustness of query execution (2009)

In database query processing, actual run-time conditions (e.g., actual selectivities and actual available memory) very often differ from compile-time expectations of run-time conditions (e.g., estimated predicate selectivities and anticipated memory availability). Robustness of query processing can be defined as the ability to handle unexpected conditions. Robustness of query execution, specifically, can be defined as the ability to process a specific plan efficiently in an unexpected condition. We focus on query execution (runtime), ignoring query optimization (compile-time), in order to complement existing research and to explore untapped potential for improved robustness in database query processing. One of our initial steps has been to devise diagrams or maps that show how well plans perform in the face of varying run-time conditions and how gracefully a system&apos;s query architecture, operators, and their implementation degrade in the face of adverse conditions. In this paper, we show several kinds of diagrams with data from three real systems and report on what we have learned both about these visualization techniques and about the three database systems. 1
Clinical study of genomic drivers in pancreatic ductal adenocarcinoma (2017)

We provide a clinically relevant framework for genomic drivers of PDA and for advancing novel treatments.
Immunologically related ketodeoxyoctonate-containing structures in Chlamydia trachomatis, Re mutants of Salmonella species, and Acinetobacter calcoaceticus var. anitratus (1984)

The lipopolysaccharides (LPS) of Chlamydia trachomatis, Acinetobacter calcoaceticus var. anitratus, and Re mutants of Salmonella sp. were shown to share related immunodeterminants , as demonstrated by double immunodiffusion and immunoblotting from sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels. The cross-reactive material in the extracellular slime of A. calcoaceticus var. anitratus was shown to be released LPS. The Acinetobacter LPS was found to separate in sodium dodecyl sulfate-polyacrylamide gel electrophoresis into three fractions. The cross-reactive component was the fraction migrating fastest, at a rate identical to Re-type LPS of Salmonella sp. The Acinetobacter LPS could be used as antigen in complement fixation assays performed on paired sera of patients with chlamydial pneumonia; it gave results identical to those of the chlamydial complement fixation glycolipid antigen conventionally used in such assays in 9 of 10 patients.
Time-efficient and cost-effective network hardening using attack graphs (2012)

Attack graph analysis has been established as a powerful tool for analyzing network vulnerability. However, previous approaches to network hardening look for exact solutions and thus do not scale. Further, hardening elements have been treated independently, which is inappropriate for real environments. For example, the cost for patching many systems may be nearly the same as for patching a single one. Or patching a vulnerability may have the same effect as blocking traffic with a firewall, while blocking a port may deny legitimate service. By failing to account for such hardening interdependencies, the resulting recommendations can be unrealistic and far from optimal. Instead, we formalize the notion of hardening strategy in terms of allowable actions, and define a cost model that takes into account the impact of interdependent hardening actions. We also introduce a near-optimal approximation algorithm that scales linearly with the size of the graphs, which we validate experimentally.
Ultra High Power 10 kV, 50 A SiC PiN Diodes (2005)

Ultra high power 10 kV, 50 A SiC PiN diodes have been developed with a low forward voltage drop (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">F</sub> ) of 3.75 V and a fast reverse recovery time of 150 nsec. This is the highest reported power rating for a single SiC chip (dimensions: 8.7 mm times 8.7 mm). Furthermore, all of the historical problems with the SiC PiN diode technology such as ineffective edge termination (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">BD</sub> increased to > 70% of ideal breakdown voltage), poor ohmic contacts to p-type SiC (rho <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> reduced to < 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-4</sup> Omegacm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ), and forward voltage drift (DeltaV <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">F</sub> reduced to < 0.1 V) have been solved with design, material, and process improvements which have resulted in high overall device yields. A combination of performance, reliability, and yield has the SiC PiN diode technology poised for a revolutionary impact in the world of power semiconductor devices
Dibenzo[<i>c</i>,<i>h</i>][1,5]naphthyridinediones as Topoisomerase I Inhibitors: Design, Synthesis, and Biological Evaluation (2012)

Dibenzo[c,h][1,5]naphthyridinediones were prepared via a novel synthetic pathway. The compounds were designed as topoisomerase I (Top1) inhibitors based on the indenoisoquinoline series of drugs. The results of biological evaluation demonstrate that, unlike very closely related dibenzo[c,h][1,6]naphthyridinediones, dibenzo[c,h][1,5]naphthyridinediones retain the Top1 inhibitory activity of similarly substituted indenoisoquinolines.
Technology Implementation Plan. Fully Ceramic Microencapsulated Fuel for Commercial Light Water Reactor Application (2015)

This report is an overview of the implementation plan for ORNL's fully ceramic microencapsulated (FCM) light water reactor fuel. The fully ceramic microencapsulated fuel consists of tristructural isotropic (TRISO) particles embedded inside a fully dense SiC matrix and is intended for utilization in commercial light water reactor application.
High Energy Level Raman-Assisted Fiber Optical Parametric Chirped Pulse Amplification (2019)

Fiber Optical Parametric Chirped Pulse Amplification (FOPCPA) consists of amplifying temporally stretched short pulses in an optical fiber by a high intensity pump beam through a four-wave mixing process. Such amplification scheme presents high gain, large bandwidth, repetition rate and wavelength broad flexibility and tunability but provides up to now only very weak signal energies (below the nJ level).
Simultaneous Removal of Gas and Dust by Activated Carbon Coated Electrode (2013)

This study aimed to develop a new dust collecting system equipped with an activated carbon (A.C.) coated electrode. Before fabrication, pre-treatment of A.C. was performed to remove metal ions within the A.C. to enlarge its specific surface area. Then, pre-treated A.C., black carbon, polyvinyl acetate (PVAc), and methanol were mixed to make a gel compound, which was coated onto aluminum plates to fabricate electrodes. The optimal mixing ratio of A.C., black carbon, PVAc, and methanol was found to be 10 g: 2 g: 3 g: 20 mL. After fabrication, the electrodes were used in the batch-type experiment for NH3 and H2S removal. The reduction rates of the gases were high at the beginning and slowly reduced with time. Dust collection experiments were conducted in continuous flow, with various voltages applied. Compared to 5 kV, dust removal efficiency was 1.5 times higher when 10 kV was applied. Increasing the number of electrodes applied also increased the collecting efficiency. The correlation coefficient between actual collecting efficiency and trend line was higher than 99%. Consequently, the novel dust collection system equipped with A.C. coated electrode appears to be a promising substitute for existing dust-control devices. Keywords: Activated carbon coated electrode, Dust collecting, Electrostatic precipitator, Gravity precipitator
Optimized Transition Path of a Transformable HOvering Rotorcraft (THOR) (2018)

Hybrid aerial vehicles which combine two or more flight configurations have gained popularity due to their increased flight envelope and versatility. With the inclusion of two or more flight modes, the transition phases between these modes are equally as crucial. While many have worked on the transition phases of more popular hybrid aerial vehicle configurations, this paper builds upon a novel aerial platform that combines the maneuverability and hover capability of a rotor-wing with the speed and endurance of a fixed-wing aircraft, previously established as the Transformable HOvering Rotorcraft (THOR). THOR uses a structurally efficient combination of a single-axis rotor (monocopter) type with a tailless fixed wing configuration, utilizing all flight surfaces in both modes. The hover-to-cruise transition of THOR is explored in the form of a trajectory optimization problem. The formulation of the cost function, vehicle model, and constraints are discussed in this paper. The open-loop control inputs that minimize the objective function were determined, simulated and flight tested experimentally.
Third-generation GFP biosensors for real-time readout of pH and redox potential in living cells (2004)

Green fluorescent protein variants have been developed that report real-time change in pH and redox potential in living cells. The variants involve cysteine substitutions near the chromophore, which greatly alter the sensitivity of the protein to changes in its environment. Measurements can be made on single living cells in the fluorescence microscope or in cell suspension with an ordinary fluorimeter. The indicators are ratiometric by emission and/or excitation, which means that measurements at two different wavelengths are sufficient to determine both the quantity being measured and the indicator GFP concentration. The photophysics of a novel blue/green dual emission GFP variant will be presented. The design principles, crystal structures and ultrafast spectroscopic analysis of probe response will be discussed in terms of atomic models involving excited state proton transfer. Some applications in living cells will be presented.
The Second Spacer Cation Assisted Growth of a 2D Perovskite Film with Oriented Large Grain for Highly Efficient and Stable Solar Cells (2019)

The fabrication of high-quality film with large grains oriented along the direction of film thickness is important for 2D Ruddlesden-Popper perovskite-based solar cells (PVSCs). High-quality 2D BA<sub>2</sub> MA<sub>n-1</sub> Pb<sub>n</sub> I<sub>3n+1</sub> (BA<sup>+</sup> =butylammonium, MA<sup>+</sup> =methylammonium, n=5) perovskite films were fabricated with a grain size of over 1 μm and preferential orientation growth by introducing a second spacer cation (SSC<sup>+</sup> ) into the precursor solution. Dynamic light scattering showed that SSC<sup>+</sup> addition can induce aggregation in the precursor solution. The precursor aggregates are favorable for the formation of large crystal grains by inducing nucleation and decreasing the nucleation sites. Applying phenylethylammonium as SSC<sup>+</sup> , the optimized inverted planar PVSCs presented a maximum PCE of 14.09 %, which is the highest value of the 2D BA<sub>2</sub> MA<sub>n-1</sub> Pb<sub>n</sub> I<sub>3n+1</sub> (n=5) PVSCs. The unsealed device shows good moisture stability by maintaining around 90 % of its initially efficiency after 1000 h exposure to air (Hr=25±5 %).
A systematic error in X-ray grating interferometry due to asymmetric scattering distributions (2012)

The high sensitivity provided by x-ray grating interferometry is one of the distinct characteristics of this phase contrast imaging technique. Up to now, several contributions to the uncertainty of the determined phase signal are known, which can be addressed by adapting total acquisition time or improving the mechanics of the experimental setup. Here, we demonstrate the occurrence of an additional systematic error, which is intrinsic to the physics of the contrast formation process. Based on a recently established scattering-based description of grating interferometry, we demonstrate analytically that asymmetric scattering distributions lead to a systematic error in the determined phase signal.
Discerning Risk of Disease Transition in Relatives of Systemic Lupus Erythematosus Patients Utilizing Soluble Mediators and Clinical Features (2016)

Preclinical alterations in levels of soluble mediators may predict transition to classified disease in relatives of SLE patients. Thus, immune perturbations precede SLE classification and can help identify high-risk relatives for rheumatology referral and potential enrollment in prevention trials.
Evaluation of large girth LDPC codes for PMD compensation by turbo equalization (2008)

Large-girth quasi-cyclic LDPC codes have been experimentally evaluated for use in PMD compensation by turbo equalization for a 10 Gb/s NRZ optical transmission system, and observing one sample per bit. Net effective coding gain improvement for girth-10, rate 0.906 code of length 11936 over maximum a posteriori probability (MAP) detector for differential group delay of 125 ps is 6.25 dB at BER of 10(-6). Girth-10 LDPC code of rate 0.8 outperforms the girth-10 code of rate 0.906 by 2.75 dB, and provides the net effective coding gain improvement of 9 dB at the same BER. It is experimentally determined that girth-10 LDPC codes of length around 15000 approach channel capacity limit within 1.25 dB.
Using Polymers to Impart Lubricity and Biopassivity to Surfaces: Are These Properties Linked? (2019)

Abstract Polymer brushes have been widely applied for the reduction of both friction and non‐specific protein adsorption. In many (but not all) applications, such as contact lenses or medical devices, this combination of properties is highly desirable. Indeed, for many polymer‐brush systems, lubricity and resistance to biofouling appear to go hand in hand, with modifications of brush architecture, for example, leading to a similar degree of enhancement (or degradation) in both properties. In the case of poly(ethylene glycol) (PEG) brushes, this has been widely demonstrated. There are, however, examples where this behavior breaks down. In systems where linear brushes are covalently crosslinked during surface‐initiated polymerization (SIP), for example, the presence and the chemical nature of links between grafted chains might or might not influence biopassivity of the films, while it always causes an increment in friction. Furthermore, when the grafted‐chain topology is shifted from linear to cyclic, chemically identical brushes show a substantial improvement in lubrication, whereas their protein resistance remains unaltered. Architectural control of polymer brush films can provide another degree of freedom in the design of lubricious and biopassive coatings, leading to new combinations of surface properties and their independent modulation.
New modified fourier algorithm to eliminate the effect of the DC offset on phasor estimation using DFT (2008)

This paper proposes a new modified Fourier algorithm to eliminate the adverse influence of a decaying dc offset when Discrete Fourier transform (DFT) is used to estimate the phasor of the fundamental frequency component. The proposed algorithm decomposes the DFT process into even sample set DFT and odd sample set DFT. The effect of the dc offset is eliminated by using the recursive relationship between the outputs of even sample set DFT and odd sample set DFT. The performance of the algorithm is evaluated by using computer-simulated signals and EMTP-generated signals. The evaluation results indicate that the proposed algorithm can estimate the accurate phasor of the fundamental frequency component regardless of not only the primary decaying dc offset but also the secondary decaying dc offset caused by CT circuit itself including its burden.
274. One-Step Generation of Universal CAR T Cells (2016)

Adoptive immunotherapy using chimeric antigen receptors (CARs) has shown remarkable clinical results in the treatment of leukemia and is one of the most promising new strategies to treat cancer. Current clinical protocols utilize autologous T cells that are collected by apheresis and engineered with retroviral vectors to stably express the CAR. This approach therefore requires patient-specific cell manufacturing, which unavoidably results in patient-to-patient variability in the final cell product. Widespread implementation of this approach will further require progress in automation and miniaturization of cell manufacturing to meet the demand for CAR T cells. Furthermore, current approaches utilize randomly integrating vectors, including gamma-retroviral, lentiviral and transposons, which all result in semi-random integration and variable expression of the CAR owing to transgene variegation. Position effects may result in heterogeneous T cell function, transgene silencing and, potentially, insertional oncogenesis. Thus, the conjunction of autologous cell sourcing and random vector integration is prone to generating cell products with variable potency. Here we utilize gene editing to generate histocompatible T cell products with consistent and homogeneous CAR expression. Different tailored nucleases, including CRISPR/Cas9 system, Zinc Finger Nucleases or TAL effector nucleases (TALENs), have been previously used for gene disruption in a wide range of human cells including primary T cells. In some instances, these nucleases have been used to generate so-called “universal T cells” for allogeneic administration, by disrupting T cell receptor (TCR) or HLA class I expression, but viral vectors or the sleeping beauty transposon were used to deliver the CAR cDNA, all of which result in semi-random transgene integration and its downstream consequences. We present here a novel strategy for one-step generation of universal CAR T cells. We first compared the efficiency of TALEN and CRISPR/Cas9 to promote homologous recombination using AAV6 donor template in T cells and established conditions yielding more than 50% of universal CAR T cells combining target gene disruption and CAR insertion in a single single step. We molecularly confirmed the targeted integration of the CAR transgene, which results in highly homogeneous and stable CAR expression in human peripheral blood T cells. These T cells exhibited the same in vitro tumor lysis activity and proliferation than retrovirally transduced CAR T cells, which augur favorably for their in vivo anti-tumor activity. Deep sequencing analyses to evaluate off-target effects of the nucleases and random AAV integration are in progress, as are in vivo experiments comparing the anti-tumor activity and graft-versus-host disease potential of edited T cells vs conventional CAR T cells. The process we describe here, which combines the scalability of universal T cell manufacturing with the uniformity and safety of targeted CAR gene integration, should be useful for the development of off-the-shelf CAR therapy.
VARIABLE-RATE, DIGITALLY CONTROLLED METERING DEVICE (2000)

During the past decade, there has been increasing interest in applying water and chemicals to crops based onneed or yield potential rather than applying uniformly to the entire field. While ground-driven variable-rate chemicalapplication equipment is now being used, most irrigation systems continue to apply nominally uniform water depths. Ourobjective was to make variable-rate irrigation applications possible by developing a digitally controlled metering device.The device consists of a reservoir that is alternately filled and emptied at a rate determined by a digital pulse from anexternal source and requires pressurized sources of water and air. The flow rate can be altered by changing the cycleduration and frequency, by changing air and water pressure, or by exchanging the reservoir with one of different volume.Tests with prototypes indicate reproducible flow rates for a range of operating pressures and discharge cycle durations.Various sprinklers or nozzles may be attached to the outlet if specific distribution patterns are desired. Additionally, themetering device can be used in a wide variety of applications with a variety of fluids or gases for variable-rate flow orinjection of a fluid into either another fluid or gas.
Cryogenic Memory Architecture Integrating Spin Hall Effect based\n Magnetic Memory and Superconductive Cryotron Devices (2019)

One of the most challenging obstacles to realizing exascale computing is\nminimizing the energy consumption of L2 cache, main memory, and interconnects\nto that memory. For promising cryogenic computing schemes utilizing Josephson\njunction superconducting logic, this obstacle is exacerbated by the cryogenic\nsystem requirements that expose the technology's lack of high-density,\nhigh-speed and power-efficient memory. Here we demonstrate an array of\ncryogenic memory cells consisting of a non-volatile three-terminal magnetic\ntunnel junction element driven by the spin Hall effect, combined with a\nsuperconducting heater-cryotron bit-select element. The write energy of these\nmemory elements is roughly 8 pJ with a bit-select element, designed to achieve\na minimum overhead power consumption of about 30%. Individual magnetic memory\ncells measured at 4 K show reliable switching with write error rates below\n$10^{-6}$, and a 4x4 array can be fully addressed with bit select error rates\nof $10^{-6}$. This demonstration is a first step towards a full cryogenic\nmemory architecture targeting energy and performance specifications appropriate\nfor applications in superconducting high performance and quantum computing\ncontrol systems, which require significant memory resources operating at 4 K.\n
The ArsQ permease and transport of the antibiotic arsinothricin (2023)

The pentavalent organoarsenical arsinothricin (AST) is a natural product synthesized by the rhizosphere bacterium Burkholderia gladioli GSRB05. AST is a broad-spectrum antibiotic effective against human pathogens such as carbapenem-resistant Enterobacter cloacae. It is a non-proteogenic amino acid and glutamate mimetic that inhibits bacterial glutamine synthetase. The AST biosynthetic pathway is composed of a three-gene cluster, arsQML. ArsL catalyzes synthesis of reduced trivalent hydroxyarsinothricin (R-AST-OH), which is methylated by ArsM to the reduced trivalent form of AST (R-AST). In the culture medium of B. gladioli, both trivalent species appear as the corresponding pentavalent arsenicals, likely due to oxidation in air. ArsQ is an efflux permease that is proposed to transport AST or related species out of the cells, but the chemical nature of the actual transport substrate is unclear. In this study, B. gladioli arsQ was expressed in Escherichia coli and shown to confer resistance to AST and its derivatives. Cells of E. coli accumulate R-AST, and exponentially growing cells expressing arsQ take up less R-AST. The cells exhibit little transport of their pentavalent forms. Transport was independent of cellular energy and appears to be equilibrative. A homology model of ArsQ suggests that Ser320 is in the substrate binding site. A S320A mutant exhibits reduced R-AST-OH transport, suggesting that it plays a role in ArsQ function. The ArsQ permease is proposed to be an energy-independent uniporter responsible for downhill transport of the trivalent form of AST out of cells, which is oxidized extracellularly to the active form of the antibiotic.