gebhart/patrepeval huggingface dataset:
Graph summarization for indexing paths in graph-structured data (2003)

With the rapidly increasing popularity of XML for data representation, there is a lot of interest in query processing over data that conforms to a labeled-tree or labeled-graph data model. An important component in querying such data involves traversing the labeled-graph by forming path expressions. This thesis studies auxiliary data structures known as path indexes that are intended to speed up the evaluation of path expressions. The approach adopted towards path indexing in this thesis is to construct a smaller summary graph and then evaluate path expressions over this smaller graph. 
We first describe formally why this problem of path indexing is different from the traditional indexing problem in database systems. Next, we propose an index specification framework that can be used to define a wide variety of path indexes, each covering a different set of path expressions. The techniques used in this framework are such that for a large class of index specifications, the resulting path index is the smallest index that is suitable for the respective set of path expressions. These techniques are based on the notion of graph bisimilarity. 
We then study how XML queries can be processed in a native XML database management system using path indexes in conjunction with inverted lists. We also analyze how this integration of path indexing and inverted lists can be used to answer information retrieval style relevance-based queries. The algorithms we obtain in this context have the property of instance optimality, a notion of optimality recently introduced by Fagin et al. in the published literature. Finally, in the last part of this thesis, we study how the path indexes we propose can be maintained as the underlying data changes.
Benzothiophene and Naphthalene Derived Constrained SERMs. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Soluble Spike DNA Vaccine Provides Long-Term Protective Immunity against SARS-CoV-2 in Mice and Nonhuman Primates (2021)

The unprecedented and rapid spread of SARS-CoV-2 (severe acute respiratory syndrome-coronavirus-2) has motivated the need for a rapidly producible and scalable vaccine. Here, we developed a synthetic soluble SARS-CoV-2 spike (S) DNA-based vaccine candidate, GX-19. In mice, immunization with GX-19 elicited not only S-specific systemic and pulmonary antibody responses but also Th1-biased T cell responses in a dose-dependent manner. GX-19-vaccinated nonhuman primates seroconverted rapidly and exhibited a detectable neutralizing antibody response as well as multifunctional CD4+ and CD8+ T cell responses. Notably, when the immunized nonhuman primates were challenged at 10 weeks after the last vaccination with GX-19, they had reduced viral loads in contrast to non-vaccinated primates as a control. These findings indicate that GX-19 vaccination provides a durable protective immune response and also support further development of GX-19 as a vaccine candidate for SARS-CoV-2.
Robust H&#x221E; controller design for microgrid-tied inverter applications (2015)

This paper proposes an H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</sub> mixed sensitivity design of output current tracking controller in a stationary reference frame for general microgrid-tied inverter applications. Variations in a microgrid impedance values have been modeled as multiplicative uncertainty in the plant model. Equivalent microgrid voltage has been considered as the output disturbance acting on the plant. Particular weighting functions have been introduced as part of the H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</sub> algorithm. Weighting functions have been used for performance tuning by shaping the sensitivity and complementary sensitivity functions of the closed loop system. An 8th order H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">∞</sub> controller has been synthesized and system robust stability has been evaluated using modified impedance stability criterion. Controller regulating performance has been validated using PSIM software simulation. Despite the fact that no resonance damping technique is applied, system has shown to be robustly stable under predefined microgrid parameters variations.
Using a PCR‐Based Method To Analyze and Model Large, Heterogeneous Populations of DNA (2019)

The study of populations of large size and high diversity is limited by the capability of collecting data. Moreover, for a pool of individuals, each associated with a unique characteristic feature, as the pool size grows, the possible interactions increase exponentially and quickly go beyond the limit of computation and experimental studies. Herein, the design of DNA libraries with various diversity is reported. By using a facile analytical method based on real-time PCR, the diversity of a pool of DNA can be evaluated to allow extraordinarily high heterogenicity (e.g., >1 trillion). It is demonstrated that these DNA libraries can be used to model heterogeneous populations; these libraries exhibit functions such as self-protection, suitability for biased expansion, and the possibility to evolve into amorphous structures. The method has shown the remarkable power of parallel computing with DNA, since it can resemble an analogue computer and be applied in selection-based biotechnology methods, such as DNA-encoded chemical libraries. As a chemical approach to solve problems traditionally for genetic and statistical analysis, the method provides a quick and cost-efficient evaluation of library diversity for intermediate steps through a selection process.
Crystal Growth and Scintillation Properties of Ce-Doped ${\rm K}_{2}{\rm NaLuF}_{6}$ (2013)

Ce 0.1, 0.5, 1.0, and 2.0 mol%-doped K <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> NaLuF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> crystals with 2 mm in diameter and 30-50 mm in length were grown by micro-pulling-down method. The photoluminescence spectra under ultraviolet excitation showed intense emission ascribed to 5d-4f transitions of Ce <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> replacing Lu <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> isolated octahedral site. In the radioluminescenced spectra under alpha-ray irradiation, the emission band is due to the transition from the lowest 5d excited state of Ce <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> to <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">F</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5/2</sub> ground state level is dominant. The light yields of Ce:K <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> NaLuF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> under 5.5-MeV alpha-ray excitation was estimated to be approximately 1.2 to 1.8% of those of BGO.
Generating synthetic contrast enhancement from non-contrast chest computed tomography using a generative adversarial network (2021)

This study aimed to evaluate a deep learning model for generating synthetic contrast-enhanced CT (sCECT) from non-contrast chest CT (NCCT). A deep learning model was applied to generate sCECT from NCCT. We collected three separate data sets, the development set (n = 25) for model training and tuning, test set 1 (n = 25) for technical evaluation, and test set 2 (n = 12) for clinical utility evaluation. In test set 1, image similarity metrics were calculated. In test set 2, the lesion contrast-to-noise ratio of the mediastinal lymph nodes was measured, and an observer study was conducted to compare lesion conspicuity. Comparisons were performed using the paired t-test or Wilcoxon signed-rank test. In test set 1, sCECT showed a lower mean absolute error (41.72 vs 48.74; P < .001), higher peak signal-to-noise ratio (17.44 vs 15.97; P < .001), higher multiscale structural similarity index measurement (0.84 vs 0.81; P < .001), and lower learned perceptual image patch similarity metric (0.14 vs 0.15; P < .001) than NCCT. In test set 2, the contrast-to-noise ratio of the mediastinal lymph nodes was higher in the sCECT group than in the NCCT group (6.15 ± 5.18 vs 0.74 ± 0.69; P < .001). The observer study showed for all reviewers higher lesion conspicuity in NCCT with sCECT than in NCCT alone (P ≤ .001). Synthetic CECT generated from NCCT improves the depiction of mediastinal lymph nodes.
Constitutive NF-kappa B activation, enhanced granulopoiesis, and neonatal lethality in I kappa B alpha-deficient mice. (1995)

Transcription factors belonging to the NF-kappa B family are controlled by inhibitory I kappa B proteins, mainly I kappa B alpha and I kappa B beta. Apparently normal at birth, I kappa B alpha-/- mice exhibit severe runting, skin defects, and extensive granulopoiesis postnatally, typically dying by 8 days. Hematopoietic tissues from these mice display elevated levels of both nuclear NF-kappa B and mRNAs of some, but not all, genes thought to be regulated by NF-kappa B. NF-kappa B elevation results in these phenotypic abnormalities because mice lacking both I kappa B alpha and the p50 subunit of NF-kappa B show a dramatically delayed onset of abnormalities. In contrast to hematopoietic cells, I kappa B alpha-/- embryonic fibroblasts show minimal constitutive NF-kappa B, as well as normal signal-dependent NF-kappa B activation that is concomitant with I kappa B beta degradation. Our results indicate that I kappa b beta, but not I kappa B alpha, is required for the signal-dependent activation of NF-kappa B in fibroblasts. However, I kappa B alpha is required for the postinduction repression of NF-kappa B in fibroblasts. These results define distinct roles for the two forms of I kappa B and demonstrate the necessity for stringent control of NF-kappa B.
Initial binding of 2‘-deoxynucleoside 5‘-triphosphates to human immunodeficiency virus type 1 reverse transcriptase. (1991)

Human immunodeficiency virus type 1 reverse transcriptase (EC 2.7.7.49), a heterodimer consisting of two polypeptide chains of molecular weights 66,000 and 51,000, fluoresces due to the presence of 36 tryptophan residues with an emission peak centered at 338 nm. The association of 2'-deoxynucleoside 5'-triphosphates with the enzyme results in a decrease in the intensity of the tryptophan emission spectrum, which can be used to calculate apparent dissociation constants. The Kd values determined for binding of the four natural 2'-deoxynucleoside 5'-triphosphates to the free enzyme range from 36.7 +/- 1.8 microM for dTTP to 47.3 +/- 3.9 microM for dATP. The 5'-triphosphate of zidovudine has a Kd of 54.1 +/- 1.3 microM. The enzyme shows no preference for purine or pyrimidine nucleotides. Hill coefficients and the results of dual ligand titration experiments demonstrate that the free enzyme possesses a single dNTP binding site for which the four natural substrates and the 5'-triphosphate of zidovudine compete. The presence of homopolymeric template-primers does not result in selective binding of the complementary 2'-deoxynucleoside 5'-triphosphate, indicating that Watson-Crick base pairing is not involved in the initial binding reaction. The major force driving the association of the ligands with the binding site is hydrophobic. Approximately 14% of the binding energy is derived from electrostatic interactions. Although Mg2+ is required for catalytic activity, it is not absolutely required for initial binding.
Is This Article Consistent with Hinchliffe's Rule? (2015)

I demonstrate that Hinchliffe’s rule – if the title of a scholarly article is a yes-no question, the answer is “no” – is paradoxical, by providing an article whose title is a question whose answer is “no” if and only if its answer is “yes”.
Connecting the legs with a spring improves human running economy (2019)

Human running is inefficient. For every 10 calories burned, less than 1 is needed to maintain a constant forward velocity - the remaining energy is, in a sense, wasted. The majority of this wasted energy is expended to support the bodyweight and redirect the center of mass during the stance phase of gait. An order of magnitude less energy is expended to brake and accelerate the swinging leg. Accordingly, most devices designed to increase running efficiency have targeted the costlier stance phase of gait. An alternative approach is seen in nature: spring-like tissues in some animals and humans are believed to assist leg swing. While it has been assumed that such a spring simply offloads the muscles that swing the legs, thus saving energy, this mechanism has not been experimentally investigated. Here, we show that a spring, or 'exotendon', connecting the legs of a human reduces the energy required for running by 6.4±2.8%, and does so through a complex mechanism that produces savings beyond those associated with leg swing. The exotendon applies assistive forces to the swinging legs, increasing the energy optimal stride frequency. Runners then adopt this frequency, taking faster and shorter strides, and reduce the joint mechanical work to redirect their center of mass. Our study shows how a simple spring improves running economy through a complex interaction between the changing dynamics of the body and the adaptive strategies of the runner, highlighting the importance of considering each when designing systems that couple human and machine.
Cobaltoceniumethynyl gold(i) as an unusual heterodinuclear bioorganometallic fragment to study the biological properties of alkynyl gold complexes (2015)

A cobaltoceniumethynyl gold(i) complex with a triphenylphosphane ligand triggered efficient cytotoxic effects in cancer cells in contrast to a derivative with two cobaltocenium moieties. The complex effectively inhibited the enzyme thioredoxin reductase (TrxR) suggesting this enzyme as a possible biological target. The cellular uptake of both metal fragments of the active complex was studied by atomic absorption spectroscopy and indicated a high biological stability of the complex.
Analysis of Hairpin Ribozyme Base Mutations in Loops 2 and 4 and Their Effects on cis-Cleavage in Vitro (1997)

In order to determine base requirements in loops 2 and 4 of the hairpin ribozyme, a comprehensive mutational analysis of the wild type sequence was done. Each base position in these two loops was mutated to contain each of the three non-wild type bases, and the effects of these mutations were analyzed using cis-cleavage assays. The method of data analysis allowed for the determination of self-cleavage rates as well as the fraction of transcripts produced which were uncleavable. Three positions in loop 2 (A22, A23, and C25) and one position in loop 4 (A38) resulted in no detectable self-cleavage when mutated to any of the non-wild type bases. The remainder of the base positions showed varying degrees of tolerance to base mutations with respect to their support of cis-cleavage. Evidence was obtained for the presence of a non-Watson-Crick base pair between A26 and G36 in the catalytic conformation of the hairpin ribozyme. On the basis of these results, a two-dimensional model for the hairpin ribozyme is presented.
Platelet-collagen adhesion: inhibition by a monoclonal antibody that binds glycoprotein IIb. (1984)

To identify platelet surface structures involved in adhesion to collagen, the effect of 16 murine antiplatelet membrane hybridoma antibodies were tested in a defined, in vitro assay. Four of these antibodies inhibited platelet-collagen adhesion and reacted with a polypeptide with Mr approximately 125,000, as determined by immunoblots after gel electrophoresis under reducing conditions. Through detailed studies with one of these antibodies, the monoclonal antibody PMI-1, the relevant antigen was identified as platelet glycoprotein IIb alpha, based upon (a) co-migration with this glycoprotein in two-dimensional gel electrophoresis and (b) co-purification by immunoaffinity chromatography with a protein with apparent Mr identical to that of glycoprotein III, under conditions in which glycoproteins IIb and III form a complex. Univalent antibody fragments prepared from monoclonal antibody PMI-1 inhibited greater than 80% of platelet-collagen adhesion, and inhibition was completely blocked by the immunopurified antigen. These results indicate that glycoprotein IIb participates in some aspect of platelet-collagen adhesion. In contrast, the purified antigen only partially neutralized a polyclonal antiserum that blocked platelet-collagen adhesion, to a maximum of approximately 25%, at saturating antigen concentrations. Thus, by these immunological criteria, glycoprotein IIb is not the only molecule involved in this process.
Conservation plan report: opportunities for energy conservation in California (1977)

This report is in part aimed at fulfilling the mandates of the Warren-Alquist Energy Act that the Energy Resources Conservation and Development Commission's Biennial Report to the Governor and to the Legislature contains an analysis of means for reducing growth in energy demand. The Warren-Alquist Energy Act is the enabling legislation for the California ERCDC. The first stages of work by the Energy Commission in preparing an Energy Conservation Action Plan for Federal funding under the provisions of Energy Policy and Conservation Act (PL 94-163) and the Energy Conservation and Production Act (PL 94-385) are also reflected. This report consists of a summary, the rationale for conservation, general strategies, proposed conservation policies, existing and proposed conservation programs, and appendices. Conservation programs, listed by sectors, make up the majority of the report. Estimates of potential savings and cost-effectiveness are presented for most programs. Recommendations for implementation are given for each of the programs. Derivations of all the numerical values presented in the report and a summary of revisions from the preliminary to the final draft are given in the Appendices.
Low-loss low-crosstalk silicon rib waveguide crossing with tapered multimode-interference design (2012)

We report the design and fabrication of silicon rib-waveguide crossings based on taper-integrated multimode-interference. Measured devices built in a 130nm SOI CMOS process showed an insertion loss of 0.1dB/crossing, and an extracted crosstalk below -35dB.
Structural studies in the [M(bidentate ligand)(unidentate ligand)5] system. A new co-ordination type for [Ml2(CO)3{Ph2P(CH2)nPPh2}](M = Mo or W; n= 1—3) (1980)

The crystal structures of [Mol2(CO)3{Ph2P(CH2)2PPh2}]·CH2Cl2(1), [Mol2(CO)3{Ph2P(CH2)3PPh2}](2), and [Wl2(CO)3[{Ph2P(CH2)PPh2}](3) have been determined by single-crystal X-ray methods at 295 K and refined by least squares to residuals of 0.082, 0.061, and 0.051 for 7 358, 4 572, and 4 522′ observed' reflections respectively. Crystals of (1) are monoclinic, space group P21/n, with a= 19.338(6), b= 14.674(6), c= 11.577(5)Å, β= 92.39(3)°, and Z= 4; (2) is monoclinic, space group P21/n, with a= 20.85(1), b= 14.64(2), c= 10.510(4)Å, β= 104.11 (5)°, and Z= 4; (3) is monoclinic, space group P21/c, with a= 20.880(5), b= 8.646(5), c= 16.706(6)Å, β= 104.17(2)°, and Z= 4. For compounds (1) and (2), with bidentate ligands of large bite, the metal-atom stereochemistry is that usually found for complexes of this type, a capped trigonal prism with the bidentate ligand spanning one of the prism edges. For (3), in which the ligand has only one methylene group bridging the two phosphorus atoms, the bite is smaller and a novel stereochemistry is observed, a pentagonal bi-pyramid with the bidentate ligand spanning one of the pentagonal edges.
Deep Learning-Enabled Point-of-Care Sensing Using Multiplexed Paper-Based Sensors (2019)

ABSTRACT We present a deep learning-based framework to design and quantify point-of-care sensors. As its proof-of-concept and use-case, we demonstrated a low-cost and rapid paper-based vertical flow assay (VFA) for high sensitivity C-Reactive Protein (hsCRP) testing, a common medical test used for quantifying the degree of inflammation in patients at risk of cardio-vascular disease (CVD). A machine learning-based sensor design framework was developed for two key tasks: (1) to determine an optimal configuration of immunoreaction spots and conditions, spatially-multiplexed on a paper-based sensing membrane, and (2) to accurately infer the target analyte concentration based on the signals of the optimal VFA configuration. Using a custom-designed mobile-phone based VFA reader, a clinical study was performed with 85 human serum samples to characterize the quantification accuracy around the clinically defined cutoffs for CVD risk stratification. Results from blindly-tested VFAs indicate a competitive coefficient of variation of 11.2% with a linearity of R 2 = 0.95; in addition to the success in the high-sensitivity CRP range (i.e., 0-10 mg/L), our results further demonstrate a mitigation of the hook-effect at higher CRP concentrations due to the incorporation of antigen capture spots within the multiplexed sensing membrane of the VFA. This paper-based computational VFA that is powered by deep learning could expand access to CVD health screening, and the presented machine learning-enabled sensing framework can be broadly used to design cost-effective and mobile sensors for various point-of-care diagnostics applications.
Multi‐Functional MoO3 Doping of Carbon‐Nanotube Top Electrodes for Highly Transparent and Efficient Semi‐Transparent Perovskite Solar Cells (2022)

Abstract MoO 3 doping of carbon‐nanotube top electrodes in perovskite solar cells is multi‐functional and facilitates p‐doping, favorable energy‐level alignment, and enhanced hole transport. The optimal layer thickness of MoO 3 (8 nm) is determined for decreasing the sheet resistance of carbon‐nanotube electrodes without damaging the perovskite film. The sheet resistance decreases by approximately one‐third from its original value, which is a substantially better result than that previously reported for acid doping of carbon‐nanotube top electrodes. MoO 3 deposition lowers the Fermi level of the carbon‐nanotube electrode, improving its energy‐level alignment and hole‐transfer performance. When coated with 2,2′,7,7′‐tetrakis[N,N‐di(4‐methoxyphenyl)amino]‐9,9′‐spirobifluorene (spiro‐MeOTAD), MoO 3 crystallizes on the carbon nanotubes and further enhances hole collection. Semi‐transparent perovskite solar cells with MoO 3 ‐doped carbon‐nanotube electrodes have a power conversion efficiency of 17.3% with a transmittance of approximately 60% (at a wavelength of 1000 nm). Because of their favorable transparency in the infrared region, these perovskite solar cells are evaluated for use in a tandem structure with silicon solar cells via computational simulations. The predicted device efficiency (23.7%) exceeds that of conventional indium‐tin‐oxide‐based tandem solar cells (23.0%).
Signal Analysis of Phase Inversion in Oil-Water Mixtures (2019)

Abstract The present paper is concerned with an experimental study of the acoustic signature of phase inversion in an oil-water mixture system. The experimental results from a batch system revealed that the correlation between the acoustic fields produced by a water-continuous dispersion has a different signature from an oil-continuous dispersion. Phase inversion could be clearly identified based on the acoustic field generated by the stirrer. This dynamic characteristic of the phase inversion phenomenon could be of use in a practical system, such as a mixing system or flowlines to detect phase inversion when it occurs.