gebhart/patrepeval huggingface dataset:
Program verification as probabilistic inference (2007)

In this paper, we propose a new algorithm for proving the validity or invalidity of a pre/postcondition pair for a program. The algorithm is motivated by the success of the algorithms for probabilistic inference developed in the machine learning community for reasoning in graphical models. The validity or invalidity proof consists of providing an invariant at each program point that can be locally verified. The algorithm works by iteratively randomly selecting a program point and updating the current abstract state representation to make it more locally consistent (with respect to the abstractions at the neighboring points). We show that this simple algorithm has some interesting aspects: (a) It brings together the complementary powers of forward and backward analyses; (b) The algorithm has the ability to recover itself from excessive under-approximation or over-approximation that it may make. (Because the algorithm does not distinguish between the forward and backward information, the information could get both under-approximated and over-approximated at any step.) (c) The randomness in the algorithm ensures that the correct choice of updates is eventually made as there is no single deterministic strategy that would provably work for any interesting class of programs. In our experiments we use this algorithm to produce the proof of correctness of a small (but non-trivial) example. In addition, we empirically illustrate several important properties of the algorithm.
Tomato Fructokinases Exhibit Differential Expression and Substrate Regulation1 (1998)

Two divergent genes encoding fructokinase, Frk1 and Frk2, have been previously shown to be expressed in tomato (Lycopersicon esculentum L.) and have now been further characterized with regard to their spatial expression and the enzymic properties of the encoded proteins. Frk1 and Frk2 mRNA levels were coordinately induced by exogenous sugar, indicating that both belong to the growing class of sugar-regulated genes. However, in situ hybridization indicated that Frk1 and Frk2 were expressed in a spatially distinct manner, with Frk2 mRNA primarily localized in cells of the fruit pericarp, which store starch, and Frk1 mRNA distributed ubiquitously in pericarp tissue. To evaluate the biochemical characteristics of the products of the Frk1 and Frk2 genes, each cDNA was expressed in a mutant yeast (Saccharomyces cerevisiae) line defective in hexose phosphorylation and unable to grow on glucose or fructose (Fru). Both Frk1 and Frk2 proteins expressed in yeast conferred the ability to grow on Fru and exhibited fructokinase activity in vitro. Although both Frk1 and Frk2 both utilized Fru as a substrate, only Frk2 activity was inhibited at high Fru concentrations. These results indicate that Frk2 can be distinguished from Frk1 by its sensitivity to substrate inhibition and by its temporal and spatial pattern of expression, which suggests that it plays a primary role in plant cells specialized for starch storage.
Photoaffinity labelling of human leukotriene C<sub>4</sub> synthase in THP‐1 cell membranes (1993)

Human leukotriene C4 synthase specific activity in the human monocytic leukemia cell line THP-1 (0.302 +/- 0.062 nmol LTC4 formed.min-1 x mg-1) was 7.6-fold higher than in U937 cells (0.040 +/- 0.017 nmol LTC4 formed.min-1 x mg-1) and comparable to dimethylsulfoxide-differentiated U937 cells (0.399 +/- 0.084 nmol LTC4 formed.min-1 x mg-1). Using the photoaffinity probe, azido[125I]-LTC4, a single polypeptide with a molecular mass of 18 kDa was specifically labelled in THP-1 microsomal membranes. The rank order of potencies for competition of azido[125I]-LTC4 photolabelling of the 18 kDa protein by glutathione, leukotrienes and their analogs was found to be LTC2 > (azido[127I]-LTC4 approximately LTC4) > (LTD4 approximately LTE4) > (LTA4 approximately LTB4) > S-hexyl glutathione > glutathione, corresponded with the rank order of potencies for inhibition of LTC4 synthase activity but not inhibition of microsomal glutathione S-transferase activity. The 18 kDa protein specifically labelled by azido[125I]-LTC4 had high specificity for LTC4 and closely related leukotrienes and was separable from microsomal glutathione S-transferase. We conclude that azido[125I]-LTC4 specifically photolabels LTC4 synthase which is an 18 kDa polypeptide or contains an 18 kDa subunit.
On Extended Transform Partitions For The Next Generation Video CODEC (2020)

AV1, AOMedia's royalty free codec, has enjoyed a great amount of success since its 2018 release. It currently achieves 31% BDRATE gains over VP9, and is on its way to becoming YouTube's default codec. Although the industry is currently focused on the implementation and optimization of AV1, AOMedia Research continues to develop new coding tools that deliver higher coding gains within acceptable complexity bounds. Here, we focus on improving transform coding. While AV1 has made great strides in transform coding over VP9, the residue signal still consumes a large portion of the bitstream. In this paper, we describe a more flexible transform partitioning scheme, which will allow the next generation codec to more efficiently target areas in the residue signal with high energy, leading to better residue compression.
Primate Animal Models and Titered Inocula for the Study of Human Hepatitis A, Hepatitis B, and Non‐A, Non‐B Hepatitis (1983)

Although many primate species have been inoculated with the agents of human hepatitis A, B, and non‐A, non‐B, only a small number of species have been shown to be susceptible, and only the chimpanzee (Pan troglodytes) has been shown to be reproducibly susceptible to all three types of human hepatitis. Infectious inocula containing each agent have been identified in different laboratories and the end‐point titers of infectivity determined, in most cases by inoculation of chimpanzees. These inocula and the nonhuman primate models have permitted investigators to study the inactivation of these agents and to evaluate passive and active immunization against the agents.
Windmill artifact in multislice helical CT (2003)

Multi-slice helical CT-systems suffer from windmill artifacts: black/white patterns that spin off of features with high longitudinal gradients. The number of black/white pairs matches the number of slices (detector rows) in the multi-slive detector. The period of spin is the same as the helical pitch. We investigate the cause of the pattern by following the traces of selected voxels through the multi-slive detector array as a function of view position. This forms an "extracted sinogram" which represents the data used to reconstruct the specific voxel. Now we can determine the cause of the artifact by correlating the windmill streak in the image with the extracted data. The investigation shows that inadequate sampling along the longitudinal direction causes the artifact.
Rational design strategies for FimH antagonists: new drugs on the horizon for urinary tract infection and Crohn’s disease (2017)

The bacterial adhesin FimH is a virulence factor and an attractive therapeutic target for urinary tract infection (UTI) and Crohn's Disease (CD). Located on type 1 pili of uropathogenic E. coli (UPEC), the FimH adhesin plays an integral role in the pathogenesis of UPEC. Recent efforts have culminated in the development of small-molecule mannoside FimH antagonists that target the mannose-binding lectin domain of FimH, inhibiting its function and preventing UPEC from binding mannosylated host cells in the bladder, thereby circumventing infection. Areas covered: The authors describe the structure-guided design of mannoside ligands, and review the structural biology of the FimH lectin domain. Additionally, they discuss the lead optimization of mannosides for therapeutic application in UTI and CD, and describe various assays used to measure mannoside potency in vitro and mouse models used to determine efficacy in vivo. Expert opinion: To date, mannoside optimization has led to a diverse set of small-molecule FimH antagonists with oral bioavailability. With clinical trials already initiated in CD and on the horizon for UTI, it is the authors, opinion that mannosides will be a 'first-in-class' treatment strategy for UTI and CD, and will pave the way for treatment of other Gram-negative bacterial infections.
Preliminary Component Design and Cost Estimation of a Novel Electric-Thermal Energy Storage System Using Solid Particles (2021)

Abstract Energy storage will become indispensable to complement the uncertainty of intermittent renewable resources and to firm the electricity supply as renewable power generation becomes the mainstream new-built energy source and fossil fuel power plants are phased out to meet carbon-neutral utility targets. Current energy storage methods based on pumped storage hydropower or batteries have many limitations. Thermal energy storage (TES) has unique advantages in scale and siting flexibility to provide grid-scale storage capacity. A particle-based TES system is projected to have promising cost and performance characteristics to meet the future growing energy storage needs. This paper introduces the system and components required for particle TES to become technically and economically competitive. The system integrates electric particle heaters, particle TES within insulated concrete silos, and an efficient air-Brayton combined-cycle power system to provide power for storage durations up to several days via low-cost, high-performance storage cycles. Design specifications and cost estimation of major components in a commercial-scale system are presented in this paper. A techno-economic analysis based on preliminary component designs and performance indicates that particle TES integrated with an air-Brayton combined-cycle power system has a path to achieve the targeted levelized cost of storage of 5 ¢/kWh-cycle at a round-trip efficiency of 50% when taking low-cost energy-specific components and leveraging basic assets from existing thermal power plants. The cost model provides insights for further development and economic potentials for long-duration energy storage.
<title>TE/TM cross-polarization laser diodes using tensile-strained quantum wells</title> (1996)

Polarization characteristics of TE/TM cross-polarization semiconductor laser diodes are discussed in this paper. Broad area lasers fabricated from tensile strained In<SUB>0.5+(delta</SUB> )Ga<SUB>0.5-(delta</SUB> )P/(AlGa)<SUB>0.5</SUB>In<SUB>0.5</SUB>P quantum well laser structures oscillate in TE/TM dual polarizations. Polarization dominance changes from TE to TM as the cavity length of the laser is increased from 250 micrometers to 650 micrometers. The polarization-dependent gain property of a tensile-strained quantum well laser is analyzed from a simple theoretical model. In a slightly tensile strain quantum well, where light-hole and heavy-hole ground states are nearly degenerate in the valence band due to the strain and quantization effect, gain is provided for TM and TE modes simultaneously, and the two mode gain curves cross at certain injection level. Polarization switching is made possible by changing the threshold gain of the laser. The threshold gain dependent polarization switching is utilized to fabricate closely spaced independently-addressable dual beam cross polarization lasers. Results on 650 nm broad area dual beam cross polarization laser are presented. For dual polarization infrared lasers, a dual quantum well structure in which gains for TE and TM modes are provided by lattice-matched and tensile-strained quantum wells separately is designed. Eight-hundred-thirty-five nm broad area laser fabricated from a GaAs and GaAs<SUB>0.95</SUB>P<SUB>0.05</SUB> dual quantum well structure oscillating in TE/TM dual polarizations is demonstrated.
The MPSim‐Dock hierarchical docking algorithm: Application to the eight trypsin inhibitor cocrystals (2004)

To help improve the accuracy of protein-ligand docking as a useful tool for drug discovery, we developed MPSim-Dock, which ensures a comprehensive sampling of diverse families of ligand conformations in the binding region followed by an enrichment of the good energy scoring families so that the energy scores of the sampled conformations can be reliably used to select the best conformation of the ligand. This combines elements of DOCK4.0 with molecular dynamics (MD) methods available in the software, MPSim. We test here the efficacy of MPSim-Dock to predict the 64 protein-ligand combinations formed by starting with eight trypsin cocrystals, and crossdocking the other seven ligands to each protein conformation. We consider this as a model for how well the method would work for one given target protein structure. Using as a criterion that the structures within 2 kcal/mol of the top scoring include a conformation within a coordinate root mean square (CRMS) of 1 A of the crystal structure, we find that 100% of the 64 cases are predicted correctly. This indicates that MPSim-Dock can be used reliably to identify strongly binding ligands, making it useful for virtual ligand screening.
Characterization of a superconductive sigma-delta analog to digital converter (1995)

Sigma-delta analog to digital converters (ADCs) use a combination of oversampling and feedback to concentrate quantization noise outside the frequency band of interest. Subsequent digital filtering can then be used to suppress the quantization noise and yield a large signal to noise ratio. Sigma-delta ADCs dominate the high performance audio market, where the signal band is limited to frequencies below 50 kHz and 8 octave oversampling requires a sampling rate of only 25.6 MHz. Przybysz et al. have described a superconductive circuit capable of >40 GHz sampling, thereby extending the useful bandwith to tens of MHz. In this paper, we describe the realization of that circuit and present measurements of its performance. Spectral analysis of the modulator performance shows spur-free dynamic range of over 78 dB and third order intermodulation products less than -68 dBc. Quantization noise shaping is also demonstrated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Automated analysis of eddy current data from inspection of PWR steam generator tubing (1985)

This paper describes the initial successful application of a computer system for the automatic data analysis of steam generator tubing inspection. The system is titled Intelligent Eddy Current Data Analysis (IEDA) System. The results of the IEDA system analysis are compared with the results obtained by the independent analysis done by human analysts per current standard industry procedures. The IEDA system is equivalent to the current practice in terms of speed, accuracy, and precision. It also provides an extensive data base of eddy current signals identified as dents, distorted support plates, etc. which are normally not provided in the results of ''conventional'' inspection data analysis on tubing condition. These signals can be used as input to diagnostic evaluation of the steam generator operating conditions. Results of these evaluations can be used in trend analysis that can point to necessary corrective actions required to extend the useful life of the steam generators.
Piezoelectric composite based on the enhanced flexoelectric effects (2006)

In this study, a piezoelectric composite is fabricated from a Ba0.67Sr0.33TiO3 (BST) composition and air, and measured at room temperature (24°C) where the BST is in its paraelectric centric phase. The charge separation mechanism is flexoelectricity, driven by the strain gradient introduced by the pyramidal boundary shapes of each BST building unit of the composite. In spite of the macro (millimeter) dimensions of the building units that inhibit a steep strain gradient, the composite is sufficiently active to be measured by using a conventional Berlincourt d33 meter. The measured values are in good agreement with expectation from the earlier measured flexoelectric coefficient μ11 of the BST and the finite element simulation results of the strain gradient in the pyramid BST units.
Bioengineered vocal fold mucosa for voice restoration (2015)

Patients with voice impairment caused by advanced vocal fold (VF) fibrosis or tissue loss have few treatment options. A transplantable, bioengineered VF mucosa would address the individual and societal costs of voice-related communication loss. Such a tissue must be biomechanically capable of aerodynamic-to-acoustic energy transfer and high-frequency vibration and physiologically capable of maintaining a barrier against the airway lumen. We isolated primary human VF fibroblasts and epithelial cells and cocultured them under organotypic conditions. The resulting engineered mucosae showed morphologic features of native tissue, proteome-level evidence of mucosal morphogenesis and emerging extracellular matrix complexity, and rudimentary barrier function in vitro. When grafted into canine larynges ex vivo, the mucosae generated vibratory behavior and acoustic output that were indistinguishable from those of native VF tissue. When grafted into humanized mice in vivo, the mucosae survived and were well tolerated by the human adaptive immune system. This tissue engineering approach has the potential to restore voice function in patients with otherwise untreatable VF mucosal disease.
Proteomic analysis of ascending colon biopsies from a paediatric inflammatory bowel disease inception cohort identifies protein biomarkers that differentiate Crohn's disease from UC (2016)

This study has identified two panels of candidate biomarkers for the diagnosis of IBD and the differentiation of IBD subtypes to guide appropriate therapeutic interventions in paediatric patients.
Voiceband signal classification using statistically optimal combinations of low-complexity discriminant variables (1999)

This paper considers the problem of classifying voiceband modem, facsimile, native binary data, and speech signals on a 64-kb/s digital channel using low complexity discriminant functions similar to those investigated by Benvenuto (1989). Benvenuto's method is simplified by replacing an approximate demodulation step with rectification of the passband signal and improved by using statistical analysis to select and combine the most effective variables into statistically optimal discriminant functions.
Jitter Detection and Image Restoration Based on Continue Dynamic Shooting Model for High-Resolution TDI CCD Satellite Images (2020)

Although time delay integration charge-coupled devices (TDI CCDs) have been widely used in high-resolution spaceborne optical cameras, they are sensitive to satellite jitter: the images obtained by them are affected by both distortion and blur. Therefore, according to the multistage integral imaging characteristics of TDI CCDs, this article not only proposes a continue dynamic shooting model (CDSM) to reflect the real push-broom mode of the satellite but also presents a method containing jitter detection and image restoration based on it. In the presented method, the CDSM subdivides the TDI CCD integration intervals. The subdivision number of CDSM is determined by the proposed integral transformation function (ITF). Then, it feeds back into the ITF and also contributes to the point spread function (PSF) estimation. Among the abovementioned, ITF defines the relationship between the parallax images and the jitter curve, and aims to improve the jitter detection performance. Finally, an adaptive image restoration based on context is conducted, which combines time, space, and spectrum information. Besides the simulated images, multispectral images of GaoFen-1 02 satellite were also adopted to validate the performance of the presented method. Experimental results indicate that the accuracy of the jitter detection is increased, and the geometric and radiometric qualities of restored images are also improved.
Differences in Erythrocyte Receptor Specificity of Different Parts of the Plasmodium falciparum Reticulocyte Binding Protein Homologue 2a (2011)

The Plasmodium falciparum reticulocyte-binding-like protein homologue (RH) and erythrocyte binding-like (EBL) protein families play important roles during invasion, though their exact roles are not clear. Both EBL and RH proteins are thought to directly bind different receptors on the surface of the erythrocyte, and the binding properties for a number of EBLs and RHs have been described. While P. falciparum RH1 (PfRH1) and PfRH4 have been shown to act directly in two alternative invasion pathways used by merozoites, the functions of PfRH2a and PfRH2b during invasion are less defined. Here, using monoclonal antibodies raised against a unique region of PfRH2a, we show that PfRH2a moves from the rhoptry neck to the moving junction during merozoite invasion. The movement of PfRH2a to the junction is independent of the invasion pathway used by the merozoite, suggesting an additional function of the protein that is independent of receptor binding. We further show that PfRH2a is processed both in the schizont and during invasion, resulting in proteins with different erythrocyte binding properties. Our findings suggest that PfRH2a and, most likely, the other members of the RH family, depending on their processing stage, can engage different receptors at different stages of the invasion process.
Validation Of An Optical Fiber Based Smart Textile: A Clinical Tool For Predicting Diabetic Foot Ulceration (2014)

Background: Undetected repeated foot loading and temperature changes during walking in diabetic patients with peripheral neuropathy significantly increases risk of foot ulceration. Early detection of inflammation due to foot temperature and pressure changes from walking has shown to be a potentially effective strategy in prevention of foot ulcers. Therefore, a clinically feasible assessment of these changes is vital to measure pre-ulcerative inflammation and predict DFUs. The current study is aimed to validate effectiveness of an innovative fiber optics embedded smart textile for simultaneous measurement of plantar pressure and temperature. Methods: The study recruited 21 diabetic patients (Age: 57.8±7.9 years, BMI: 31.6±8.0 kg/m2, VPT: 26.8±15 volt, 68% diagnosed with peripheral neuropathy) at high risk for foot ulcers from Wound and Diabetic Foot Center at Hamad Medical Co. Doha. A series of sensors were juxtaposed on the length of an optical fiber integrated in a comfortable sock (Novinoor LLC, IL) for measuring temperature and pressure changes under anatomical regions of the heel, midfoot, 1st and 5th metatarsal heads, and big toe based on changes in wavelength of light. A thermal image was acquired after five-minute temperature acclimation before walking for validating temperature changes. Participants walked 200 steps to induce thermal stress and follow up thermal image was acquired. Participants also wore F-scan insoles (TekScan®Inc) during walk for pressure validation. Results: All the recruited patients perceived the device as comfortable. A significant correlation was observed between both pressure (r=0.67, p<0.05) and temperature (r=0.55, p<0.05) measurements between the sock and the reference systems under different anatomical regions of interest. Conclusion: This study demonstrates the proof of concept for an innovative smart textile in simultaneous assessment of the key parameters associated with risk of foot ulcer in patients with diabetes. Given the correlation values, additional studies will larger sample size is required to further validate and address whether the technology can predict and better manage diabetic foot ulcers. Funding source: NPRP 4-1026-3-277