gebhart/patrepeval huggingface dataset:
Brave New World (2013)

D r Rastan and colleagues 1 are to be congratulated for per- forming a well-designed multicenter, prospective, randomized, controlled trial comparing primary stenting with provisional stenting for moderate-length (42 mm) popliteal artery stenoses in primarily claudicators (79%) with one third having total occlusions. 1 The Endovascular Treatment of Atherosclerotic Popliteal Artery Lesions-Balloon Angioplasty Versus Primary Stenting (ETAP) trial confirms, for what seems to be the bazillionth time, that provisional stenting, properly performed, achieves functional and patency outcomes equal to those of primary stenting. This has been shown for femoral lesions in multiple trials that often included lesions extending into the popliteal artery, and now it has been shown for the isolated popliteal disease. Although not reported in this article, we would expect a cost analysis to demonstrate that provisional stenting, for appropriate indications, would be resource sparing compared with primary stenting.
Inferring early genetic progression in cancers with unobtainable premalignant disease (2023)

Analysis of premalignant tissue has identified the typical order of somatic events leading to invasive tumors in several cancer types. For other cancers, premalignant tissue is unobtainable, leaving genetic progression unknown. Here, we demonstrate how to infer progression from exome sequencing of primary tumors. Our computational method, PhylogicNDT, recapitulated the previous experimentally determined genetic progression of human papillomavirus-negative (HPV<sup>-</sup>) head and neck squamous cell carcinoma (HNSCC). We then evaluated HPV<sup>+</sup> HNSCC, which lacks premalignant tissue, and uncovered its previously unknown progression, identifying early drivers. We converted relative timing estimates of driver mutations and HPV integration to years before diagnosis based on a clock-like mutational signature. We associated the timing of transitions to aneuploidy with increased intratumor genetic heterogeneity and shorter overall survival. Our approach can establish previously unknown early genetic progression of cancers with unobtainable premalignant tissue, supporting development of experimental models and methods for early detection, interception and prognostication.
Dense motion fields for digital video processing and compression (2003)

This paper presents novel algorithms that perform motion estimation for video processing and compression. We observe that "smoothness" is a very important and intuitive property in the estimation of motion fields. It is pointed out that most current motion estimation techniques implement smoothness as a constraint, differing only in terms of the specific type of smoothness demanded from video data. This paper views smoothness as a property that is determined by the underlying video data rather than a predetermined and specific property that is imposed on video data. Instead of forcing the available video data to conform to an abstract smoothness model, we try to select the "smoothest" motion field that conforms to the available data. We propose fast and efficient techniques that determine a set of possible motion fields and that select the smoothest field from this set. Issues like quantization and embedded video compression (via embedded motion fields) are discussed.
High-Throughput Chlorophyll and Carotenoid Profiling Reveals Positive Associations with Sugar and Apocarotenoid Volatile Content in Fruits of Tomato Varieties in Modern and Wild Accessions (2021)

Flavor and nutritional quality has been negatively impacted during the course of domestication and improvement of the cultivated tomato (<i>Solanum</i>&nbsp;<i>lycopersicum</i>). Recent emphasis on consumers has emphasized breeding strategies that focus on flavor-associated chemicals, including sugars, acids, and aroma compounds. Carotenoids indirectly affect flavor as precursors of aroma compounds, while chlorophylls contribute to sugar production through photosynthesis. However, the relationships between these pigments and flavor content are still unclear. In this study, we developed a simple and high-throughput method to quantify chlorophylls and carotenoids. This method was applied to over one hundred tomato varieties, including <i>S</i>. <i>lycopersicum</i> and its wild relatives (<i>S</i>. <i>l</i>. var. <i>cerasiforme</i> and <i>S</i>. <i>pimpinellifolium</i>), for quantification of these pigments in fruits. The results obtained by integrating data of the pigments, soluble solids, sugars, and aroma compounds indicate that (i) chlorophyll-abundant varieties have relatively higher sugar accumulations and (ii) prolycopene is associated with an abundance of linear carotenoid-derived aroma compounds in one of the orange-fruited varieties, "Dixie Golden Giant". Our results suggest the importance of these pigments not only as components of fruit color but also as factors influencing flavor traits, such as sugars and aroma.
Amphoteric, Sulfonamide-Functionalized “Polysoaps”: CO2-Induced Phase Separation for Water Remediation (2018)

Amphoteric polysoaps have been prepared via statistical RAFT copolymerization using either methacryloyl sulfacetamide (mSAC) or methacryloyl sulfmethazine (mSMZ) and 4-hexylphenyl methylacrylamide (4HPhMA). These copolymers form pH- and CO2-responsive polymeric micelles capable of sequestering hydrophobic molecules in water. The composition and structure of the respective copolymers can be changed to tailor the onset and extent of CO2-dependent phase behavior. When CO2 is introduced into the system, resulting in carbonic acid formation, the pH drops below the pKa of the sulfonamide units along the copolymer backbone, and phase separation occurs. Purging with N2 results in an increase in pH and redissolution of the polysoap; this process can be repeated multiple times. The mSMZ polysoaps, which show complete phase transitions using this reversible process, were especially efficient in removing the model contaminants pyrene and 9-anthracenemethanol from water. The feasibility of recovering and reusing these copolymers is demonstrated, pointing to the potential utility of such CO2-responsive systems in water treatment and related environmental remediation applications.
Robust engineering design optimization with non-uniform rational B-splines-based metamodels (2012)

Abstract Non-uniform rational B-splines (NURBs) demonstrate properties that make them attractive as metamodels, or surrogate models, for engineering design purposes. Previous research has resulted in the development of algorithms capable of fitting NURBs-based metamodels to engineering design spaces, and optimizing these models. This article presents an approach to robust optimization that employs NURBs-based metamodels. This robust optimization technique exploits the unique structure of NURBs-based metamodels to derive a simple but effective robustness metric. An algorithm is demonstrated that uses this metric to weigh robustness against optimality, and visualizes the trade-offs between these metamodel properties. This approach is demonstrated with test problems of increasing dimensionality, including several practical design challenges. Keywords: robust designNURBsmetamodelssplines Acknowledgements This research would not have been possible without the support of the National Science Foundation under grant no. CMMI-0900182 and the Colorado School of Mines, College of Engineering and Computer Science. Any opinions, findings and conclusions are those of the authors and do not necessarily reflect the views of the National Science Foundation or the Colorado School of Mines.
Failure Analysis of InP-Based Edge-Emitting Buried Heterostructure Laser Diodes Degraded by Forward-Biased Electrostatic Discharge Tests (2009)

We investigated the forward-biased electrostatic discharge (ESD)-induced degradation that is one of the important reliability issues for InP-based edge-emitting buried heterostructure laser diodes. Although it has been suggested that the degradation mechanism is related to optical damage, the detailed mechanism has not been established. Thus, we carried out failure analysis. Two elliptically shaped degraded regions, which were introduced by the first and second ESD pulses, were observed in an active layer. A peculiar chain-like degradation was created along the longitudinal axis. This degradation was caused by light absorption at an active layer. We also investigated the relationship between forward-biased ESD tolerance and an aging test. We observed a decrease in tolerance as a result of the aging test for laser diodes with cleaved facets. This decrease was sufficiently suppressed by facet coating. We identified two reasons why facet coating is important. One is to obtain sufficient ESD tolerance under initial conditions, and the other is to suppress the decrease in ESD tolerance during aging.
Coarse‐graining: A procedure to generate equilibrated and relaxed models of amorphous polymers (2007)

We present a coarse-graining procedure to construct models of amorphous polymers. The method, which was applied to polyethylene, is based on a generation-relaxation strategy previously developed to provide independent atomistic microstructures. The coarse-graining was performed by assigning positions to mesoscopic particles denoted blobs, which represent groups of atoms, through distance, angle and dihedral distribution functions. The interaction energy between pairs of blobs was evaluated through a soft potential, whose parameters were derived from atomistic models. Three levels of coarse-graining that differ in the number of atoms included in the blob have been considered. The structural and energy-related properties calculated using the coarse-grained models developed in this study are in good agreement with those obtained using atomistic simulations.
Overcoming the Photovoltage Plateau in Large Bandgap Perovskite Photovoltaics (2018)

Development of large bandgap (1.80-1.85 eV E<sub>g</sub>) perovskite is crucial for perovskite-perovskite tandem solar cells. However, the performance of 1.80-1.85 eV E<sub>g</sub> perovskite solar cells (PVKSCs) are significantly lagging their counterparts in the 1.60-1.75 eV E<sub>g</sub> range. This is because the photovoltage ( V<sub>oc</sub>) does not proportionally increase with E<sub>g</sub> due to lower optoelectronic quality of conventional (MA,FA,Cs)Pb(I,Br)<sub>3</sub> and results in a photovoltage plateau ( V<sub>oc</sub> limited to 80% of the theoretical limit for ∼1.8 eV E<sub>g</sub>). Here, we incorporate phenylethylammonium (PEA) in a mixed-halide perovskite composition to solve the inherent material-level challenges in 1.80-1.85 eV E<sub>g</sub> perovskites. The amount of PEA incorporation governs the topography and optoelectronic properties of resultant films. Detailed structural and spectroscopic characterization reveal the characteristic trends in crystalline size, orientation, and charge carrier recombination dynamics and rationalize the origin of improved material quality with higher luminescence. With careful interface optimization, the improved material characteristics were translated to devices and V<sub>oc</sub> values of 1.30-1.35 V were achieved, which correspond to 85-87% of the theoretical limit. Using an optimal amount of PEA incorporation to balance the increase in V<sub>oc</sub> and the decrease in charge collection, a highest power conversion efficiency of 12.2% was realized. Our results clearly overcome the photovoltage plateau in the 1.80-1.85 eV E<sub>g</sub> range and represent the highest V<sub>oc</sub> achieved for mixed-halide PVKSCs. This study provides widely translatable insights, an important breakthrough, and a promising platform for next-generation perovskite tandems.
Transient Colloidal Stability Controls the Particle Formation of SBA-15 (2012)

A hypothesis about (transient) colloidal stability as a controlling mechanism for particle formation in SBA-15 is presented. The hypothesis is based on results from both in situ and ex situ investigations, including cryogenic transmission electron microscopy (cryo-TEM), UV-vis spectroscopy, and dynamic light scattering (DLS). Cryo-TEM images show that particles grow via the formation of silica-Pluronic-water "flocs", which coalesce in a seemingly arbitrary manner. Despite this, the final material consists of well-defined particles with a small size distribution. We argue that the interface between the flocs and surrounding media is covered by Pluronic molecules, which provide steric stabilization. As the flocs grow, the coverage of polymers at the interface is increased until a stable size is reached, and that regulates the particle size. By targeting the characteristics of the Pluronic molecules, during the on-going synthesis, the hypothesis is tested. The results are consistent with the concept of (transient) colloidal stability.
Vanadate Has no Effect on Insulin-Extraction by the Rat Liver (1994)

The mechanism(s) responsible for the insulin-like effects of vanadate are still unclear, although several possible explanations have been raised. However, the possibility that vanadate induces inhibition of insulin degradation in the liver was not examined yet. Therefore, in the present study we examined the effect of vanadate on the extraction of insulin by the perfused rat liver using an open, non-recycling system. Baseline insulin extraction (44 ± 2% and 37±3%) was not affected by the administration of 1 and 5 μM vanadate (decreased to 42±2% and 36±1%, respectively, p = NS). Vanadate had no adverse effects on liver viability, and the bile flow remained stable during and after vanadate administration (0.87±0.08 μl/min/g liver prior to Vs. 0.084 ± 0.11 μl/min/g liver following vanadate administration). This study shows that vanadate does not inhibitinsulin extraction by the perfused liver, and that doses of vanadate that effectively inhibit hepatic glucose production possess no adverse effects on liver viability.
High Yield Expression of Human BACE Constructs in Eschericia coli for Refolding, Purification, and High Resolution Diffracting Crystal Forms (2008)

BACE (beta-site APP cleaving enzyme) or beta-secretase, the enzyme responsible for processing APP to give the N-terminal portion of the Abeta peptide, is a membrane bound aspartyl protease consisting of an ectodomain catalytic unit, a C-terminal transmembrane segment and a cytoplasmic domain. Three BACE constructs, pET11a-BACE, pQE80L-BACE, and pQE70-BACE were designed to terminate at a position just before the transmembrane domain (Ser(432)) and are described schematically below. (1) pET11a-T7.Tag-G-S-M-(A-8GV......QTDES(432)), (2) pQE80L-Met-R-G-S-(His)(6)-G-S-I-E-T-D-(T(1)QH...QTDES(432)), and (3) pQE70-Met-BACE (R(36)GSFVEMG....PQTDES(432) (His) (6)) Each construct was over-expressed in Escherichia coli as inclusion bodies. The inclusion body proteins were solubilized in urea and refolded by dilution in water to yield active enzyme. Maximal activity for pET11a-BACE and pQE80L-BACE was usually reached at day 3 to 4, while construct pQE70-BACE required about 21 days. Active BACE was purified to homogeneity by anion-exchange chromatography and affinity chromatography over a column of immobilized peptide inhibitor. The process, easily scalable to 60 liters of cell culture, yielded in excess of 400 mg of active enzyme for crystallographic analysis. Highly purified pET11a-BACE and pQE70-BACE formed complexes with various inhibitors, the latter protein giving crystals diffracting up to 1.45 A resolution. In addition, a crystal form that does not require the presence of an inhibitor has been obtained for pQE70-BACE. This ligand-free crystal form has proven useful for the preparation of BACE-inhibitor complexes in soaking experiments.
A luminescence-based assay of UDP-sugar producing pyrophosphorylases (2013)

A coupled luminescence assay was applied to monitor pyrophosphate (PPi) production by either purified barley UDP-glucose pyrophosphorylase (UGPase) or purified Leishmania UDP-sugar pyrophosphorylase (USPase). In the assay, the PPi produced by the pyrophosphorylases was converted to ATP by ATP-sulfurylase, and the ATP produced was linked to luminescent light formation through the action of firefly luciferase. The assay allowed for a quantitative measurement of UGPase and USPase activities, down to a pmol per min level. The activities were linear with time and proportional to the amount of the enzyme added, and were neither affected by Pi nor by DTT. For UGPase, Km values with UTP and Glc-1-P were 0.14 and 0.26 mM, respectively, whereas for USPase the respective Km values with UTP, Glc-1-P and Gal-1-P were 0.4, 2.9 and 3.9 mM. Possible applications of the luminescence-based assay for not only UDP-sugar producing pyrophosphorylases, but also other types of pyrophosphorylases are discussed.
Component segmentation of sketches used in 3D model retrieval (2015)

Sketching is a natural human practice. With the popularity of multi-touch tablets and styluses, sketching has become a more popular means of human-computer interaction. However, accurately recognizing sketches is rather challenging, especially when they are drawn by non-professionals. Therefore, automatic sketch understanding has attracted much research attention. To tackle the problem, we propose to segment sketch drawings before analyzing the semantic meanings of sketches for the purpose of developing a sketch-based 3D model retrieval system.
Is bile acid malabsorption underdiagnosed? An evaluation of accuracy of diagnosis by measurement of SeHCAT retention. (1985)

The cause of intractable chronic diarrhoea was found to be malabsorption of bile acid in five out of 42 patients thought to have the irritable bowel syndrome, six out of 29 patients with persistent diarrhoea after surgery for peptic ulcer, 23 who had undergone small bowel resection, and two others. Specific treatment brought symptomatic relief. The diagnosis was established by measuring the proportion of SeHCAT, a synthetic bile salt, retained one week after oral administration of a tracer dose of less than 100 micrograms of the compound labelled with 40 kBq (1 microCi) of selenium-75. These results indicate that malabsorption of bile acid is a more common cause of chronic diarrhoea than is generally appreciated. Measurement of retention of SeHCAT is a simple, accurate, and acceptable means of establishing the diagnosis of this debilitating but treatable condition.
Competition between ABO and Le Gene Specified Enzymes (1983)

One B- and two A-specific radioimmunoassays detected A and B antigenic determinants in saliva of ABH nonsecretors. The A or B antigens found in saliva of nonsecretors had lower efficiency and higher heterogeneity, in the inhibition of the A or B assays, as compared to A or B antigens in saliva of ABH secretors. In the 3 assays, samples of nonsecretor Lewis positive donors (Le^a) had less A or B antigens than samples of nonsecretor Lewis negative donors (Le^c), suggesting that there is a competition between A or B and Le gene-specified products.
High power piezoelectric transformer for driving a 28 W fluorescent lamp (2002)

In this study, contour-vibration-mode Pb(Ni/sub 1/2/,W/sub 1/2/)O/sub 3/-Pb(Mn/sub 1/3/, Nb/sub 2/3/)O/sub 3/-Pb(Zr, Ti)O/sub 3/ piezoelectric transformers were fabricated in the modified filter structure with ring and dot electrodes. The transformers have been developed for application in 455 kHz AM radios. The piezoelectric transformers were fabricated to the size of 31.5/spl times/31.5/spl times/2.5mm/sup 3/ by cold isostatic pressing. Driving of the piezoelectric transformer was carried out with input region for the ring electrode and output region for the dot electrode. The electrical properties and characteristic temperature rises caused by the vibration were measured at various load resistances. Efficiencies above 90% with load resistance were obtained from the transformers. A 28 W (T5) fluorescent lamp was successfully driven by the fabricated transformer. The transformer with ring/dot electrode area ratio of 1.83 exhibited the best properties in terms of output power, efficiency and characteristic temperature rise, 30.95 W, 97.57% and 8.3/spl deg/C, respectively.
Proton vibrational dynamics in lithium imide investigated through incoherent inelastic and Compton neutron scattering (2012)

In the present study we report neutron spectroscopic measurements on polycrystalline lithium imide, namely, incoherent inelastic neutron scattering at 20 K, and neutron Compton scattering from 10 K up to room temperature. From the former technique the H-projected density of phonon states up to 100 meV is derived, while the latter works out the spherically averaged single-particle (i.e., H, Li, and N) momentum distributions and, from this, the mean kinetic energies. Only for H at the lowest investigated temperature, non-gaussian components of its momentum distribution are detected. However, these components do not seem directly connected to the system anharmonicity, being fully compatible with the simple N-H bond anisotropy. Neutron data are also complemented by ab initio lattice dynamics simulations, both harmonic and, at room temperature, carried out in the framework of the so-called "quantum colored noise thermostat" method. The single-particle mean kinetic energies in lithium imide as a function of temperature show a quite peculiar behavior at the moment not reproduced by ab initio lattice dynamics methods, at least as far as H and Li are concerned. As matter of fact, neither their low temperature values nor their temperature trends can be precisely explained in terms of standard phonon calculations.