gebhart/patrepeval huggingface dataset:
Berberine potently inhibits protein tyrosine phosphatase 1B: Investigation by docking simulation and experimental validation (2006)

Berberine was investigated as an inhibitor of human protein tyrosine phosphatase 1B (h-PTP 1B) in an attempt to explain its anti-hyperglycemic activitiy. The investigation included simulated docking experiments to fit berberine within the binding pocket of h-PTP 1B. Berberine was found to readily fit within the binding pocket of h-PTP 1B in a low energy orientation characterized with optimal electrostatic attractive interactions bridging the isoquinolinium positively charged nitrogen atom of berberine and the negatively charged acidic residue of ASP 48 of h-PTP 1B. Experimentally, berberine was found to potently competitively inhibit recombinant h-PTP 1B in vitro (Ki value = 91.3 nM). Our findings strongly suggest that h-PTP 1B inhibition is at least one of the reasons for the reported anti-hyperglycemic activities of berberine.
Raging Against or With the Private Marketplace? (2008)

The rise of market logics and the spread of neoliberal policies over the past couple of decades have led to resistance and countermobilization efforts by a variety of activists and concerned citizens—recall the vivid 1999 World Trade Organization (WTO) protests in Seattle. However, contemporary modernity is more complicated than such simple movement—countermovement imageries, and instead of witnessing a leveling of previous institutional configurations with new market-oriented ones, the blending or coexistence of multiple competing and/or complementary logics has become de rigeuer. Hence, in some cases, market logics can provide a foundation for action that supports the arguments and interests of those who stand opposed on principle to market creep. Highlighting how the environmental movement has come to embrace the market as well as activism via an exploration of student eco-entrepreneurship in university settings, we argue that both researchers and skeptics need to go beyond ideological commitments to appreciate the complicated diversity of action and empirical reality that exists at the interface of business and society.
<i>RAS</i> Mutations Contribute to Evolution of Chronic Myelomonocytic Leukemia to the Proliferative Variant (2010)

Our results strongly suggest RAS mutations to function as a secondary event that contributes to development of the chronic myelomonocytic leukemia variant with the poorer prognosis (MP-CMML) and therefore advise their detection to be implemented in chronic myelomonocytic leukemia diagnostics and monitoring.
Photoemission Studies of the Noble Metals. II. Gold (1970)

New photoemission data have been obtained from evaporated films of gold in the range of photon energies between 5 and 21.2 eV. With the exception of a single direct transition, all the optical transitions appear to fit a nondirect model; consequently, it has been possible to construct an optical density of states (ODS) for gold in the region \ifmmode\pm\else\textpm\fi{}11.6 eV about the Fermi level ${E}_{F}$. Two broad peaks dominate the valence ODS. These are centered at about 3.5 and 6 eV below ${E}_{F}$. The higher-lying peak is resolved into a doublet with peaks at 3.0 and 3.8 eV. The two broad peaks correlate well with peaks observed in soft-x-ray photoemission. Positive correlation is also found with band calculations. The electron-electron scattering length for gold has been calculated as a byproduct of the analysis relating the ODS to the photoemission data, and detailed quantitative agreement is found between the calculated scattering length and Kanter's experimental values in the range between 5 and 11 eV above the Fermi level. This quantitative agreement between the calculated and experimental scattering length provides a useful cross-check in support of both the experimental data and the model used to analyze them.
Reduction of Ethylene by Ni<sup>I</sup>(cyclam)<sup>+</sup>in Aqueous Solutions (2008)

Ni(I)(1,4,8,11-tetraazacyclotetradecane)(+) reduces ethylene quantitatively to ethane plus butane (and hexane traces) in neutral aqueous solutions. A radical mechanism is proposed.
5-(5,6-Dichloro-2-indolyl)-2-methoxy-2,4-pentadienamides:  Novel and Selective Inhibitors of the Vacuolar H<sup>+</sup>-ATPase of Osteoclasts with Bone Antiresorptive Activity (1998)

The vacuolar H+-ATPase (V-ATPase), located on the ruffled border of the osteoclast, is a proton pump which is responsible for secreting the massive amounts of protons that are required for the bone resorption process. With the aim to identify new agents which are able to prevent the excessive bone resorption associated with osteoporosis, we have designed a novel class of potent and selective inhibitors of the osteoclast proton pump, starting from the structure of the specific V-ATPase inhibitor bafilomycin A1. Compounds 3a-d potently inhibited the V-ATPase in chicken osteoclast membranes (IC50 = 60-180 nM) and were able to prevent bone resorption by human osteoclasts in vitro at low-nanomolar concentrations. Notably, the EC50 of compound 3c in this assay was 45-fold lower than the concentration required for half-maximal inhibition of the V-ATPase from human kidney cortex. These results support the validity of the osteoclast proton pump as a useful molecular target to produce novel inhibitors of bone resorption, potentially useful as antiosteporotic agents.
Simultaneous wide‐angle X‐ray diffraction and differential scanning calorimetry analysis of the melting and recrystallization behavior of polyethylene and isotactic polypropylene containing cyclopentane units in the main chain (2004)

Abstract The melting and crystallization behavior of polyethylene and isotactic polypropylene containing 1,2‐ or 1,3‐disubstituted cyclopentane units in the main chain has been studied with simultaneous wide‐angle X‐ray diffraction (WAXD) and differential scanning calorimetry. For the ethylene‐based copolymers, the position of a reflection peak in the WAXD patterns shifts to a low angle with the increasing acquired temperature. The temperature dependence on the axial length of the crystal lattice is more marked in the copolymers forming orthorhombic crystals (containing 1,2‐cyclopentane or 5.6 mol % 1,3‐cyclopentane units) than in those forming hexagonal crystals (containing 8.1 mol % 1,3‐cyclopentane units). For the isotactic propylene‐based copolymers, the position of the reflection peaks in the WAXD patterns is independent of the acquired temperature. The proportion of the γ form in the copolymer containing the 1,2‐cyclopentane units is higher than that in the copolymers containing the 1,3‐cyclopentane units. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 1457–1465, 2004
Type I collagen expression contributes to angiogenesis and the development of deeply invasive cutaneous melanoma (2007)

Tumors are complex tissues composed of neoplastic cells, soluble and insoluble matrix components and stromal cells. Here we report that in melanoma, turn-over of type I collagen (Col(I)), the predominant matrix protein in dermal stroma affects melanoma progression. Fibroblasts juxtaposed to melanoma cell nests within the papillary dermis display high levels of Col(I) mRNA expression. These nests are enveloped by collagen fibers. In contrast, melanoma-associated fibroblasts within the reticular dermis express Col(I) mRNA at a level that is comparable to its expression in uninvolved dermis and reduced amount of collagen protein can be observed. To determine the significance of Col(I) expression in melanoma, we pharmacologically inhibited its transcription in a porcine cutaneous melanoma model by oral administration of halofuginone. When administered before melanoma development, it reduced melanoma incidence and diminished the transition from microinvasive toward deeply invasive growth by limiting the development of a tumor vasculature. Whereas invasive melanoma growth has been correlated with increased blood vessel density previously, our data for the first time demonstrate that the proangiogenic effect of Col(I) expression by fibroblasts and vascular cells precedes the development of invasive melanomas in a de novo tumor model.
Structural and Functional Consequences of Coenzyme Binding to the Inactive Asian Variant of Mitochondrial Aldehyde Dehydrogenase (2007)

The common mitochondrial aldehyde dehydrogenase (ALDH2) ALDH2(*)2 polymorphism is associated with impaired ethanol metabolism and decreased efficacy of nitroglycerin treatment. These physiological effects are due to the substitution of Lys for Glu-487 that reduces the k(cat) for these processes and increases the K(m) for NAD(+), as compared with ALDH2. In this study, we sought to understand the nature of the interactions that give rise to the loss of structural integrity and low activity in ALDH2(*)2 even when complexed with coenzyme. Consequently, we have solved the crystal structure of ALDH2(*)2 complexed with coenzyme to 2.5A(.) We have also solved the structures of a mutated form of ALDH2 where Arg-475 is replaced by Gln (R475Q). The structural and functional properties of the R475Q enzyme are intermediate between those of wild-type and the ALDH2(*)2 enzymes. In both cases, the binding of coenzyme restores most of the structural deficits observed in the apoenzyme structures. The binding of coenzyme to the R475Q enzyme restores its structure and catalytic properties to near wild-type levels. In contrast, the disordered helix within the coenzyme binding pocket of ALDH2(*)2 is reordered, but the active site is only partially reordered. Consistent with the structural data, ALDH2(*)2 showed a concentration-dependent increase in esterase activity and nitroglycerin reductase activity upon addition of coenzyme, but the levels of activity do not approach those of the wild-type enzyme or that of the R475Q enzyme. The data presented shows that Glu-487 maintains a critical function in linking the structure of the coenzyme-binding site to that of the active site through its interactions with Arg-264 and Arg-475, and in doing so, creates the stable structural scaffold conducive to catalysis.
Mathematical modeling of heat and water transport in human respiratory tract (1990)

Excessive heat and water losses from the airways are stimuli to asthma. To study heat and water vapor transport in the human respiratory tract, a time-dependent model, based on a single differential equation with an analytical solution, was developed that could predict the intra-airway temperatures and water vapor contents. The key feature is the dependence of the temperature and water vapor along the respiratory tract as a function of the air residence time at each location. The model assumes disturbed laminar flow leading to enhanced transport mechanisms and wall temperature profiles modeled according to experimental data (E. R. McFadden, Jr., B. M. Pichurko, H. F. Bowman, E. Ingenito, S. Burns, N. Dowling, and J. Soloway. J. Appl. Physiol. 58: 564-570, 1985). It predicts that 1) the air equilibrates with the wall before it reaches body conditions (37 degrees C, 99.5% relative humidity); 2) conditioning of the inspired air involves several generations, with the number depending on the respiratory conditions; and 3) the walls of the upper airways are unsaturated, although it is difficult to judge at this state the depth of the respiratory tract affected.
Segmentation via manipulation (1991)

A paradigm of iterative, interactive scene segmentation and simplification of random heaps of unknown objects via vision and manipulation is introduced. The scene simplification is based on the graph operations of vertex and edge removal. These operations are defined isomorphic to the pick and push manipulation actions. Sensors are used as graph generators and the manipulator is used as the decomposing mechanism of the graphs. The model is a nondeterministic finite-state Turing machine. A vision system, a manipulator, and force/torque and other sensory input are integrated into a robot work cell. Experiments conducted to test convergence and error recovery of four different strategies are discussed. It is found that under certain conditions the strategies can tolerate errors in the sensory data, recover from pathological states, and converge.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The use of cast gold pinledge retainers with pontics as an esthetic and functional restorative option in the maxillary anterior. (2004)

A restorative technique for replacing congenitally missing lateral incisors was necessary when implants were not an option. Two three-unit bridges were considered but were rejected in favor of the much more conservative pinledge retainers. Only a relatively small amount of tooth structure was removed during the preparation of the canines, compared to the amount of reduction necessary for crown abutments. Maryland-type bridges (both all-ceramic and metal-based) also were considered but were rejected due to the tight occlusion and the need to prepare the lingual of both abutments in greater amounts than necessary for the thin gold castings. From an esthetic standpoint, there was a small amount of gold showing but not enough to bother the patient, his parents, or the dentist.
Low complexity channel estimation method for TDS-OFDM based Chinese DTTB system (2009)

The Chinese digital television terrestrial broadcasting (DTTB) standard uses pseudo-noise (PN) sequence as guard interval (GI) and the training sequence. This PN sequence is used to do channel estimation and synchronization in the system. The existing channel estimation methods often have to adopt iterative scheme when the length of channel impulse response (CIR) is long, which will increase the receiver complexity dramatically. In this paper, a channel estimation scheme for time domain synchronous OFDM (TDS-OFDM) systems is proposed. Interference free CIR information can be obtained by constructing special correlation windows, rather than removing interference from the time domain sequences through iteration. Moreover, the estimation can be achieved by using correlation process. Comparing to conventional schemes, the proposed algorithm greatly reduces the computational complexity. Simulation results show that the proposed method can meet the requirement of the Chinese DTTB systems. And the scheme is also suitable for other communication OFDM systems with time domain sequence headers.
PROBABILISTIC ENTAILMENT ON FIRST ORDER LANGUAGES AND REASONING WITH INCONSISTENCIES (2022)

Abstract We investigate an approach for drawing logical inference from inconsistent premisses. The main idea in this approach is that the inconsistencies in the premisses should be interpreted as uncertainty of the information. We propose a mechanism, based on Kinght’s [14] study of inconsistency, for revising an inconsistent set of premisses to a minimally uncertain, probabilistically consistent one. We will then generalise the probabilistic entailment relation introduced in [15] for propositional languages to the first order case to draw logical inference from a probabilistic set of premisses. We will show how this combination can allow us to limit the effect of uncertainty introduced by inconsistent premisses to only the reasoning on the part of the premise set that is relevant to the inconsistency.
Nuclear Factor Kappa B Activation and Regulation of Cyclooxygenase Type-2 Expression in Human Amnion Mesenchymal Cells by Interleukin-1β1 (2002)

Interleukin-1beta (IL-1beta) has been shown in numerous studies to increase prostaglandin (PG) output by up-regulating the expression of cyclooxygenase-2 (COX-2), a rate-limiting enzyme in PG synthesis. In this study, we investigated the possible role of the nuclear factor kappa B (NFkappaB) in IL-1beta signaling, leading to the expression of COX-2 in human amnion cell culture. Fetal amnion was obtained following vaginal delivery and digested with collagenase, and the subepithelial (mesenchymal) cells were isolated. Cultures were characterized with antisera to keratin (epithelial cells) and vimentin (mesenchymal cells). Confluent cells were stimulated with human recombinant IL-1beta, and activation of NFkappaB was assessed by measuring changes in the inhibitory protein IkappaB (total IkappaB and phosphorylated IkappaB) using Western blot analysis as well as by nuclear binding of NFkappaB using an electrophoretic mobility shift assay. COX-2 protein levels were determined by Western blot analysis. After 5 min of stimulation with IL-1beta, phosphorylated IkappaB began to appear, 90% of which was degraded within 15 min. This was temporally associated with decreased total IkappaB and increased nuclear NFkappaB DNA-binding activity. In the IL-1beta-treated group, COX-2 protein began to increase after 6 h; this response was time-dependent, with a significant increase until 24 h after IL-1beta stimulation. When NFkappaB translocation was blocked by using SN50 (a cell-permeable inhibitory peptide of NFkappaB translocation), the synthesis of COX-2 protein was inhibited. These results suggest that NFkappaB is involved in the IL-1beta-induced COX-2 expression in the mesenchymal cells of human amnion.
A double bandpass N-path filter for LTE carrier aggregation receivers in 28nm CMOS (2014)

A tunable double bandpass integrated filter is introduced. The filter is designed based on the impedance transfer identity of the N-path filtering. The filter's dual bandpass nature, makes it suitable to be employed as a high Q filter at the input of LTE receivers. It can be used to suppress out-of-band blockers in the non-contiguous carrier aggregation mode. Each of the two passbands can be tuned to be centered at each of the two LTE carriers. The design is simulated for LTE band 2 and the simulation results showed blocker suppression of 10 dB for blockers at the duplex distance and 12 dB of suppression for blockers at double the duplex distance.
A high-efficiency maximum power point tracker for photovoltaic arrays in a solar-powered race vehicle (2002)

A maximum power point tracker for photovoltaic arrays is presented. Components are optimized for weight/power-loss tradeoff in a solar-powered vehicle, resulting in over 97% efficiency. The control circuit uses a robust auto-oscillation method. Measurement and multiplication of array voltage and current is shown to be unnecessary, and the control is based only on output current measurement. Multiple local maxima arising from partial shading of the solar array are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Determination of Volume of Aggregates: New Image-Analysis Approach (2000)

The importance of using quality aggregates with specific gradation and shape properties in asphalt concrete has been recognized by the Strategic Highway Research Program under a set of developed consensus aggregate properties. The flat and elongated ratio and angularity of the aggregate particles are those properties that directly influence the rutting potential of an asphalt pavement. Along with a need to develop rapid and automated methods for determining flat and elongated ratios of individual aggregate particles, there is also a need to develop an accurate and repeatable experimental technique. A new aggregate image analyzer has been recently developed at the University of Illinois that uses three video cameras for accurately determining the volume of each aggregate and for automating the determination of flat and elongated particles, angularity, and gradation. A new image-analysis approach determines the percentage by weight of the flat and elongated particles providing results comparable to the manual results from ASTM D4791 by presenting the results as ratios of weights. The significance of making such accurate volume computations of an individual aggregate using images is discussed. The computed aggregate volumes and the percentages by weight of flat and elongated ratios obtained for two bag samples were in very good agreement with the manual measurements, thus validating the correctness of the imaging technique and the effectiveness of the new aggregate image analyzer.
Computational video editing for dialogue-driven scenes (2017)

We present a system for efficiently editing video of dialogue-driven scenes. The input to our system is a standard film script and multiple video takes, each capturing a different camera framing or performance of the complete scene. Our system then automatically selects the most appropriate clip from one of the input takes, for each line of dialogue, based on a user-specified set of film-editing idioms. Our system starts by segmenting the input script into lines of dialogue and then splitting each input take into a sequence of clips time-aligned with each line. Next, it labels the script and the clips with high-level structural information (e.g., emotional sentiment of dialogue, camera framing of clip, etc.). After this pre-process, our interface offers a set of basic idioms that users can combine in a variety of ways to build custom editing styles. Our system encodes each basic idiom as a Hidden Markov Model that relates editing decisions to the labels extracted in the pre-process. For short scenes (< 2 minutes, 8--16 takes, 6--27 lines of dialogue) applying the user-specified combination of idioms to the pre-processed inputs generates an edited sequence in 2--3 seconds. We show that this is significantly faster than the hours of user time skilled editors typically require to produce such edits and that the quick feedback lets users iteratively explore the space of edit designs.
Growth of <i>Geobacter sulfurreducens</i> with Acetate in Syntrophic Cooperation with Hydrogen-Oxidizing Anaerobic Partners (1998)

Pure cultures of Geobacter sulfurreducens and other Fe(III)-reducing bacteria accumulated hydrogen to partial pressures of 5 to 70 Pa with acetate, butyrate, benzoate, ethanol, lactate, or glucose as the electron donor if electron release to an acceptor was limiting. G. sulfurreducens coupled acetate oxidation with electron transfer to an anaerobic partner bacterium in the absence of ferric iron or other electron acceptors. Cocultures of G. sulfurreducens and Wolinella succinogenes with nitrate as the electron acceptor degraded acetate efficiently and grew with doubling times of 6 to 8 h. The hydrogen partial pressures in these acetate-degrading cocultures were considerably lower, in the range of 0.02 to 0.04 Pa. From these values and the concentrations of the other reactants, it was calculated that in this cooperation the free energy change available to G. sulfurreducens should be about -53 kJ per mol of acetate oxidized, assuming complete conversion of acetate to CO2 and H2. However, growth yields (18.5 g of dry mass per mol of acetate for the coculture, about 14 g for G. sulfurreducens) indicated considerably higher energy gains. These yield data, measurement of hydrogen production rates, and calculation of the diffusive hydrogen flux indicated that electron transfer in these cocultures may not proceed exclusively via interspecies hydrogen transfer but may also proceed through an alternative carrier system with higher redox potential, e.g., a c-type cytochrome that was found to be excreted by G. sulfurreducens into the culture fluid. Syntrophic acetate degradation was also possible with G. sulfurreducens and Desulfovibrio desulfuricans CSN but only with nitrate as electron acceptor. These cultures produced cell yields of 4.5 g of dry mass per mol of acetate, to which both partners contributed at about equal rates. These results demonstrate that some Fe(III)-reducing bacteria can oxidize organic compounds under Fe(III) limitation with the production of hydrogen, and they provide the first example of rapid acetate oxidation via interspecies electron transfer at moderate temperature.