gebhart/patrepeval huggingface dataset:
Biophysical features of MagA expression in mammalian cells: implications for MRI contrast (2014)

We compared overexpression of the magnetotactic bacterial gene MagA with the modified mammalian ferritin genes HF + LF, in which both heavy and light subunits lack iron response elements. Whereas both expression systems have been proposed for use in non-invasive, magnetic resonance (MR) reporter gene expression, limited information is available regarding their relative potential for providing gene-based contrast. Measurements of MR relaxation rates in these expression systems are important for optimizing cell detection and specificity, for developing quantification methods, and for refinement of gene-based iron contrast using magnetosome associated genes. We measured the total transverse relaxation rate (R2*), its irreversible and reversible components (R2 and R2', respectively) and the longitudinal relaxation rate (R1) in MDA-MB-435 tumor cells. Clonal lines overexpressing MagA and HF + LF were cultured in the presence and absence of iron supplementation, and mounted in a spherical phantom for relaxation mapping at 3 Tesla. In addition to MR measures, cellular changes in iron and zinc were evaluated by inductively coupled plasma mass spectrometry, in ATP by luciferase bioluminescence and in transferrin receptor by Western blot. Only transverse relaxation rates were significantly higher in iron-supplemented, MagA- and HF + LF-expressing cells compared to non-supplemented cells and the parental control. R2* provided the greatest absolute difference and R2' showed the greatest relative difference, consistent with the notion that R2' may be a more specific indicator of iron-based contrast than R2, as observed in brain tissue. Iron supplementation of MagA- and HF + LF-expressing cells increased the iron/zinc ratio approximately 20-fold, while transferrin receptor expression decreased approximately 10-fold. Level of ATP was similar across all cell types and culture conditions. These results highlight the potential of magnetotactic bacterial gene expression for improving MR contrast.
Network Positions and Contributions to Online Public Goods: The Case of Chinese Wikipedia (2012)

We study the effect of collaboration network structure on the contribution behavior of participating editors in Wikipedia. Collaboration in Wikipedia is organized around articles, and any two editors co-editing an article have a collaborative relationship. Based on the economic theories about network games and social role theory, we propose that an editor's position in the collaboration network influences the editor's decisions about her total contribution as well as the allocation of her efforts. By leveraging panel data collected from the Chinese language version of Wikipedia and a natural experiment resulting from blocking it in mainland China, we find strong support for the proposed effect of network position on contribution behavior. Our analysis further reveals that different aspects of an individual's network position have distinct implications. This research enhances our understanding about how collaboration network structure shapes individual behavior in online mass collaboration platforms.
Direct Inverse Control Based on Neural Network for Unmanned Small Helicopter Attitude and Altitude Control (2017)

This paper describes the development of inner loop control of a small helicopter using artificial neural network. A Direct Inverse Control (DIC) based on Neural Network is proposed to maintain the attitude (roll, pitch, and yaw) position on the helicopter hovering state, for several different altitude values. The adopted neural networks learning method to train the network is the backpropagation algorithm. Simulations using real experimental helicopter hovering flight data were conducted to verify the performance of the proposed NN-DIC system. It was revealed that the simulated NN-DIC system can follow the hovering trajectory reference with very low error values.
Transmission-Efficient Structures of Bent and Crossing Silicon Slot Waveguides (2013)

We present transmission-efficient bent and crossing silicon slot waveguides for compact silicon slot waveguide-based circuits. To begin with, using the 3-D vector finite-element method, we investigate the transmission characteristics of a bent silicon slot waveguide with an asymmetric slot that is connected to straight waveguides. Numerical results show that the transmission efficiency can be improved by optimizing a taper structure that is introduced between the bend of an asymmetric slot waveguide and its straight input/output waveguides. Next, we investigate the transmission characteristics of a 3-D crossing silicon slot waveguide that has a vertical coupler. Numerical results show that our crossing structure can achieve a high transmission efficiency compared with conventional structures.
Achieving a Low-Voltage, High-Mobility IGZO Transistor through an ALD-Derived Bilayer Channel and a Hafnia-Based Gate Dielectric Stack (2021)

Ultrahigh-resolution displays for augmented reality (AR) and virtual reality (VR) applications require a novel architecture and process. Atomic-layer deposition (ALD) enables the facile fabrication of indium-gallium zinc oxide (IGZO) thin-film transistors (TFTs) on a substrate with a nonplanar surface due to its excellent step coverage and accurate thickness control. Here, we report all-ALD-derived TFTs using IGZO and HfO<sub>2</sub> as the channel layer and gate insulator, respectively. A bilayer IGZO channel structure consisting of a 10 nm base layer (In<sub>0.52</sub>Ga<sub>0.29</sub>Zn<sub>0.19</sub>O) with good stability and a 3 nm boost layer (In<sub>0.82</sub>Ga<sub>0.08</sub>Zn<sub>0.10</sub>O) with extremely high mobility was designed based on a cation combinatorial study of the ALD-derived IGZO system. Reducing the thickness of the HfO<sub>2</sub> dielectric film by the ALD process offers high areal capacitance in field-effect transistors, which allows low-voltage drivability and enhanced carrier transport. The intrinsic inferior stability of the HfO<sub>2</sub> gate insulator was effectively mitigated by the insertion of an ALD-derived 4 nm Al<sub>2</sub>O<sub>3</sub> interfacial layer between HfO<sub>2</sub> and the IGZO film. The optimized bilayer IGZO TFTs with HfO<sub>2</sub>-based gate insulators exhibited excellent performances with a high field-effect mobility of 74.0 ± 0.91 cm<sup>2</sup>/(V s), a low subthreshold swing of 0.13 ± 0.01 V/dec, a threshold voltage of 0.20 ± 0.24 V, and an <i>I</i><sub>ON/OFF</sub> of ∼3.2 × 10<sup>8</sup> in a low-operation-voltage (≤2 V) range. This promising result was due to the synergic effects of a bilayer IGZO channel and HfO<sub>2</sub>-based gate insulator with a high permittivity, which were mainly attributed to the effective carrier confinement in the boost layer with high mobility, low free carrier density of the base layer with a low <i>V</i><sub>O</sub> concentration, and HfO<sub>2</sub>-induced high effective capacitance.
Activation of the muscarinic K+ channel by P2‐purinoceptors via pertussis toxin‐sensitive G proteins in guinea‐pig atrial cells. (1996)

1. Whole-cell voltage clamp and cell-attached patch-clamp techniques were applied to single atrial myocytes enzymatically dissociated from adult guinea-pig hearts. 2. In whole-cell clamp conditions, external applications, of ATP activated the muscarinic K+ (KACh) current, identified by its inward rectification, its reversal potential near the calculated K+ equilibrium potential (EK) and its relaxation properties during step changes of whole-cell membrane potential. Theophylline, an antagonist for Pi-purinoceptors, did not affect the action of ATP on the KACh current, indicating that the response was evoked through P2-purinoceptors. 3. The concentration-response relationship for ATP was well described by a Hill equation with a half-maximal concentration of 1.84 microM and a Hill coefficient of 0.94. ATP (100 microM) produced a maximal increase of the KACh current to 10.92 microA microF-1, which corresponds to 44.9 and 80.9% of the maximal increases evoked by ACh (10 microM) and adenosine (100 microM), respectively. 4. The activation of KACh current gradually declined to a steady level despite the continuous presence of ATP (desensitization). Recovery from the desensitization was relatively rapid with a half-time of approximately 1.5 min. 5. The activation of KACh current by ATP was completely abolished by pre-incubating myocytes with pertussis toxin (PTX, 5 micrograms ml-1), indicating that P2-purinoceptors are coupled to PTX-sensitive G proteins to activate the KACh channel. 6. In the cell-attached patch recording, ATP (5 microM) applied to the pipette solution enhanced the activity of a channel with single-channel conductance of 52.7 +/- 0.9 pS (mean +/- S.E.M., n = 10), reversal potential near EK and mean open time of 1.1 +/- 0.1 ms. These conductance and kinetic properties are identical to those of the KACh channel in the heart. In contrast, ATP applied to the bath solution did not significantly affect the basal activity of KACh channel openings. These observations suggest that the mechanism coupling the P2-purinoceptor to the activation of the KACh channel involves membrane-delimited component(s) rather than soluble second messenger(s). 7. These results strongly suggest a direct coupling of the P2-purinoceptor to the KACh channel through PTX-sensitive G proteins, analogous to the coupling mechanism of the muscarinic ACh receptor and Pi-purinoceptor to this channel.
DEVELOPMENT OF MECHANISTIC MODELS FOR THE PREDICTION OF MACHINING PERFORMANCE: MODEL BUILDING METHODOLOGY (1998)

ABSTRACT In this paper, recent research efforts at the University of Illinois at Urbana-Champaign (UIUC) on the development of machining process models are summarized under a unified mechanistic modeling framework. The fundamental elements of the basic cutting force model are described first, which include the computation of chip load and chip flow, force transformation relations, workpiece-cutter intersection algorithm, and the model calibration procedure. Some advanced model enhancements are then presented, such as the modeling of process faults, modeling of chip-control tools, and the incorporation of ploughing and tool wear effects. The integration of the process model with the machining system dynamics is discussed next. Finally, representative results are shown to validate the mechanistic modeling approach.
Use of Tetrabenazine in Huntington Disease Patients on Antidepressants or with Advanced Disease: Results from the TETRA-HD Study (2011)

The safety and effectiveness of tetrabenazine in different sub-populations of Huntington disease (HD) is not known. In this study, we evaluated the safety of tetrabenazine in individuals on an antidepressant and its effectiveness in advanced HD. Tetrabenazine was not associated with an increased incidence of depressed mood among those taking antidepressants and was effective at reducing chorea in those with advanced HD.
The signal environment is more important than diet or chemical specialization in the evolution of warning coloration (2007)

Aposematic coloration, or warning coloration, is a visual signal that acts to minimize contact between predator and unprofitable prey. The conditions favoring the evolution of aposematic coloration remain largely unidentified. Recent work suggests that diet specialization and resultant toxicity may play a role in facilitating the evolution and persistence of warning coloration. Using a phylogenetic approach, we investigated the evolution of larval warning coloration in the genus Papilio (Lepidoptera: Papilionidae). Our results indicate that there are at least four independent origins of aposematic larval coloration within Papilio. Controlling for phylogenetic relatedness among Papilio taxa, we found no evidence supporting the hypothesis that either diet specialization or chemical specialization facilitated the origin of aposematic larvae. However, there was a significant relationship between the signal environment and the evolution of aposematic larvae. Specifically, Papilio lineages feeding on herbaceous or narrow-leaved plants, regardless of the plants' taxonomic affiliation, were more likely to evolve aposematic larvae than were lineages feeding only on trees/shrubs or broad-leaved plants. These results demonstrate that factors other than diet specialization, such as the signal environment of predator-prey interactions, may play a large role in the initial evolution and persistence of aposematic coloration.
Collagenase‐2 (MMP‐8) and collagenase‐3 (MMP‐13) in adult periodontitis: molecular forms and levels in gingival crevicular fluid and immunolocalisation in gingival tissue (2002)

Multiple species and elevated levels of both MMP-8 and MMP-13 from many rather than single cellular sources in the diseased periodontium are identified in untreated periodontitis GCF and active forms contribute to GCF collagenase activity.
Self-assembly of amphiphilic fluorescent dyes showing aggregate-induced enhanced emission: temperature dependence of molecular alignment and intermolecular interaction in aqueous environment (2009)

A 1-cyano-1,2-bis(biphenyl)ethene derivative having hexa(ethylene glycol) groups as amphiphilic side chains showed aggregate-induced enhanced emission in water; upon heating the intensity of the enhanced emission was attenuated in a lower temperature range than the temperature range where exciton interaction is still effective.
NVSleep: Using non-volatile memory to enable fast sleep/wakeup of idle cores (2014)

Spin-transfer torque random access memory (STTRAM) is an emerging memory technology with several attractive properties including non-volatility, high density, low leakage, and high endurance. These characteristics make it a potential candidate for replacing SRAM structures on processor chips. This paper presents NVSleep, a low-power microprocessor framework that leverages STT-RAM to implement fast checkpointing that enables near-instantaneous shutdown of cores without loss of the execution state. NVSleep stores almost all processor state in STT-RAM structures that do not lose content when power-gated. Memory structures that require low-latency access are implemented in SRAM and backed-up by “shadow” STT-RAM structures that are used to implement fast checkpointing. This enables rapid shutdown of cores and low-overhead resumption of execution, which allows cores to be turned off frequently and for short periods of time to take advantage of idle execution phases and save power. We present two implementations of NVSleep: NVSleepMiss which turns cores off when last level cache misses cause pipeline stalls and NVSleepBarrier which turns cores off when blocked on barriers. Evaluation of a simulated 64-core system shows average energy savings of 21% for NVSleepMiss for SPEC2000 benchmarks and 34% for NVSleepBarrier in high barrier count multi-threaded workloads from PARSEC and SPLASH2 benchmarks.
Binding Forces Contributing to the Association of Cyclodextrin with Alcohol in an Aqueous Solution (1979)

Abstract The association constants and thermodynamic parameters were determined for complexes of α- and β-cyclodextrins (CD) with a variety of alcohols (ROH) by the spectrophotometric examination of the inhibitory effect of ROH on the association of CD with azo dyes, and they were analyzed in connection with the partition coefficients of ROH in a diethyl ether–water solvent system in order to elucidate the binding forces contributing to the association of CD with an organic substrate. Hydrophobic and van der Waals interactions were of primary importance in the complexation. Among them, the latter was preferential in α-CD–1-alkanol adducts, while the former, in β-CD–1-alkanol adducts. As the bulkiness of ROH increased, the stability of the α-CD adduct was lowered owing to van der Waals repulsion between ROH and the relatively small α-CD cavity, whereas that of the β-CD adduct was enhanced by the attainment of the close van der Waals contact of ROH with the relatively large β-CD cavity.
The Role of PPAR<i>γ</i>Receptors and Leukotriene B<sub>4</sub>Receptors in Mediating the Effects of LY293111 in Pancreatic Cancer (2008)

Pancreatic cancer is a devastating disease in which current therapies are inadequate. Separate lines of research have identified the 5-lipoxygenase/leukotriene B(4) receptor pathway and the PPARgamma pathway as potential targets for prevention or treatment of this disease. LY293111 was originally designed as a potent leukotriene B(4) receptor antagonist for treatment of inflammatory conditions. LY293111 was also known to have inhibitory effects on 5-lipoxygenase, which is upstream of the production of leukotrienes. LY293111 was shown to have potent anticancer effects in pancreatic cancer and several other solid malignancies, where it caused cell cycle arrest and marked apoptosis. Subsequently, it came to light that LY293111 exhibited PPARgamma agonist activity in addition to its effects on the 5-lipoxygenase pathway. This raises the question of which of the two targets is of greatest importance with regard to the anticancer effects of this agent. The evidence to date is not conclusive, but suggests that the effects of LY293111 may be mediated by both LTB(4) receptors and PPARgamma.
The Essential Protein for Bacterial Flagella Formation FlgJ Functions as a β-N-Acetylglucosaminidase (2014)

The flagellum is a major virulence factor of motile pathogenic bacteria. This structure requires more than 50 proteins for its biogenesis and function, one of which is FlgJ. Homologs of FlgJ produced by the β- and γ-proteobacteria, such as Salmonella enterica, Vibrio spp., and both Sphingomonas sp. and Pseudomonas spp. are bifunctional, possessing an N-terminal domain responsible for proper rod assembly and a C-terminal domain possessing peptidoglycan lytic activity. Despite the amount of research conducted on FlgJ from these and other bacteria over the past 15 years, no biochemical analysis had been conducted on any FlgJ and consequently confusion exists as to whether the enzyme is a peptidoglycan hydrolase or a lytic transglycosylase. In this study, we present the development of a novel assay for glycoside lytic enzymes and its use to provide the first enzymatic characterization of the lytic domain of FlgJ from S. enterica as the model enzyme. Surprisingly, FlgJ functions as neither a muramidase nor a lytic transglycosylases but rather as a β-N-acetylglucosaminidase. As such, FlgJ represents the first autolysin with this activity to be characterized from a Gram-negative bacterium. At its optimal pH of 4.0, the Michaelis-Menten parameters of K(m) and k(cat) for FlgJ from S. enterica were determined to be 0.64 ± 0.18 mg ml(-1) and 0.13 ± 0.016 s(-1), respectively, using purified PG as substrate. Its catalytic residues were identified as Glu(184) and Glu(223).
XML-based Exploitation of Region of Interest Scalability in Scalable Video Coding (2007)

The use of Regions Of Interest (ROIs) is a useful concept for many application scenarios, especially for those applications that are deployed in heterogeneous multimedia environments. In this paper, we show how Flexible Macroblock Ordering can be used in the scalable extension of the H.264/AVC specification in order to define the ROIs in the coded bit- stream. Furthermore, we introduce an XML-driven adaptation framework based on the MPEG-21 Bitstream Syntax Description Language in order to implement the ROI extraction process. This framework gives us the opportunity to adapt scalable bitstreams by using an engine that has no knowledge of the underlying coding format. From the performance analysis of our adaptation framework, we can conclude that the ROIs can be extracted in the XML domain and that the ROIs in the adapted bitstream are still intact without quality degradation. Furthermore, the traditional drifting problem caused by the ROI extraction can be neglected. Finally, we show that the adaptation process in the XML domain can be executed in real time.
Decreased succinate dehydrogenase B in human hepatocellular carcinoma accelerates tumor malignancy by inducing the Warburg effect (2018)

Changes in TCA cycle enzymes or respiratory activity are possible mechanisms of aerobic glycolysis that contributes to tumor progression. To clarify whether the decrease of succinate dehydrogenase B (SDHB) alters energy metabolism, induces the Warburg effect and results in tumor malignancy, SDHB expression was examined and modulated in hepatocellular carcinoma (HCC) tissues and cells, respectively. SDHB level was often decreased in malignant HCC cells and tissues. Furthermore, the reduced SDHB expression was associated with advanced tumor stage and poor survival rate. Moreover, silencing of SDHB altered energy metabolism switched from aerobic respiration to glycolysis, resulted in the Warburg effect, and enhanced cell proliferation and motility. In contrast, the SDHB overexpression deregulated bioenergetic metabolism and decreased cell growth and migration. In mouse xenograft models, subcutaneous implantation and tail vein injection with SDHB knockdown cells resulted in a larger tumor volume and accelerated cancer metastasis, respectively. A mutation or decrease in SDHB induced the switch from aerobic respiration to glycolysis. This metabolic alteration was associated with tumor cell dedifferentiation, proliferation, motility and overall patient survival in HCC.
Otitis media in children: local immune response to nontypeable Haemophilus influenzae (1989)

Twenty children experienced 30 episodes of otitis media with effusion due to nontypeable (NT) Haemophilus influenzae in the first 2 years of life. The local and systemic immune responses to homologous strains of NT H. influenzae were determined by an immunodot assay. Strain-specific immunoglobulin G (IgG) antibody predominated in the middle ear fluid (MEF). It was detected in 91% of the children, compared with IgM in 48% (P less than 0.005), IgA in 52% (P less than 0.005), and secretory IgA in 18% (P less than 0.005). The titer (log2) of NT H. influenzae-specific IgG antibody (mean +/- standard error, 8.2 +/- 0.1) exceeded the titers of IgM (3.4 +/- 0.1), IgA (3.7 +/- 0.1), and secretory IgA (1.2 +/- 0.3). NT H. influenzae-specific antibody was detected exclusively in MEFs of individuals who possessed homologous serum antibody. Although antibody titers in MEF declined over time, serum antibody titers remained stable. These data suggest that immunity to NT H. influenzae in the middle ear, in part, reflects systemic immunity. Whereas local antibody disappears after resolution of the infection, systemic antibody persists.
Compression of functions defined on surfaces of 3D objects (2002)

We present a technique to compress scalar functions defined on 2-manifolds. Our approach combines discrete wavelet transforms with zerotree compression, building on ideas from three previous developments: the lifting scheme, spherical wavelets, and embedded zerotree coding methods. Applications lie in the efficient storage and rapid transmission of complex data sets. Typical data sets are Earth topography, satellite images, and surface parametrizations. Our contribution is the novel combination and application of these techniques to general 2-manifolds.