gebhart/patrepeval huggingface dataset:
A critical analysis of incremental iterative data flow analysis algorithms (1990)

A model of data flow analysis and fixed point iteration solution procedures is presented. The faulty incremental iterative algorithm is introduced. Examples of the imprecision of restarting iteration from the intraprocedural and interprocedural domains are given. Some incremental techniques which calculate precise data flow information are summarized.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Regulation of the Functions of Natural Cytotoxicity Receptors by Interactions with Diverse Ligands and Alterations in Splice Variant Expression (2017)

The natural cytotoxicity receptor (NCR) family is constituted by NKp46, NKp44, and NKp30 in humans, which are expressed mainly on natural killer (NK) cells and are encoded by the <i>ncr1, ncr2</i>, and <i>ncr3</i> genes, respectively. NCRs have classically been defined as activating receptors that trigger cytotoxicity and cytokine responses by NK cells upon engaging with ligands on tumor cells. Several new findings, however, have challenged this model and identified alternative mechanisms regulating the function of NCRs. Recent reports indicate that ligand matters, since the interaction of NKp44 with distinct ligands on target cells can either activate or inhibit NK cells. Also, the NCRs have been found to interact with distinct specificities to various heparan sulfate glycosaminoglycans, which are complex polysaccharides found in extracellular matrix or on cell surface heparan sulfate proteoglycans (HSPGs). The NCRs can engage with HSPGs in trans as a co-ligand on the target cells or in cis on the NK cell surface to regulate receptor-ligand interactions and NK cell activation. A number of splice variants of <i>ncr2</i> and <i>ncr3</i> have also been identified, and a predominant expression of certain variants results in inhibitory signaling through NKp44 and NKp30. Several recent studies have found that the selective expression of some of these inhibitory splice variants can significantly influence outcome in the contexts of cancer, infection, and pregnancy. These findings establish that NCR functions are more diverse than originally thought, and better understanding of their splice variant expression profiles and ligand interactions are needed to establish their functional regulation in the context of human health.
Physiologic Oxygen Concentration Enhances the Stem-Like Properties of CD133+ Human Glioblastoma Cells <i>In vitro</i> (2009)

In vitro investigations of tumor stem-like cells (TSC) isolated from human glioblastoma (GB) surgical specimens have been done primarily at an atmospheric oxygen level of 20%. To determine whether an oxygen level more consistent with in situ conditions affects their stem cell-like characteristics, we compared GB TSCs grown under conditions of 20% and 7% oxygen. Growing CD133(+) cells sorted from three GB neurosphere cultures at 7% O(2) reduced their doubling time and increased the self-renewal potential as reflected by clonogenicity. Furthermore, at 7% oxygen, the cultures exhibited an enhanced capacity to differentiate along both the glial and neuronal pathways. As compared with 20%, growth at 7% oxygen resulted in an increase in the expression levels of the neural stem cell markers CD133 and nestin as well as the stem cell markers Oct4 and Sox2. In addition, whereas hypoxia inducible factor 1alpha was not affected in CD133(+) TSCs grown at 7% O(2), hypoxia-inducible factor 2alpha was expressed at higher levels as compared with 20% oxygen. Gene expression profiles generated by microarray analysis revealed that reducing oxygen level to 7% resulted in the up-regulation and down-regulation of a significant number of genes, with more than 140 being commonly affected among the three CD133(+) cultures. Furthermore, Gene Ontology categories up-regulated at 7% oxygen included those associated with stem cells or GB TSCs. Thus, the data presented indicate that growth at the more physiologically relevant oxygen level of 7% enhances the stem cell-like phenotype of CD133(+) GB cells.
Engineering Thrombin for Selective Specificity toward Protein C and PAR1 (2010)

Thrombin elicits functional responses critical to blood homeostasis by interacting with diverse physiological substrates. Ala-scanning mutagenesis of 97 residues covering 53% of the solvent accessible surface area of the enzyme identifies Trp(215) as the single most important determinant of thrombin specificity. Saturation mutagenesis of Trp(215) produces constructs featuring k(cat)/K(m) values for the hydrolysis of fibrinogen, protease-activated receptor PAR1, and protein C that span five orders of magnitude. Importantly, the effect of Trp(215) replacement is context dependent. Mutant W215E is 10-fold more specific for protein C than fibrinogen and PAR1, which represents a striking shift in specificity relative to wild-type that is 100-fold more specific for fibrinogen and PAR1 than protein C. However, when the W215E mutation is combined with deletion of nine residues in the autolysis loop, which by itself shifts the specificity of the enzyme from fibrinogen and PAR1 to protein C, the resulting construct features significant activity only toward PAR1. These findings demonstrate that thrombin can be re-engineered for selective specificity toward protein C and PAR1. Mutations of Trp(215) provide important reagents for dissecting the multiple functional roles of thrombin in the blood and for clinical applications.
Toward an Organometallic Molecular Brake with a Metal Foot Pedal:  Synthesis, Dynamic Behavior, and X-ray Crystal Structure of [(9-Indenyl)triptycene]chromium Tricarbonyl (2004)

The potential use of haptotropic shifts to control rotational barriers has been initiated by the synthesis of (9-indenyl)triptycene (12) and its chromium tricarbonyl derivative (13). Both complexes have been characterized by X-ray crystallography and variable-temperature NMR spectroscopy, revealing barriers to rotation of 12 and 13 kcal mol-1, respectively. In the metal complex, the chromium carbonyl moiety coordinates to one of the blades of the triptycene unit rather than to the more crowded indenyl group.
DNA rearrangements and antigenic variation in Trypanosoma equiperdum: multiple expression-linked sites in independent isolates of trypanosomes expressing the same antigen. (1983)

African trypanosomes resist the immune response of their mammalian hosts by varying the surface glycoprotein which constitutes their antigenic identity. The molecular mechanism of this antigenic variation involves the successive activation of a series of genes which code for different variant surface glycoproteins (VSGs). We have studied the expression of two VSG genes (those of VSG-1 and VSG-28) in Trypanosoma equiperdum, and we report the following findings. (i) The expression of both VSG genes is associated with the duplication and transposition of corresponding basic copy genes. (ii) The duplicated transposed copy appears to be the expressed copy. (iii) Although there are multiple genes which cross-hybridize with the VSG-1 cDNA probe, only one of these appears to be used as a template for the expression-linked copy in four independent BoTat-1 clones. (iv) Analysis of the genomic environments of the expressed VSG-1 genes from each of four independently derived BoTat-1 trypanosome clones revealed that there are at least three different sites into which the expression-linked copy can be inserted.
Regulation of platelet activating factor‐induced equine platelet activation by intracellular kinases (2008)

Lipopolysaccharide (LPS) can activate equine platelets directly or indirectly, via leukocyte-derived platelet activating factor (PAF). Thromboxane (Tx) production by LPS-stimulated equine platelets requires p38 MAPK and this kinase has been suggested as a therapeutic target in endotoxaemia. The present study has utilised selective inhibitors to investigate the role of p38 MAPK and two other kinases, phosphatidylinositol-3 kinase (PI3K) and protein kinase C (PKC), in regulating PAF-induced Tx production, aggregation and 5-HT release in equine platelets, and the modification of these responses by LPS. LPS enhanced PAF-induced 5-HT release, an effect that was reduced by the p38 MAPK inhibitor, SB203580 (60 +/- 8% reduction; n = 6). SB203580 did not affect responses to PAF alone; whereas inhibition of PKC reduced PAF-induced 5-HT release, Tx production and aggregation (maximal inhibition by the PKCdelta inhibitor, rottlerin: 69 +/- 13%, 63 +/- 14% and 97 +/- 1%, respectively; n = 6). Wortmannin and LY249002, which inhibit PI3K, also caused significant inhibition of PAF-induced aggregation (maximal inhibition 78 +/- 3% and 88 +/- 2%, respectively; n = 6). These data suggest that inhibition of platelet p38 MAPK may be of benefit in equine endotoxaemia by counteracting some of the effects of LPS. However, detrimental effects of platelet activation mediated by PAF and not enhanced by LPS are unlikely to be markedly affected.
Digital On-Demand Computing Organism for Real-Time Systems. (2006)

We have previously reported that calcium channel antagonists can block both the growth of meningiomas in culture and the potent growth stimulation of meningioma cells by epidermal growth factor (EGF) and platelet-derived growth factor (PDGF). This study further defines the nature of this growth inhibition. Primary meningioma cultures were established, and cells were characterized. Fibroblast growth factor or insulin-like growth factor-I growth stimulation in the presence of calcium channel antagonists was examined. In addition, the effects of ethylene glycol-bis-(aminoethylether) N,N,N',N"-tetraacetic acid and Bay K 8644, a calcium channel agonist, on the growth factors were analyzed. Growth factor receptor immunohistochemistry was performed on the original tumors and the in vitro meningioma cells. Twelve of 17 (71%) meningiomas in this study were positive for the EGF receptor, and 14 of 17 (82%) were positive for the PDGF receptor. Five of six (83%) of the culture cells were positive for the EGF receptor, and four of five (80%) were positive for the PDGF receptor. Intracellular calcium changes were quantified using the intracellular calcium-chelating, fluorescent dye, Fura-2. The growth stimulation of fibroblast growth factor and insulin-like growth factor-I on meningioma cells in culture was decreased in a dose-dependent manner by calcium channel antagonists. The growth stimulation of fibroblast growth factor and insulin-like growth factor-I was not affected by a reduction of extracellular calcium, whereas the growth stimulation of EGF and PDGF was. Interestingly, intracellular calcium was not increased after exposure to growth factors but was increased after serum stimulation. This increase could be blocked by preincubation with verapamil. Calcium channel antagonists can inhibit proliferation of meningioma cells in culture after stimulation with a number of growth factors. These drugs might disrupt intracellular calcium homeostasis or interfere with key elements of the growth factor signal transduction pathways. These mechanisms as well as the potential clinical relevance of these findings are discussed.
Caribbean and La Réunion Chikungunya Virus Isolates Differ in Their Capacity To Induce Proinflammatory Th1 and NK Cell Responses and Acute Joint Pathology (2015)

The introduction of CHIKV in the Americas has heightened the risk of large-scale outbreaks due to the close proximity between the United States and the Caribbean. The immunopathogenicity of the circulating Caribbean CHIKV isolate was explored, where it was demonstrated to exhibit reduced infectivity resulting in a weakened joint pathology. Analysis of serum cytokine levels, localized immunophenotyping, and gene expression profiles in the organs revealed that a limited Th1 response and reduced NK cells activity could underlie the reduced pathology in the host. Interestingly, higher asymptomatic infections were observed in the Caribbean compared to the La Réunion outbreaks in 2005 and 2006. This is the first study that showed an association between key proinflammatory factors and pathology-mediating leukocytes with a less severe pathological outcome in Caribbean CHIKV infection. Given the limited information regarding the sequela of Caribbean CHIKV infection, our study is timely and will aid the understanding of this increasingly important disease.
Evidence for Superconductivity above 260 K in Lanthanum Superhydride at Megabar Pressures (2019)

Recent predictions and experimental observations of high T_{c} superconductivity in hydrogen-rich materials at very high pressures are driving the search for superconductivity in the vicinity of room temperature. We have developed a novel preparation technique that is optimally suited for megabar pressure syntheses of superhydrides using modulated laser heating while maintaining the integrity of sample-probe contacts for electrical transport measurements to 200 GPa. We detail the synthesis and characterization of lanthanum superhydride samples, including four-probe electrical transport measurements that display significant drops in resistivity on cooling up to 260 K and 180-200 GPa, and resistivity transitions at both lower and higher temperatures in other experiments. Additional current-voltage measurements, critical current estimates, and low-temperature x-ray diffraction are also obtained. We suggest that the transitions represent signatures of superconductivity to near room temperature in phases of lanthanum superhydride, in good agreement with density functional structure search and BCS theory calculations.
Structure Characterization of Tetra-PEG Gel by Small-Angle Neutron Scattering (2009)

The structure of Tetra-PEG gel, a new class of biocompatible, easy-made, and high-strength hydrogel consisting of a four-arm polyethylene glycol (PEG) network, has been investigated by means of small-angle neutron scattering (SANS). Since the Tetra-PEG gel is prepared by cross-end-coupling two kinds of four-arm PEG macromers having different functional groups at the ends, i.e., amine group and succinimidyl ester group respectively, the coupling reaction occurs exclusively between PEG chains carrying different functional groups. SANS results showed that the four-arm PEG macromer aqueous solutions and Tetra-PEG gels were successfully described by the theoretical scattering function for multiarm Gaussian chains and the Ornstein−Zernike function, respectively. Surprisingly, no noticeable excess scattering that originated from cross-linking was observed in Tetra-PEG gels, suggesting that its network structure is extremely uniform. Investigations on nonstoichiometric Tetra-PEG gels showed weakening of the mechanical properties as well as an increase of dangling chains (defects) in the network. It is concluded that Tetra-PEG gels have an extremely uniform network structure, probably mimicking a diamond-like structure, and this is one of the reasons for the advanced mechanical properties of Tetra-PEG gels.
Role of reactive oxygen species in sodium selenite induced DNA damage in HepG2 cells (2006)

ObjectiveTo investigate the mechanisms of sodium selenite induced DNA damage in HepG2 cells.Methods HepG2 cells were treated with the designed concentrations of sodium selenite and the selenite (10μmol/L) added simultaneously with GSH(10mmol)and NAC(5mmol).Then the cell viability was detected by MTT, and the flurescent intensity of reactive oxygen species(ROS) was determined by flow cytometry, and DNA damage was detected by commet assay. Results The level of ROS was increased after HepG2 was treated with 5,10,20μmol/L sodium selenite for one hour, and the cell viability was decreased after 12 hours, and the DNA damage was enhanced. Compared with the control group, the difference was statistically significant(P0.05). GSH and NAC effectively inhibited the ROS increased and cell viability decreased and DNA damage weakened.Conclusion ROS may be the important reason that sodium selenite induced HepG2 cells DNA damage.
Compositional dependence of the stability of AuCu alloy nanoparticles (2012)

The oxidation of AuCu nanoparticles was studied as a function of composition and temperature. Oxidation rates at 110 °C were higher for NPs with higher Cu content, showing that Au stabilized the Cu. Electrochemistry measurements show that AuCu could be a promising catalyst for lowering the over potential of CO(2) reduction.
El Niño-Southern Oscillation Events Recorded in the Stratigraphy of the Tropical Quelccaya Ice Cap, Peru (1984)

Snow accumulation measured during 1982-1983 on the Quelccaya ice cap, Peru, was 70 percent of the average from 1975 through 1983. Inspection of 19 years (1964 through 1983) of accumulation measured near the summit of Quelccaya reveals a substantial decrease ( approximately 30 percent) in association with the last five El Niño-Southern Oscillation (ENSO) occurrences in the equatorial Pacific. The ENSO phenomenon is now recognized as a global event arising from large-scale interactions between the ocean and the atmosphere. Understanding this extreme event, with the goal of prediction, requires a record of past occurrences. The Quelccaya ice cap, which contains 1500 years of annually accumulated ice layers, may provide a long and detailed record of the most extreme ENSO events.
Effect of Carbon Dioxide-Enriched Water and Fresh Water on the Cutaneous Microcirculation and Oxygen Tension in the Skin of the Foot (1997)

The effects of immersion of the lower leg and foot in fresh water and in carbon dioxide (CO2)-enriched water (1200 mg CO2 per kg water; succinate+sodium bicarbonate: Actibath, KAO Tokyo) on cutaneous circulation, vasomotion and oxygen tension (PO2) were measured by laser Doppler flowmetry and transcutaneous oximetry. On the first of two consecutive days patients were randomly assigned to have the lower extremities immersed in either fresh water or CO2-enriched water under standardized conditions (temperature, 34 degrees C; depth, 35 cm; immersion time, twenty minutes) with concurrent measurement. On the second day patients were switched to the other bath type. For both sets of measurements probes were attached symmetrically to the dorsum of each foot. Included in the study were 18 patients with mild, bilateral, peripheral, occlusive arterial disease (intermittent claudication, femoral or iliac type). During immersion in CO2-enriched water the Doppler laser signal and vasomotion amplitude rose by 300%, while PO2 increased by 10%. These increases were still apparent during the latter part of the measurement period, following withdrawal of the limbs from the bath, while patients were seated and supine. During immersion in fresh water and thereafter the Doppler laser signal was unchanged and the PO2 increase was considerably less marked. The authors were thus able to demonstrate vasodilation and increased oxygen utilization (Bohr effect) resulting from topical CO2 application, and hence, that the use of topical CO2 has an objective basis.
Dual Mode Patterning of Fluorine-Containing Block Copolymers through Combined Top-down and Bottom-up Lithography (2012)

Integrated nanopatterns were successfully obtained from a combination of high lateral ordering of newly designed self-assembling fluorine-containing block copolymers and degradation of the fluorine-containing polymer nanodomains in e-beam irradiated areas. The fluorine-containing block copolymers of poly(styrene-block-2,2,2-trifluoroethyl methacrylate) (PS-b-PTFEMA) and poly[styrene-block-(methyl methacrylate-co-2,2,2-trifluoroethyl methacrylate)] (PS-b-(PMMA-co-PTFEMA)), which are capable of both top-down and bottom-up lithography, were developed. The reported block copolymers were synthesized by either anionic polymerization or atom transfer radical polymerization (ATRP). Characterization of bulk and thin films were carried out using differential scanning calorimetry (DSC), transmission electron microscopy (TEM), and small-angle X-ray scattering (SAXS), and these studies revealed the formation of highly ordered self-assembled structures. Lateral ordering of arrays of PS dots was observed in the thin film of PS-b-PTFEMS, in which PS was the minor block, and the thin film of PS-b-(PMMA-co-PTFEMA), in which PS was the major block. These thin films were subjected to conventional lithographic processing using e-beam and deep-UV radiation to create integrated patterns such as “dots in lines”.
Investigation of merging/reconnection heating during solenoid-free startup of plasmas in the MAST Spherical Tokamak (2017)

We present results of recent studies of merging/reconnection heating during central solenoid (CS)-free plasma startup in the Mega Amp Spherical Tokamak (MAST). During this process, ions are heated globally in the downstream region of an outflow jet, and electrons locally around the X-point produced by the magnetic field of two internal P3 coils and of two plasma rings formed around these coils, the final temperature being proportional to the reconnecting field energy. There is an effective confinement of the downstream thermal energy, due to a thick layer of reconnected flux. The characteristic structure is sustained for longer than an ion–electron energy relaxation time, and the energy exchange between ions and electrons contributes to the bulk electron heating in the downstream region. The peak electron temperature around the X-point increases with toroidal field, but the downstream electron and ion temperatures do not change.
A Vigilance Explanation of Musical Chills? Effects of Loudness and Brightness Manipulations (2020)

Recent research has suggested that low-level psychoacoustic parameters such as loudness and spectral brightness are correlated with musical chills, a subjective emotional experience accompanied by goosebumps, shivers, and tingling sensations. These relationships may be explained by a vigilance theory of chills, through the process of auditory looming; however, these correlations or theories have never been causally tested. In the current study, participants ( N = 40) listened to five variations (original, low loudness, high loudness, low brightness, high brightness) of an experimental and control piece of chills music, characterized by a crescendo and guitar solo respectively; this qualitative distinction was made based on whether the underlying musical structure of the pieces was or was not capable of engaging auditory looming processes. It was predicted that increases in loudness would result in increased chills frequency across participants, indicated by button presses; brightness was included as an exploratory parameter. Results show that for the experimental piece, increases in loudness resulted in significantly more frequent chills experiences, and increases in brightness significantly reduced the frequency of chills, whereas no effects were found for the control piece. Findings are discussed in terms of vigilance and social bonding theories of chills, and the complex interactions between low-level psychoacoustic properties and higher-level musical structures.