gebhart/patrepeval huggingface dataset:
Expanded Tropism of Primary Human Immunodeficiency Virus Type 1 R5 Strains to CD4 <sup>+</sup> T-Cell Lines Determined by the Capacity To Exploit Low Concentrations of CCR5 (1999)

Human immunodeficiency virus type 1 (HIV-1) non-syncytium-inducing (NSI) strains predominantly use the chemokine receptor CCR5, while syncytium-inducing (SI) strains use CXCR4. In vitro, SI isolates infect and replicate in a range of CD4(+) CXCR4(+) T-cell lines, whereas NSI isolates usually do not. Here we describe three NSI strains that are able to infect two CD4(+) T-cell lines, Molt4 and SupT1. For one strain, a variant of JRCSF selected in vitro, replication on Molt4 was previously shown to be conferred by a single amino-acid change in the V1 loop (M.T. Boyd et al., J. Virol. 67:3649-3652, 1993). On CD4(+) cell lines expressing different coreceptors, these strains use CCR5 predominantly and do not replicate in CCR5-negative peripheral blood mononuclear cells derived from individuals homozygous for Delta32 CCR5. Furthermore, infection of Molt4 and SupT1 by each of these three strains is potently inhibited by ligands for CCR5, including 2D7, a monoclonal antibody specific for CCR5. CCR5 mRNA was present in both Molt4 and SupT1 by reverse transcription-PCR, although CCR5 protein could not be detected either on the cell surface or in intracellular vesicles. The expanded tropism of the three strains shown here is therefore not due to adaptation to a new coreceptor but due to the capacity to exploit extremely low levels of CCR5 on Molt4 and SupT1 cells. This novel tropism observed for a subset of primary HIV-1 isolates may represent an extended tropism to new CD4(+) cell types in vivo.
Hard real-time motion planning for autonomous vehicles (2011)

Motion planning is the problem of finding a continuous collision free path from an initial configuration (or state) to a goal. On board an autonomous vehicle, the capability to prevent collisions also depends on the sensing and control. Critically, motion planning is a necessary component for the safe operation of an autonomous vehicles. This work focuses on the problem of embedding a motion planner into a software system in which all tasks are required to satisfy hard deadlines. The key contribution of this work is to present a framework that can be used as a basis for incorporating approximately complete motion planning algorithms within a hard real-time system. This framework ensures that deadlines can be satisfied, with only mild constraints on other software. Two motion planning algorithms are presented as a verification of the framework, and are applied to solving dynamic motion planning problems related to the safe and efficient navigation of autonomous systems.
Increased Activity and Phase Delay in Circadian Motility Rhythms in Geriatric Depression (1988)

Locomotor activity levels and rhythms of eight hospitalized geriatric unipolar depressed patients (DSM-III criteria) were compared with those of eight healthy elderly controls in a similar environment. Activity was measured using a wrist-worn electronic activity monitor with solid-state memory. Depressed patients had a 29% higher mean total 24-hour activity level, with no change in circadian amplitude or frequency. Daily peak activity (acrophase) averaged 2.05 hours later in depressed patients, with no overlap between the groups. The degree of phase delay correlated significantly with the 4 PM postdexamethasone serum cortisol level. These tentative findings suggest that elderly unipolar depressed patients have prominent chronobiological disturbances in the modulation of activity levels and possibly other physiological processes. These differ strikingly from reported disturbances in younger or bipolar depressed patients.
Quantification in tissue near–infrared spectroscopy (1997)

In near–infrared spectroscopy (NIRS) of tissue, light attenuation is due to: (i) absorption from chromophores of fixed concentration, (ii) absorption from chromophores of variable concentration, and (iii) light scatter. NIRS is usually concerned with trying to quantify the concentrations of chromophores in category (ii), in particular oxy– and deoxyhaemoglobin (HbO 2 and Hb) and cytochrome oxidase. In the absence of scatter the total light absorption in the medium is a linear sum of that due to each chromophore. In a scattering medium like tissue, this linear summation is distorted because the optical path length at each wavelength may differ. This distorted spectrum is then superimposed upon a further wavelength–dependent attenuation arising from light loss due to scatter, which is a complex function of the tissue absorption and scattering coefficients ( μ a and μ s ), scattering phase function, and tissue and measurement geometry. Consequently, quantification of NIRS data is difficult. Over the past 20 years many differing approaches to quantification have been tried. The development of methods for measuring optical path length in tissue initially enabled changes in concentration to be quantified, and subsequently methods for absolute quantification of HbO 2 and Hb were developed by correlating NIRS changes with an independent measurement of arterial haemoglobin saturation. Absolute determination of tissue optical properties, however, requires additional information over and above the detected intensity at the tissue surface, which must then be combined with a model of light transport to derive μ a and μ s . The additional data can take many forms, e.g. the change in intensity with distance, the temporal dispersion of light from an ultrashort input light pulse, or phase, and modulation depth changes of intensity–modulated light. All these approaches are now being actively pursued with considerable success. However, all the approaches are limited by the accuracy of the light transport models, especially in inhomogeneous media.
Synapse formation between clonal neuroblastoma X glioma hybrid cells and striated muscle cells. (1976)

Clonal neuroblastoma X glioma hybrid cells were shown to form synapses with cultured, striated muscle cells. The properties of the synapses between hybrid and muscle cells were similar to those of the normal, neuromuscular synapse at an early stage of development. The number of synapses formed and the efficiency of transmission across synapses were found to be regulated, apparently independently, by components in the culture medium. Under appropriate conditions synapses were found with 20% of the hybrid-muscle cell pairs examined; thus, the hybrid cells form synapses with relatively high frequency.
Anticalins: Exploiting a non‐Ig scaffold with hypervariable loops for the engineering of binding proteins (2013)

Antibodies, which can recognize a plethora of possible antigens, have been considered as a paradigm of protein engineering performed by nature itself. Lipocalins constitute a distinct family of proteins with functions in ligand binding and transport that occur in many organisms, including man. Like antibodies, lipocalins exhibit a structurally conserved framework – a β‐barrel with an attached α‐helix – which supports four structurally hypervariable loops forming a cup‐shaped binding site. Thus, lipocalins offer an ideal platform for protein engineering to generate novel binding reagents. Using recombinant/synthetic DNA technology and methods of combinatorial library selection, ‘Anticalins’ with prescribed target specificities can be easily generated. Anticalins with picomolar affinities have been developed for three classes of ligands having relevance in basic research and/or medical application: small molecules, peptides, and proteinaceous signalling molecules as well as cell surface receptors. Anticalins derived from human lipocalins have already reached the clinical trial stage. Due to their very small size and simple composition of a single polypeptide chain, which also facilitates the construction of bifunctional fusion proteins, Anticalins promise benefits as a next class of biopharmaceuticals.
Quaternary ammoniums and other preservatives' contribution in oxidative stress and apoptosis on Chang conjunctival cells. (2001)

The quaternary ammoniums tested (BAC, BOB, and Cet) were the most cytotoxic preservatives in the current model. An apoptotic mechanism appeared to be present at low concentrations of quaternary ammoniums, whereas a necrotic process appeared at higher concentrations. Superoxide anions may play an important role in tissue damage induced by preservatives in ocular surface disorders.
Influence of Ionic Liquids Bearing Functional Groups in Dye-Sensitized Solar Cells (2006)

Ionic liquids containing the nitrile and vinyl functional groups attached to imidazolium cations combined with various anions, e.g., iodide, bis[(trifluoromethyl)sulfonyl]imide ([TFSI]-), or dicyanamide ([N(CN)2]-), have been prepared and characterized. These ionic liquids have been successfully used as electrolytes for dye-sensitized solar cells based on nanocrystalline TiO2 with the amphiphilic ruthenium sensitizer [ruthenium (4,4'-dicarboxylic acid-2,2'-bipyridine)(4,4'-bis(p-hexyloxystyryl)-2,2'-bipyridine)][NCS]2 (coded K-19). The iodide salt was used in 3-methoxypropionitrile-based electrolytes, and the performances of both types of devices were evaluated on the basis of their photocurrent density-voltage characteristics and dark current measurements, demonstrating that the functional groups do not exert a detrimental effect on the performance. The solid-state structure of the nitrile-functionalized salt [C1C3CN(im)]I has also been established by single-crystal X-ray diffraction, revealing extensive hydrogen bonding between the cation protons and the iodide.
Real-Time Camera Pose Estimation for Wide-Area Augmented Reality Applications (2010)

Achieving accurate registration between real and synthetic worlds is one of augmented reality's biggest challenges. A real-time camera-pose estimation method, based on multiple maps and local bundle adjustment, enables the registration to work without prior knowledge of natural scenes. This method can significantly enhance AR systems' usability.
Low complexity power allocation for hybrid amplify-and-forward opportunistic relay ordering cooperation (2013)

在这份报纸，对连接不平衡提高坚韧性，一个混合合作协议为 amplify-and-forward ( AF )被建议机会主义的合作，在机会主义的中继和多跳跃的地方，有继电器订的合作( RO )动态地被选择最大化结束结束信号噪音比率( SNR )，并且力量分配系数因此在全部的力量限制下面被优化。而且，有低复杂性的一个 suboptimum 分配计划被采用泛音平均数的上面的界限建议。模拟结果证明建议计划超过常规 AF 在线类型拓扑学的变化的机会主义的合作。而且，建议 suboptimum 分配的效率也在大 SNR 被验证区域。
Two MAPK cascades, NPR1, and TGA transcription factors play a role in Pto‐mediated disease resistance in tomato (2003)

The tomato Pto kinase confers resistance to the causative agent of bacterial speck disease, Pseudomonas syringae pv. tomato, by recognizing the pathogen effector proteins AvrPto or AvrPtoB. Pto-mediated resistance requires multiple signal transduction pathways and has been shown to activate many defense responses including an oxidative burst, rapid changes in the expression of over 400 genes, and localized cell death. We have tested the role in Pto-mediated resistance in tomato of a set of 21 genes from other species known to be involved in defense-related signaling. Expression of each gene was suppressed by virus-induced gene silencing (VIGS) and the effect on disease symptoms and bacterial growth during the tomato-Pseudomonas incompatible interaction was determined. We found that Pto-mediated resistance was compromised by silencing of genes encoding two mitogen-activated protein (MAP) kinase kinases, MEK1 and MEK2, two MAP kinases, NTF6 and wound-induced protein kinase (WIPK), a key regulator of systemic acquired resistance (SAR), NPR1, and two transcription factors, TGA1a and TGA2.2. A lesser impact on Pto-mediated resistance was observed in plants silenced for RAR1 and COI1. The identification of nine genes that play a role in resistance to bacterial speck disease both advances our knowledge of Pto signal transduction and demonstrates the conservation of many defense signaling components among diverse plant species.
Role of multiple efflux pumps in<i>Escherichia coli</i>in indole expulsion (1999)

Escherichia coli chromosome encodes several multidrug transporters. Despite their protective function against antibacterial agents, the specific physiological actions of these transporters are not fully understood. E. coli produces indole, a metabolite of tryptophan, under physiological conditions. Defined inactivation of the acrEF gene, the product of which is known as an energy-dependent multiple drug efflux pump, decreased indole excretion while reintroduction of the acrEF gene restored it. A DeltaacrEF mutant accumulated more intracellular indole than the parent. This mutant was more susceptible to the growth-inhibitory effect of indole than the parent. These results indicate that the AcrEF system plays a significant role in indole efflux.
Binding Affinity of Hydrolyzable Tannins to Parotid Saliva and to Proline-Rich Proteins Derived from It (2000)

Proline-rich proteins (PRP) in human parotid saliva have a high affinity for dietary polyphenolic compounds (tannins), forming stable complexes that may modulate the biological and nutritional properties of the tannin. The formation of such complexes may also have an important role in the modulation or promotion of the sensation of oral astringency perceived when tannin-rich foods and beverages are consumed. The major classes of PRP (acidic, basic, and glycosylated) have been isolated from human saliva, and the relative binding affinities of a series of hydrolyzable tannins, which are found in a number of plant-derived foods and beverages, to these PRP classes have been determined using a competition assay. All of the classes of PRP have a high capacity for hydrolyzable tannins. Within the narrow range of binding affinities exhibited, structure/binding relationships with the levels of tannin galloylation, hexahydroxydiphenoyl esterification, and degree of polymerization were identified. No individual class of human salivary PRP appears to have an exclusive affinity for a particular type of hydrolyzable tannin.
Solubilization of nonaqueous phase liquids and their mixtures in micellar solutions of ethoxylated nonionic surfactants. (1995)

ICU patients typically lack decision-making capacity, and physicians know patients' wishes in only 20% of EOL decisions. There were regional differences in discussions of EOL decisions with families and other physicians. In European ICUs there seems to be a need to improve communication.
A bidirectional NMOSFET current reduction model for simulation of hot-carrier-induced circuit degradation (1993)

An approach for modeling hot-electron induced change in drain current that significantly improves the ease of parameter extraction and provides new capabilities for modeling the effect of bidirectional stressing and the asymmetrical I-V characteristics after stressing is presented. The change in the drain current, Delta I/sub D/ is implemented as an asymmetrical voltage-controlled current source and the new Delta I/sub D/ model is independent of the MOSFET model used for circuit simulation. The physical basis of the model, the analytical model equations, the implementation scheme in BERT (BErkeley Reliability Tools) simulator and simulation results for uni- and bidirectional circuit stressing are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A new incremental data mining algorithm using pre-large itemsets1 (2001)

Due to the increasing use of very large databases and data warehouses, mining useful information and helpful knowledge from transactions is evolving into an important research area. In the past, researchers usually assumed databases were static to si
Cavity ringdown strain gauge (2004)

Biconical tapered single-mode fiber, which is common in many telecommunications components, offers an alternative sensor to typical optical fiber strain gauges that are susceptible to temperature and pressure effects and require expensive and sophisticated signal acquisition systems. Cavity ringdown spectroscopy, a technique commonly applied to high-sensitivity chemical analysis, offers detection sensitivity advantages that can be used to improve strain measurement with biconical tapers. Combining these two technologies in a spatially extended resonator, we demonstrate a minimum detectable change in ringdown time of 0.08%, corresponding to a minimum detectable displacement of 4.8 nm, and a sensitivity to strain as small as 79 n epsilon/square root(Hz) over a 5-mm taper length.
Use of Multiple Antigenic Peptides as Coating Antigens in Detection of Antibody (1996)

The protein conjugates of two peptides (P1 and P2) with the sequences 101-116 and 253274 of the human immunodeficiency virus type 1 (HIV1) gp120 protein, respectively, showed high reactivity against an anti-gp120 goat antibody, whereas the peptides only displayed low reactivity when used as coating antigens in indirect enzyme linked immuno sorbent assay (ELISA). However, P1 and P2 effectively inhibited the binding of the anti-HIV1 gp120 goat antibody with their peptide-ovalbumin conjugates in competitive ELISA, suggesting that the low reactivity of P1 and P2 in indirect ELISA resulted from their low coating efficiency on the microtiter plates. To increase coating efficiency of synthetic peptides without conjugation, four multiple antigenic peptides (MAP) for each peptide were synthesized. Their antigenicity was determined against the anti-HIV1 gp120 goat antibody and anti-peptide antisera by indirect and competitive ELISA. The MAPs for both P1 and P2 showed almost similar reactivity with the peptide-bovine serum albumin conjugates in indirect ELISA. MAPs with four peptide branches were more effective than MAPs with two peptide branches. The high efficiency of the MAPs seems to be related to the cumulative effects of their high coating efficiency and high affinity conformation on the microtiter plate to the antibodies. These results suggest that multi-branched MAPs are useful as coating peptide antigens in the development of analytical systems for disease diagnosis.
Contrasting levels of variability between cytoplasmic genomes and incompatibility types in the mosquito<i>Culex pipiens</i> (1997)

Reproductive incompatibilities called cytoplasmic incompatibilities are known to affect a large number of arthropod species and are mediated by Wolbachia, a maternally transmitted microorganism. The crossing relationships between strains of potential hosts define their incompatibility types and it is generally assumed that differences between strains of Wolbachia induce different crossing types. Among all the described host species, the mosquito, Culex pipiens, displays the greatest variability of cytoplasmic incompatibility crossing types. We analysed mitochondrial and bacterial DNA variability in Culex pipiens in order to investigate some possible causes of incompatibility crossing type variability. We sequenced fragments of the ftsZ gene, and the A + T-rich control region of the mtDNA. We also sequenced the second subunit of the mitochondrial cytochrome oxidase (COII) gene, in Culex pipiens and a closely related species, C. torrentium, in order to verify the usefulness of the A + T-rich region for the present purposes. No variability was found in the Wolbachia ftsZ gene fragment, and very limited variation of the mitochondrial marker whatever the compatibility type or the origin of the host. A low variability was found in the A + T-rich region and comparison of divergence of the A + T-rich region and COII gene between C. pipiens and C. torrentium did not reveal any special constraints affecting this region. In contrast to observations in other host species, variability of incompatibility crossing types is not due to multiple infections by distantly related Wolbachia strains.
A Fluid Film Squeezed Between Two Rotating Parallel Plane Surfaces (1985)

This paper is concerned with the motion of a fluid film squeezed between two rotating parallel plane surfaces. Attention is given to the case of impulsive squeezing and impulsive rotation. Approximate analytic solutions are obtained and a numerical solution to the full nonlinear equations of motion is presented. The results show that the centrifugal inertial forces increase the radial outflow and reduce considerably the load capacity while the noncentrifugal inertial forces increase the torque.
The Effect of Monopolar Radiofrequency Treatment Pattern on Joint Capsular Healing (2000)

The purpose of this study was to compare joint capsular healing after two delivery patterns of monopolar radiofrequency energy: 1) uniform treatment of the joint capsule (paintbrush pattern) and 2) multiple single linear passes (grid pattern). First, an in vitro study was performed to compare the percent shrinkage of these two treatment patterns using the femoropatellar joints (stifles) of six sheep. Monopolar radiofrequency energy (settings, 70 degrees C/15W) was applied to the lateral joint capsule; the treated area was approximately 10 x 10 mm. There was no significant difference in shrinkage between the grid (27% +/- 8.7%) and paintbrush (29% +/- 7.9%) patterns. In the in vivo study, stifles of 24 sheep were randomly assigned to the paintbrush or the grid pattern groups and treatment was performed arthroscopically. Sheep were sacrificed immediately after surgery, or at 2, 6, or 12 weeks after surgery. At 6 weeks after surgery, confocal microscopy demonstrated that treated areas had almost completely repaired in the grid group; some nonviable areas were still present in the paintbrush group. Mechanical testing at 6 weeks indicated that joint capsule in the grid group had better mechanical properties than capsule in the paintbrush group. This study revealed that radiofrequency treatment of joint capsule in a grid pattern allowed faster healing than tissue treated in a paintbrush pattern.
Simian Immunodeficiency Virus-Producing Cells in Follicles Are Partially Suppressed by CD8<sup>+</sup>Cells<i>In Vivo</i> (2016)

HIV- and SIV-specific CD8<sup>+</sup> T cells are typically largely excluded from lymphoid B cell follicles, where virus-producing cells are most highly concentrated, suggesting that B cell follicles are somewhat of an immunoprivileged site where virus-specific CD8<sup>+</sup> T cells are not able to clear all follicular HIV- and SIV-producing cells. To gain insights into follicular CD8<sup>+</sup> T cell function, we characterized follicular virus-specific CD8<sup>+</sup> T cells in situ by using an SIV-infected rhesus macaque model of HIV. We found that subsets of follicular SIV-specific CD8<sup>+</sup> T cells are able to migrate throughout the follicle, are likely inhibited by Foxp3<sup>+</sup> cells, and are likely exhausted but that, nonetheless, subsets are likely functional, as they express markers consistent with effector function and show signs of suppressing viral replication in vivo These findings support HIV cure strategies that increase the frequency of functional follicular virus-specific CD8<sup>+</sup> T cells.
Texture displays (2009)

In this paper, we consider a passive approach to tactile presentation based on changing the surface textures of objects that might naturally be handled by a user. This may allow devices and other objects to convey small amounts of information in very unobtrusive ways and with little attention demand. This paper considers several possible uses for this style of display and explores implementation issues. We conclude with results from our user study, which indicate that users can detect upwards of four textural states accurately with even simple materials.