gebhart/patrepeval huggingface dataset:
Antigenic Stimulation Specifically Reactivates the Replication of Archived Simian Immunodeficiency Virus Genomes in Chronically Infected Macaques (2005)

Human immunodeficiency virus/simian immunodeficiency virus (SIV) diversification is a direct consequence of viral replication and occurs principally in secondary lymphoid organs where CD4(+) T cells are activated and proliferate. However, the evolution of viral quasispecies may also be driven by various nonexclusive mechanisms, including adaptation to specific immune responses and modification of viral fitness. Analysis of viral quasispecies in SIV-infected macaques subjected to repeated antigenic stimulations allowed us to demonstrate transient expansions of SIV populations that were highly dependent upon activation of antigen-specific T cells. T-cell clones expanded in response to a particular antigen were infected by a specific viral population and persisted for prolonged periods. Upon a second stimulation by encounter with the same antigen, these specific genomes were at the origin of a new burst of replication, leading to rapid but transient replacement of the viral quasispecies in blood. Finally, longitudinal analysis of SIV sequence variation during and between antigenic stimulations revealed that viral evolution is mostly constrained to periods of strong immunological activity.
Morbid Obesity: Increased Risk of Failure After Aseptic Revision TKA (2015)

Level III, therapeutic study.
Interrupted Arterial Occlusion Reduces Ischemic Damage in a Focal Cerebral Ischemia Model of Rats (1995)

It is generally thought by neurosurgeons that when temporary clipping of a major cerebral vessel is necessary during aneurysm surgery, repeated short periods of cerebral ischemia are safer for the brain than a single long episode. This study was performed to investigate whether repetitive short episodes of cerebral ischemia would alter the resulting brain injury as compared with a single long period of ischemia in a rat model for focal cerebral ischemia. Middle cerebral artery occlusion and reperfusion were performed by the intraluminal thread technique. The experimental design consisted of a single 90-minute occlusion period in the continuous ischemia group versus three 30-minute occlusion periods with 15-minute reperfusion periods in the repetitive group. Local cerebral blood flow was measured by the hydrogen clearance technique. During the ischemic period, local cerebral blood flow values significantly decreased in both the continuous and the repetitive groups. Cerebral blood flow restoration was demonstrated after each episode of reperfusion in both groups. The neurological status scores 2 hours after surgery in the rats subjected to repetitive insults were significantly better compared with those in the rats of the continuous ischemia group. However, the scores on Days 1, 3, and 7 did not show a significantly better difference. The animals were killed 7 days after the induction of ischemia for the measurement of the infarction area under the microscope. The total area of infarction was significantly reduced (4.05 +/- 4.56 versus 47.2 +/- 37.3 mm2, P < 0.001) by interruption of the ischemic time period.(ABSTRACT TRUNCATED AT 250 WORDS)
Bond-orientational order in liquids and glasses (1983)

Bond-orientational order in molecular-dynamics simulations of supercooled liquids and in models of metallic glasses is studied. Quadratic and third-order invariants formed from bond spherical harmonics allow quantitative measures of cluster symmetries in these systems. A state with short-range translational order, but extended correlations in the orientations of particle clusters, starts to develop about 10% below the equilibrium melting temperature in a supercooled Lennard-Jones liquid. The order is predominantly icosahedral, although there is also a cubic component which we attribute to the periodic boundary conditions. Results are obtained for liquids cooled in an icosahedral pair potential as well. Only a modest amount of orientational order appears in a relaxed Finney dense-random-packing model. In contrast, we find essentially perfect icosahedral bond correlations in alternative "amorphon" cluster models of glass structure.
Manual for Assessing Safety Hardware TL-4 Evaluation of Critical Flare Rate for Cast-in-Place Concrete Barrier (2022)

Concrete median barriers are used by Departments of Transportation (DOTs) to provide separation of traffic. Typically, the crashworthiness of these barriers is tested and evaluated in full-scale crash testing conducted according to current roadside safety device standards. Occasionally, DOTs need to flare the concrete barrier length of need (LON) around fixed objects, such as bridge piers. Flaring a concrete barrier increases the effective impact angle which consequently increases the impact severity of the vehicle creating an opportunity for vehicle instability or excessive occupant risk factors. No current recommendations are available to guide the installation of flared barriers around such fixed objects, while still maintaining barrier crashworthiness. Although the current practice is to flare the cast-in-place (CIP) concrete barrier at a maximum 20:1 rate, no full-scale crash testing has been conducted to determine the crashworthiness of the system at this condition or at a flare rate that might be considered more critical. The crash tests reported in this paper were performed according to the Manual for Assessing Safety Hardware (MASH) Tests 4–10 (with the use of a passenger car), 4–11 (a pickup truck), and 4–12 (a single unit truck) for LON, which represent the tests considered necessary to demonstrate the MASH compliance of the device. The 40-in. single slope CIP concrete barrier with a 20:1 flare rate met MASH requirements and is considered MASH compliant for Test Level (TL) 4. The system is considered suitable for implementation where there is a need to flare the concrete barrier around a fixed object.
Supplementary Methods from PlGF/VEGFR-1 Signaling Promotes Macrophage Polarization and Accelerated Tumor Progression in Obesity (2023)

&lt;p&gt;Supplementary Methods&lt;/p&gt;
Electrocoating of stainless steel coronary stents for extended release of paclitaxel (2008)

Nonbiodegradable polymer coating based on N-(2-carboxyethyl)pyrrole (PPA) and butyl ester of PPA (BuOPy) were successfully electrodeposited on a stainless steel stent surface using cyclic voltammetry. Chemical composition of the coating was examined by X-ray photoelectron spectroscopy. Polymer stability was examined by immersing the coated stent into 1:1 solution of fetal calf serum:seline solution up to 1 year and implantation subcutaneously in mouse for 1 week. Morphology changes were then recorded by scanning electron microscopy. Paclitaxel loading was carried out by immersion into drug solution and its release was detected by HPLC. The results show that thin (single micrometers), uniform coating with various morphology and hydrophobicity can be created by electrochemical deposition. The polymer did not show significant histopathological or morphological changes in vitro and in vivo. The surface properties allow loading appropriate amounts of paclitaxel and release it slowly up to a month.
Temperature Dependence of a Modified Pitzer Equation for Strong Electrolytes Systems (2003)

We have established the temperature dependence for a modified Pitzer model. This model adequately correlates osmotic and activity coefficient data together with the dilution enthalpy for single-electrolyte solutions. For multisalt aqueous solutions, the modified model can successfully predict the behavior of the osmotic coefficient and the enthalpy at different temperatures. For the new model, the total average percentage error in the osmotic and activity coefficients is 3.1%.
Frequency Entrainment of a Forced van der Pol Oscillator (1978)

A van der Pol relaxation oscillator that is subjected to external sinusoidal forcing can exhibit stable and unstable periodic and almost periodic responses. For some forcing amplitudes it even happens that two stable subharmonics having different periods may coexist. We investigate here the stable responses of such forced oscillators. By numerically computing the rotation number of stable oscillations for various values of the forcing amplitude and oscillator tuning, we obtain descriptions of regions of phase locking, successive bifurcation of stable subharmonic and almost periodic oscillations, and overlap regions where two distinct stable oscillations can coexist.
Implementation of x-ray energy detection and photon counting using a silicon field-emission imaging array (2007)

A silicon field-emission array (FEA) was proposed for the implementation of x-ray energy detection and photon counting. The response of single X-ray photon events of differing X-ray energies is modeled showing two pulses with different widths and amplitudes. To verify the theory, a 2cm x 2cm silicon field emission array has been fabricated by subtractive etching and oxidation sharpening techniques. At 450 mum cathode to anode distance and at a vacuum level of 5x107 Torr, the device was biased at 1400V, field emitting at an integrated current of 32pA. When the device was excited by a 100muCi Fe55 X-ray source, an average increase of 24pA was observed.
Channel and Substrate Currents in GaAs FETS Due to Ionizing Radiation (1983)

Measurements of photocurrents due to pulsed ionizing radiation are reported and analyzed for planar, ion implanted GaAs junction field-effect transistors fabricated on semi-insulating GaAs substrates. With the help of various device geometries and contact arrangements, it will be shown that the primary photocurrent of the pn-junction gate of the JFET is much smaller than the additional photocurrent originating in the semi-insulating substrate by electron hole pair generation. For a 3 μm contact separation the substrate photocurrent in amperes is empirically given by Ips = 6 × 10-11 VAWγ, where VA is the applied voltage in volts, W the width of the contacts in cm and γ the dose rate in rad(GaAs)/s. The relation for Ips has also been theoretically assessed in good agreement with the experimental results. Since the primary photocurrent Ipp, is much smaller than Ips, the prediction of logic upset due to ionizing radiation dose rate has to be expanded to include this induced substrate photocurrent.
Low-Defect, High Molecular Weight Indacenodithiophene (IDT) Polymers Via a C–H Activation: Evaluation of a Simpler and Greener Approach to Organic Electronic Materials (2021)

The development, optimization, and assessment of new methods for the preparation of conjugated materials is key to the continued progress of organic electronics. Direct C–H activation methods have emerged and developed over the last 10 years to become an invaluable synthetic tool for the preparation of conjugated polymers for both redox-active and solid-state applications. Here, we evaluate direct (hetero)arylation polymerization (DHAP) methods for the synthesis of indaceno[1,2-b:5,6-b′]dithiophene-based polymers. We demonstrate, using a range of techniques, including direct visualization of individual polymer chains via high-resolution scanning tunneling microscopy, that DHAP can produce polymers with a high degree of regularity and purity that subsequently perform in organic thin-film transistors comparably to those made by other cross-coupling polymerizations that require increased synthetic complexity. Ultimately, this work results in an improved atom economy by reducing the number of synthetic steps to access high-performance molecular and polymeric materials.
Detection of Diverse Variants of Human Immunodeficiency Virus–1 Groups M, N, and O and Simian Immunodeficiency Viruses from Chimpanzees by Using GenericpolandenvPrimer Pairs (2000)

Human immunodeficiency virus type 1 (HIV-1) infection of humans is the result of independent cross-species transmissions of simian immunodeficiency viruses (SIVcpz) from naturally infected chimpanzees (Pan troglodytes troglodytes) to man. To develop a polymerase chain reaction-based assay capable of detecting members of all major phylogenetic SIVcpz and HIV-1 lineages (groups M, N, and O), primer pairs in conserved pol and env regions were designed. Both primer sets amplified </=10 copies of selected group M reference clones (subtypes A-H), proviral DNA or RNA of group N (YBF30), and group O of HIV-1 and also amplified divergent SIVcpz from cultured isolates (SIVcpzGAB1 and SIVcpzANT), uncultured spleen tissue (SIVcpzUS), and plasma (SIVcpzANT and SIVcpzUS). Sequences of the 2 amplicons (445 bp for gp41 and 261 bp for integrase) are of sufficient length for phylogenetic analyses, allowing both group and subtype classifications of the human viruses. Finally, both primer pairs are highly sensitive (>99%) in amplifying viral sequences from plasma taken from patients infected with HIV-1 group M (n=226) and O (n=17) viruses.
Folded reflectarray antenna with partial grid and director for high aperture efficiency (2018)

In this Letter, a new polarising grid for a folded reflectarray is proposed to improve the aperture efficiency of the antenna. This polarising grid is designed using a partial grid and a director which can improve the antenna radiation characteristic. Consequently, the measured aperture efficiency of the proposed antenna with the new polarising grid is 60.49% at 77 GHz.
Communication Through Jamming Over a Slotted ALOHA Channel (2008)

This correspondence derives bounds on the jamming capacity of a slotted ALOHA system. A system with n legitimate users, each with a Bernoulli arrival process is considered. Packets are temporarily stored at the corresponding user queues, and a slotted ALOHA strategy is used for packet transmissions over the shared channel. The scenario considered is that of a pair of <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">illegitimate</i> users that jam legitimate transmissions in order to communicate over the slotted ALOHA channel. Jamming leads to binary signaling between the illegitimate users, with packet collisions due to legitimate users treated as (multiplicative) noise in this channel. Further, the queueing dynamics at the legitimate users stochastically couples the jamming strategy used by the illegitimate users and the channel evolution. By considering various independent and identically distributed (i.i.d.) jamming strategies, achievable jamming rates over the slotted ALOHA channel are derived. Further, an upper bound on the jamming capacity over the class of all ergodic jamming policies is derived. These bounds are shown to be tight in the limit where the offered system load approaches unity.
Preclinical investigations of drug resistance (1995)

The effectiveness of antileukemic therapy is limited by intrinsic and acquired cellular resistance. Preclinical investigations support a complex and redundant network of cytoprotective mechanisms resulting from decreased drug accumulation, intracellular drug detoxification, alterations in nuclear targets of the antineoplastic agent, impaired transduction of growth arrest signals, and inherent cytokinetic resistance to S-phase active agents. Some, but not all, of these mechanisms are coordinately regulated, and correlative studies suggest that some may indeed contribute to clinical chemotherapy resistance. Current Opinion in Oncology 1995, 7:19-27
Advanced fusion power; a preliminary assessment. Final report, 1986-1987 (1987)

This report reviews research and studies of fusion with low neutron emission and advanced fuels (such as deuterium with helium 3); it assesses the feasibility of developing advanced fuels as a fusion power source for space propulsion and electrical power generation.
Multi-omics colocalization with genome-wide association studies reveals a context-specific genetic mechanism at a childhood onset asthma risk locus (2021)

This study provides evidence of functional effects for asthma risk variants in AECs and insight into RV-mediated transcriptional and epigenetic response mechanisms that modulate genetic effects in the airway and risk for asthma.
A current-switched full adder fabricated by photolithographic techniques (1978)

We describe a one‐bit full‐adder based on Josephson tunnel junctions and fabricated by photolithographic techniques. The design employs current‐switched gates with latching characteristics, direct‐coupled control currents and parallel fanout. The linewidths are 25 μm. Simulated and indirectly measured delays/gate are approximately 100 psec.
Determination, diversification and multipotency of mammalian myogenic cells (2000)

In amniotes, myogenic commitment appears to be dependent upon signaling from neural tube and dorsal ectoderm, that can be replaced by members of the Wnt family and by Sonic hedgehog. Once committed, myoblasts undergo different fates, in that they can differentiate immediately to form the myotome, or later to give rise to primary and secondary muscle fibers. With fiber maturation, satellite cells are first detected; these cells contribute to fiber growth and regeneration during post-natal life. We will describe recent data, mainly from our laboratory, that suggest a different origin for some of the cells that are incorporated into the muscle fibers during late development. We propose the possibility that these myogenic cells are derived from the vasculature, are multi-potent and become committed to myogenesis by local signaling, when ingressing a differentiating muscle tissue. The implications for fetal and perinatal development of the whole mesoderm will also be discussed.
Analysis of a brain-specific isozyme. Expression and chromatin structure of the rat aldolase C gene and transgenes (1994)

International audience
High Selectivity in Dry Etching of Silicon Nitride over Si Using a Novel Hydrofluorocarbon Etch Gas in a Microwave Excited Plasma for FinFET (2014)

Increased etch selectivity of SiN x over Si is required for the gate spacer formation in miniaturized MISFETs, especially in the FinFET. In this work, the selectivity of SiN x over Si is evaluated using a novel hydrofluorocarbon etch gas with a microwave excited high-density plasma. By using this novel etchant gas, a higher selectivity of SiN x over Si was obtained compared to CH3F. The etch rate of Si was suppressed due to the deposition of a hydrocarbon film on Si surface without O 2 gas. It was found that the selectivity of SiN x over Si near the SiN x sidewall decreased compared that far from the SiN x sidewall. By using flow rates of more than 12 sccm of the novel C x H y F z gas, the gate spacer was formed without Si recess even after the SiN x was overetched for an equivalent thickness of 40 nm.
Effect of Single-Dose Subarachnoid Spinal Anesthesia on Pain and Recovery after Unilateral Percutaneous Nephrolithotomy (2002)

A single preoperative dose of subarachnoid spinal analgesia provides a statistically significant decrease in postoperative parenteral pain medication and earlier ambulation. It also appears to reduce the amount of postoperative pain and decrease nausea.
Estimating optical turbulence using the PAMELA model (2004)

We present an optical turbulence model that has evolved from the PAMELA model. After a preliminary report in SPIE 2003 it became apparent that more data was needed to refine this adaptive model. This led us to take twelve months of over-land data (~100 meters pathlength) at the Chesapeake Bay Detachment of the Naval Research Lab. We present data throughout the year with varying environments with comparison with the model prediction. Our recent modification includes segmenting the windspeed to 3 sections, morning, afternoon, and night for better fitting. This is an attempt to incorporate variable wind speed into the model which is known to contribute significantly to the turbulence in the atmosphere. In addition, we present preliminary results from the over-the-bay data (10 km pathlength).
Cardiac dysfunction and impaired compensatory response to pressure overload in mice deficient in stem cell antigen‐1 (2011)

Stem cell antigen-1 (Sca-1) has been used to identify cardiac stem cells in the mouse heart. To investigate the function of Sca-1 in aging and during the cardiac adaptation to stress, we used Sca-1-deficient mice. These mice developed dilated cardiomyopathy [end-diastolic left ventricular diameter at 18 wk of age: wild-type (WT) mice, 4.2 mm ± 0.3; Sca-1-knockout (Sca-1-KO) mice, 4.6 mm ± 0.1; ejection fraction: WT mice, 51.1 ± 2.7%; Sca-1-KO mice, 42.9 ± 2.7%]. Furthermore, the hearts of mice lacking Sca-1 demonstrated exacerbated susceptibility to pressure overload [ejection fraction after transaortic constriction (TAC): WT mice, 43.5 ± 3.2%; Sca-1-KO mice, 30.8% ± 4.0] and increased apoptosis, as shown by the 2.5-fold increase in TUNEL(+) cells in Sca-1-deficient hearts under stress. Sca-1 deficiency affected primarily the nonmyocyte cell fraction. Indeed, the number of Nkx2.5(+) nonmyocyte cells, which represent a population of cardiac precursor cells (CPCs), was 2-fold smaller in Sca-1 deficient neonatal hearts. In vitro, the ability of CPCs to differentiate into cardiomyocytes was not affected by Sca-1 deletion. In contrast, these cells demonstrated unrestricted differentiation into cardiomyocytes. Interestingly, proliferation of cardiac nonmyocyte cells in response to stress, as judged by BrdU incorporation, was higher in mice lacking Sca-1 (percentages of BrdU(+) cells in the heart after TAC: WT mice, 4.4 ± 2.1%; Sca-1-KO mice, 19.3 ± 4.2%). These data demonstrate the crucial role of Sca-1 in the maintenance of cardiac integrity and suggest that Sca-1 restrains spontaneous differentiation in the precursor population. The absence of Sca-1 results in uncontrolled precursor recruitment, exhaustion of the precursor pool, and cardiac dysfunction.
Normal force and behavior of containing water during the compression of PVA brush (2015)

Polyvinyl acetal (PVA) brushes have been widely used in the Post CMP cleaning applications. To better understanding the mechanical characteristics of the PVA brushes, we measured the normal force during the compression and its relation to the water behavior contained inside the brushes. The normal force is directly related to the shear force which is important to the cleaning performance. In this study, especially we focus on the brush compression speed. As a result, the increase with compression speeds the maximum value of normal force also increased in the all brushes of several shapes. The normal force reached the order of several N, even in the single nodules of small size. In addition, water is spattered to the surrounding air just after the brush compression, and the region where water seeping out is depends on the brush shape and surface structure. From these results, we conclude that the PVA brushes have viscoelastic properties, and behavior of water inside the brushes and the shape are greatly affect the normal force.
Investigation of Multi‐Nickel‐Substituted Tungstophosphates and Their Stability and Electrocatalytic Properties in Aqueous Media. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Nonlinear optimization framework for image-based modeling on programmable graphics hardware (2005)

Graphics hardware is undergoing a change from fixed-function pipelines to more programmable organizations that resemble general purpose stream processors. In this paper, we show that certain general algorithms, not normally associated with computer graphics, can be mapped to such designs. Specifically, we cast nonlinear optimization as a data streaming process that is well matched to modern graphics processors. Our framework is particularly well suited for solving image-based modeling problems since it can be used to represent a large and diverse class of these problems using a common formulation. We successfully apply this approach to two distinct image-based modeling problems: light field mapping approximation and fitting the Lafortune model to spatial bidirectional reflectance distribution functions. Comparing the performance of the graphics hardware implementation to a CPU implementation, we show more than 5-fold improvement.