gebhart/patrepeval huggingface dataset:
Dissociation of the CD4 downregulation and viral infectivity enhancement functions of human immunodeficiency virus type 1 Nef (1995)

Recent evidence indicates that the nef gene of human immunodeficiency virus type 1 augments rather than inhibits viral replication in both cell culture and in vivo models. In addition, nef alters various normal cellular processes, including the display of CD4 on the cell surface. However, it remains unknown whether the enhancement of infectivity and the downregulation of CD4 represent linked or independent biologic properties of this single protein. In the present studies, mutational analyses were performed to define structure-function relationships within the Nef protein that mediate these effects. To assess the functional consequences of these mutations, sensitive and reliable assays were developed to quantitate the viral infectivity enhancement and CD4 downregulation functions of Nef. The results indicate that membrane-targeting sequences at the N terminus of Nef are important for both functions of Nef, while certain other conserved regions are dispensable for both functions. A conserved proline-X-X repeat segment in the central core of the protein, which is reminiscent of an SH3-binding domain, is critical for the enhancement of infectivity function but is dispensable for CD4 downregulation. However, the downregulation of CD4 by Nef appears to involve a two-step process requiring the initial dissociation of p56lck from CD4 to permit engagement of the endocytic apparatus by CD4. Together, these findings demonstrate that the infectivity enhancement and CD4 downregulation activities of human immunodeficiency virus type 1 Nef can be dissociated. Thus, these processes may be independent of one another in the viral replication cycle.
Method to Extract System-Independent Material Properties From Dual-Energy X-Ray CT (2019)

In 2016, we published a method for processing dual-energy computed tomography (DECT) data called system-independent rho-e/Z-e (ρ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> /Z <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> ) or SIRZ. Using data from multiple DECT systems and spectra, SIRZ estimated the electron density ρ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> and effective atomic number Z <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> (based on published X-ray cross sections), for a set of known specimens. However, the decomposition process required complex spectral modeling of the DECT system, which made SIRZ difficult to implement and automate. This paper describes the subsequent work on “SIRZ-2” to simplify the spectral modeling, automate the process, and improve its range and versatility. The SIRZ-2 basis functions are more accurate for the X-ray energy range (<;200 keV) and materials that are common to DECT applications in security and nondestructive characterization. To evaluate the SIRZ-2 performance, eight well-characterized specimens (with Z <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> of 6-20) were scanned with multiple spectral pairs (up to 200 keV) on seven different DECT systems, including a commercial airport luggage scanner. For these varied tests, the average SIRZ-2 relative errors for ρ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> estimates were four times lower (0.7% compared to 3.0% for SIRZ), while average Z <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> relative errors were comparably low for both methods (<;1.5%). Average precision errors were also low (<;2.3% for both). SIRZ-2 produces accurate, repeatable, and system-independent material property estimates of (ρ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> , Z <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e</sub> ) that can be directly compared across DECT systems and over time.
ChemInform Abstract: AMMONOLYSIS OF ESTERS OF AZIRIDINECARBOXYLIC ACIDS (1983)

Abstract Die Ammonolyse der Aziridincarbonsäureester (I) mit Ammoniak in Methanol oder anderen Alkoholen führt zu den Amiden (ll).
Secure content delivery in information-centric networks (2013)

In this paper, we propose a novel secure content delivery framework, for an information-centric network, which will enable content providers (e.g., Netflix and Youtube) to securely disseminate their content to legitimate users via content distribution networks (CDNs) and Internet service providers (ISPs). Use of our framework will enable legitimate users to receive/consume encrypted content cached at a nearby router (CDN or ISP), even when the providers are offline. Our framework would slash system-downtime due to server outages, such as that recently experienced by Netflix, Pinterest, and Instagram users in the US (October 22, 2012). It will also help the providers utilize in-network caches for shaping content transmission and reducing delivery latency. We discuss the handling of security, access control, and system dynamics challenges and demonstrate the practicality of our framework by implementing it on a CCNx testbed.
The determination of the parameters of sub- and supercritical extraction of plant raw materials (2010)

The extraction of biologically active substances by carbon dioxide from various plant raw materials (amaranth seeds, Sophora japonica flower buds, Stephania rotunda stems, and Stevia rebaudiana leaves) was studied at sub- and supercritical parameters. A laboratory unit for the extraction of plant raw materials by liquefied gases and supercritical fluids at 5–35 MPa pressures and 285–350 K temperatures was developed. The maximum yield of the extracted substances from plants specified was obtained at temperature and pressure exceeding the critical parameters of CO2 (320–330 K, 28–30 MPa).
Supplementary Table 1 from Enhancement of Antitumor Immunity in Lung Cancer by Targeting Myeloid-Derived Suppressor Cell Pathways (2023)

&lt;p&gt;PDF file - 18K, Antibodies used for characterization of Immune Cell Phenotypes.&lt;/p&gt;
Software for x-ray optics research instrumentation. Final report, 1991 (1992)

The statement of work for this contract between The Regents of the University of California and Brigham Young University called for the implementation of computer controlled substrate motion in an existing DC magnetron sputtering system. This task entailed the design and fabrication of a vacuum compatible motor drive and substrate holder, the system had to be capable of closed loop microcomputer control which required the development of a suitable computer interface and control software. Concurrent with this task, the existing magnetron sputtering system was to be upgraded to permit ion assisted deposition. This required modification of the existing sputtering hardware to permit independent control of voltages applied to the substrate and other additional electrode assemblies. In addition to design, fabrication and installation of the system modifications a systematic study of Mo-Si multilayer coatings grown using ion assisted deposition was undertaken. These studies served, in part, as training of LLNL personnel in the ion assisted deposition technique.
Origin of preferential grain orientation in excimer laser-induced crystallization of silicon thin films (2012)

The origin of the formation of {100} and {111} grain textures in polycrystalline silicon thin films prepared with multiple excimer laser shots at the super-lateral-growth crystallization regime is investigated in this study. Our results demonstrate that the type of texture formed is determined solely by the thickness of the silicon layer. At a critical value of 40 nm, a transition from {100} to {111} texture is observed with increasing layer thickness. It is therefore proposed that below this critical value, the texture formation is governed by surface energy anisotropy whereas above it, the kinetics of the solidification process predominate.
Assessing Hurricane Rainfall Mechanisms Using a Physics-Based Model: Hurricanes Isabel (2003) and Irene (2011) (2018)

Abstract We examine a recently developed physics-based tropical cyclone rainfall (TCR) model and apply it to assess the mechanisms that dominate the magnitude and spatial distribution of TC rainfall, with Hurricanes Isabel (2003) and Irene (2011) as study cases. We evaluate the TCR model using Weather and Research Forecasting (WRF) Model simulations. TCR-generated rainfall fields for the two storms compare well with WRF estimates in terms of both azimuthal mean and spatial distributions. When coupled with a hydrologic model, TCR generates flood peaks over the Delaware River basin for Irene as accurately as WRF. TCR accounts for four major rainfall mechanisms: surface frictional convergence, vortex stretching, interaction of the storm with topography, and interaction of the storm with large-scale baroclinity. We show that these rainfall mechanisms affected the rainfall pattern differently for Isabel and Irene. Frictional convergence is the dominant factor, while other mechanisms are also significant. The frictional convergence depends on the boundary layer formulation, which is relatively simple in TCR and may require calibration of boundary layer parameters. Furthermore, we find that the TC rainfall distribution is strongly dependent on the temporal and spatial variation of the TC wind field, mediated by the physical mechanisms represented by TCR. When coupled with various analytical wind models, TCR generally captures the rainfall distribution, with the Holland wind model performing the best. Given its high computational efficiency, TCR can be coupled with an analytical wind model, a hydrological model, and a TC climatology model to generate large numbers of synthetic events to assess the risk associated with TC rainfall and inland flooding.
Eye movement abnormalities correlate with genotype in autosomal dominant cerebellar ataxia type I (1998)

We compared horizontal eye movements (visually guided saccades, antisaccades, and smooth pursuit) in control subjects (n = 14) and patients with three forms of autosomal dominant cerebellar ataxias type I: spinocerebellar ataxias 1 and 2 (SCA1, n = 11; SCA2, n = 10) and SCA3/Machado-Joseph disease (MJD) (n = 16). In SCA1, saccade amplitude was significantly increased, resulting in hypermetria. The smooth pursuit gain was decreased. In SCA2, saccade velocity was markedly decreased. The percentage of errors in antisaccades was greatly increased and was significantly correlated with age at disease onset. In addition, a correlation between smooth pursuit gain and the number of trinucleotide repeats was found. In SCA3, gaze-evoked nystagmus was often present as was saccade hypometria and smooth pursuit gain was markedly decreased. Three major criteria, saccade amplitude, saccade velocity, and presence of gaze-evoked nystagmus, permitted the correct assignment of 90% of the SCA1, 90% of the SCA2, and 93% of the patients with SCA3 to their genetically confirmed patient group and, therefore, may help orient diagnoses of SCA1, SCA2, and SCA3 at early clinical stages of the diseases.
Rapid screening of lignans from Phyllanthus myrtifolius and stilbenoids from Syagrus romanzoffiana by HPLC‐SPE‐NMR (2011)

HPLC-SPE-NMR associated with HR-ESI/MS, which consumed only analytical amounts of partially purified mixtures, was demonstrated to be a good tool for rapid screening of both known and new natural products.
Anti‐LPS factor in the horseshoe crab, Tachypleus tridentatus (1984)

Anti-LPS factor, which inhibits the endotoxin mediated coagulation system in the horseshoe crab, Tachypleus tridentatus, was found to lyse red blood cells sensitized with gram-negative bacterial LPS, but not to lyse unsensitized cells. This hemolysis occurred even at 0 degree C and was completed within 1 min. The binding of anti-LPS factor to LPS must be essential for the hemolysis, because free LPS inhibited the hemolytic action of anti-LPS factor.
Post-bond sub-500 nm alignment in 300 mm integrated face-to-face wafer-to-wafer Cu-Cu thermocompression, Si-Si fusion and oxideoxide fusion bonding (2010)

We report recent advances in tool and process hardening of a first of its kind 300 mm wafer-to-wafer (WtW) preprocessing, aligning, and bonding integrated tool. We have demonstrated sub-500 nm post-bond alignment accuracies for 300 mm WtW face-to-face (FtF) Cu-Cu thermocompression bonds, WtW FtF Si-Si fusion bonds, and WtW FtF oxideoxide fusion bonds. All process of record (POR) recipes that were developed had undetectable voids based on scanning acoustic microscope (C-SAM) measurements on representative bonded Cu, oxide, and Si blanket wafers. Optimized bonded patterned wafer splits in the Cu-Cu WtW thermocompression bonding step have shown alignment accuracies down to ∼190 nm, the highest accuracy to date. Using an infrared-enabled, high speed focused ion beam (FIB) system (with XeF <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> ) with a CAD overlay function to assist in selective sample preparation, we have verified that the bonding interfaces at the via chain structures with 1–5 μm diameter vias show no interfacial voids. Also, there is evidence of Cu interdiffusion, as supported by transmission electron microscopy (TEM) and electron backscattering diffraction (EBSD) data.
Continuous cultivation of photosynthetic microorganisms: Approaches, applications and future trends (2015)

The possibility of using photosynthetic microorganisms, such as cyanobacteria and microalgae, for converting light and carbon dioxide into valuable biochemical products has raised the need for new cost-efficient processes ensuring a constant product quality. Food, feed, biofuels, cosmetics and pharmaceutics are among the sectors that can profit from the application of photosynthetic microorganisms. Biomass growth in a photobioreactor is a complex process influenced by multiple parameters, such as photosynthetic light capture and attenuation, nutrient uptake, photobioreactor hydrodynamics and gas-liquid mass transfer. In order to optimize productivity while keeping a standard product quality, a permanent control of the main cultivation parameters is necessary, where the continuous cultivation has shown to be the best option. However it is of utmost importance to recognize the singularity of continuous cultivation of cyanobacteria and microalgae due to their dependence on light availability and intensity. In this sense, this review provides comprehensive information on recent breakthroughs and possible future trends regarding technological and process improvements in continuous cultivation systems of microalgae and cyanobacteria, that will directly affect cost-effectiveness and product quality standardization. An overview of the various applications, techniques and equipment (with special emphasis on photobioreactors) in continuous cultivation of microalgae and cyanobacteria are presented. Additionally, mathematical modeling, feasibility, economics as well as the applicability of continuous cultivation into large-scale operation, are discussed.
Electrically Switchable and Permanently Stable Light Scattering Modes by Dynamic Fingerprint Chiral Textures (2016)

Negative dielectric nematic liquid crystals (LCs) doped with two azobenzene materials provide electrically switchable and permanently stable scattering mode light modulators based on dynamic fingerprint chiral textures (DFCT) with inhomogeneously helical axes. These light modulators can be switched between transparent (stable large domains of DFCT) states and scattering (stable small domains of DFCT) states by applying electric fields with different frequencies. The generation of DFCT results from the long flexible side chains of the doped chiral dopant. That is, if the DFCT can be obtained, then the large domains of DFCT reflect an intrinsically stable state. Moreover, the stabilization of the small domains of DFCT are caused by the terminal rigid restricted side chains of the other doped chiral dopant. Experimentally, the required amplitude to switch the light modulator from a scattering (transparent) state to a transparent (scattering) state decreases as the frequency of the applied electric field increases (decreases) within the set limits. This study is the first report on the advantages of the light scattering mode of DFCT, including low operating voltage, permanently stable transmission, wide viewing angle, high contrast, and polarization-independent scattering and transparency.
Acute noncontrast T1‐weighted magnetic resonance imaging predicts chronic radiofrequency ablation lesions (2018)

Native T1w MRI acquired acutely after RF ablation is a good predictor of chronic lesion size. Acute LGE-MRI significantly overestimates the chronic lesion size.
Synthetic dual inhibitors of DNA topoisomerase I and II. (1996)

A new type of synthetic dual inhibitor of DNA topoisomerase I and II was explored. This series of compounds shows high antineoplastic activities against cancer cells, but in vivo activity against P388 was not as high as in vitro activities.
Synthesis of A New Series of Tetrachalcogen Fulvalenes and Their Charge Transfer Cohpiexes (1985)

Abstract The synthesis of a new series of fulvalene-type π-donors and their charge-transfer complexes are described together with the crystal structure of the tetratellurafulvalene derivative.
Polysilicon TFT circuit design and performance (1992)

Both n- and p-channel polysilicon TFTs can be fabricated, allowing CMOS circuit techniques to be used. However, TFT characteristics are poor in comparison to conventional single-crystal MOSFETs, and relatively coarse design rules must be used to be compatible with processing on large-area glass plates. The authors examine these issues and describe the performance of a range of digital and analog circuit elements built using polysilicon TFTs. Digital circuit speeds in excess of 20 MHz are reported, along with operational amplifiers with over 80 dB of gain and more than 1-MHz unity-gain frequency. Several polysilicon TFT switched-capacitor circuits are also reported and shown to have adequate linearity, output swing, and settling time to form integrated data line drivers on an active-matrix liquid crystal display.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Full-range imaging of eye accommodation by high-speed long-depth range optical frequency domain imaging (2010)

We describe a high-speed long-depth range optical frequency domain imaging (OFDI) system employing a long-coherence length tunable source and demonstrate dynamic full-range imaging of the anterior segment of the eye including from the cornea surface to the posterior capsule of the crystalline lens with a depth range of 12 mm without removing complex conjugate image ambiguity. The tunable source spanned from 1260 to 1360 nm with an average output power of 15.8 mW. The fast A-scan rate of 20,000 per second provided dynamic OFDI and dependence of the whole anterior segment change on time following abrupt relaxation from the accommodated to the relaxed status, which was measured for a healthy eye and that with an intraocular lens.
Evidence that a significant number of naive T cells enter non‐lymphoid organs as part of a normal migratory pathway (2006)

Only activated and effector memory T cells are thought to access non-lymphoid tissues. In contrast, naive T cells are thought to circulate only between the blood, lymph and secondary lymphoid organs. We examined the phenotype of endogenous T cells in various non-lymphoid organs and showed that a subset of cells exhibited an apparently naive phenotype and were functionally inactive. FTY720 treatment selectively depleted this population from the non-lymphoid tissues. In addition, RAG-deficient TCR transgenic CD4 and CD8 T cells were present in non-lymphoid tissues in bone marrow chimeric mice and in situ imaging analysis revealed their location in the parenchymal tissues. Moreover, migration of TCR transgenic T cells to non-lymphoid tissues after adoptive transfer was pertussis-toxin resistant. Overall, the results suggest that naive T cells may circulate through non-lymphoid tissues as part of their normal migratory pathway.
Screenless Completions as a Viable Through-Tubing Sand Control Completion (2007)

Abstract Screenless sand control completions provide a cost-effective means of completing wells in the Gulf of Mexico by eliminating the need to have a rig on location. To date, six screenless completions have been performed for a major operator in the Gulf of Mexico. Each of the six treatments provided significant cost savings, as well as excellent return on investment for the operator. Screenless completions are an integrated solution that involve many field-proven technologies such as reservoir characterization, perforating, coiled-tubing intervention, matrix acidizing, resin consolidation, optimized fracturing with proppant flowback control, and fines migration prevention. The proper candidate selection, treatment design, treatment execution, production management and co-ordination of all services are essential to the success of the screenless completion. In this paper, the common sequence of events for a screenless completion is presented as well as the key technologies involved, from perforating to production. Each of the six case histories are examined in detail and will show that screenless completions provide effective through-tubing sand control in a variety of well conditions. Screenless completions have been proven effective in reservoirs from 10 to 60 ft in thickness, at depths from 4,000 to 10,500-ft true vertical depth, in casings from 3-1/2 to 9-5/8-in. and in oil and gas reservoirs at rates of up to 600 BOPD, 1750 BFPD or 3.5 MMSCFD and in wells deviated as high as 42o. The technique can also be applied in different wellbore configurations to target pay behind casing, and also zones that are located behind both tubing and casing.
Physiological Transport Forces Govern Drug Distribution for Stent-Based Delivery (2001)

Because local concentrations and gradients are inextricably linked to biological effect, our results provide a potential explanation for the variable success of stent-based delivery. We conclude that mere proximity of delivery devices to tissues does not ensure adequate targeting, because physiological transport forces cause local concentrations to deviate significantly from mean concentrations.
Nuclear localization signal binding protein from Arabidopsis mediates nuclear import of Agrobacterium VirD2 protein (1997)

T-DNA nuclear import is a central event in genetic transformation of plant cells by Agrobacterium. Presumably, the T-DNA transport intermediate is a single-stranded DNA molecule associated with two bacterial proteins, VirD2 and VirE2, which most likely mediate the transport process. While VirE2 cooperatively coats the transported single-stranded DNA, VirD2 is covalently attached to its 5' end. To better understand the mechanism of VirD2 action, a cellular receptor for VirD2 was identified and its encoding gene cloned from Arabidopsis. The identified protein, designated AtKAPalpha, specifically bound VirD2 in vivo and in vitro. VirD2-AtKAPalpha interaction was absolutely dependent on the carboxyl-terminal bipartite nuclear localization signal sequence of VirD2. The deduced amino acid sequence of AtKAPalpha was homologous to yeast and animal nuclear localization signal-binding proteins belonging to the karyopherin alpha family. Indeed, AtKAPalpha efficiently rescued a yeast mutant defective for nuclear import. Furthermore, AtKAPalpha specifically mediated transport of VirD2 into the nuclei of permeabilized yeast cells.