gebhart/patrepeval huggingface dataset:
TP53 genetic alterations in head‐and‐neck carcinomas from Brazil (1998)

In this study we investigated the incidence of mutations and loss of heterozygosity (LOH) of the TP53 gene in DNA samples from paired tumor and adjacent normal tissue from 90 patients with untreated squamous-cell carcinoma of the head and neck. Evidence for TP53 mutations were demonstrated in 53% (48/90) of the cases analyzed. All cases were also examined for loss of heterozygosity, using a PCR-based polymorphic marker at TP53. LOH was found in 36 out of 72 (50%) informative cases. Direct sequencing of PCR products was performed in 45 cases with evidence of mutations. The sequencing results revealed the presence of base-substitutions (67%), deletions (29%) and insertions (4%). Of the base-substitutions, 70% were transitions and 30% were transversions. Demographic variables, tumor site, stage (TNM), family history of cancer, lymph-node involvement and histological grade were not important predictors of TP53 mutations. Nor did TP53 genetic alterations correlate with survival status. In conclusion, we show that TP53 genetic alterations are frequent in head-and-neck tumors, but are not associated with clinicopathological variables or disease progression. Our study provides an evaluation of the spectrum of TP53 mutations in the pathogenesis of head-and-neck carcinoma in Brazil. Int. J. Cancer 76:13–18, 1998.© 1998 Wiley-Liss, Inc.
Submicrometer Surface Patterning Using Interfacial Colloidal Particle Self-Assembly (2009)

Hexagonal noncontiguously packed (HNCP) arrays of submicrometer-sized particles trapped at an air-water interface are successfully transferred to solid substrates. The long-range order of the hexagonal arrays at the interface can be improved by compression-relaxation cycles. The interparticle distance (i.e., the periodicity of the hexagonal array) can be controlled by varying the degree of compression of the particle film. The critical characteristics of the substrate surface are hydrophobicity (advancing water contact angle of >70 degrees) and a charge complementary to the surface of the particles. Suitable silicon and glass substrates are easily prepared by treatment with commercially available organosilicon compounds. Two transfer processes have been developed. When the parallel transfer process is used, the HNCP arrays are deposited on the solid substrates with minimal pattern distortion. The vertical dipping transfer distorts the pattern and renders a sense of directionality perpendicular to the dipping direction. This surface patterning technique is applied to fabrication of subwavelength grating for antireflection in the visible region. Antireflective HNCP arrays comprising varied particle diameters and pattern periodicities are fabricated on glass substrates to demonstrate the effects of these parameters on the antireflection performance.
Application of heat shock promoter in transgenic zebrafish (2008)

The heat shock promoter is useful for regulating transgene expression in small water-living organisms. In zebrafish embryos, downstream gene expression can be greatly induced throughout the body by raising the temperature from 28.5 degrees C to 38.0 degrees C. By manipulating the local temperature within an embryo, spatial control of transgene expression is also possible. One such way for inducing heat shock response in targeted cells is by using a laser microbeam under the microscope. In addition, random mosaic expression by transient gene expression and transplantation of the transgenic embryo into a wild type host can be considered a powerful tool for studying gene functions using this promoter. In this paper, we review the applications of the zebrafish heat shock protein promoter as a gene expression tool and for lineage labeling and transcription enhancer screening.
Transient response of <i>Enterobacter aerogenes</i> under a dual nutrient limitation in a chemostat (1976)

Utilizing a chemostat with a dual nutrient limitation of nitrogen and phosphate, we examined the transient response of the culture following a pulse of one of the limiting nutrients (ammonia). This method provided quantitative evidence that cells can be grown under dual nutrient limitation. Furthermore, the pattern of response was consistent with the hypothesis that phosphate limitation restricts nucleic acid synthesis in the cell and that nitrogen limitation restricts protein synthesis. The net result is that under a phosphate limitation there is a restricted biosynthetic capacity which we feel is closely associated with the RNA content of the cell.
The use of machine-readable astronomical catalogs at small observatories (1986)

The development of computer controlled telescopes at small observatories has dramatically increased the demand for and potential usefulness of astronomical catalogs in machine-readable form. The compilation and storage of catalogs containing program and standard stars are obvious necessities for the operation of an automatic telescope, but to date most observers have been collecting their own data and manually entering them into microcomputer disk storage. (This is clear from the small number of machine catalogs distributed by the ADC to smaller observatories.) Astronomical data centers located in several countries around the world currently archive, maintain and disseminate a wide variety of machine catalogs in virtually every discipline of astronomy, and these facilities can provide observers with nearly any kind of data needed for controlling telescopes (positional catalogs), reducing data (catalogs of all types of photometry, spectroscopy, etc.) and providing access to fundamental quantities needed for the interpretation of observations (catalogs of binaries, variables, radial and rotational velocities, etc.). The ADC presently has approximately 450 machine catalogs in its archives and these are available to observatories upon request. Procedures for obtaining data from the ADC and policies for distribution are described in this paper, while a list of all catalogs available can be obtained by contacting the ADC.
Experimental observation of hairpin auto-generation events in a turbulent boundary layer (2016)

Time-resolved tomographic particle image velocimetry experiments show that new hairpin vortices are generated within a fully developed and unperturbed turbulent boundary layer. The measurements are taken at a Reynolds number based on the momentum thickness of 2038, and cover the near-wall region below $y^{+}=140$ , where $y^{+}$ is the wall-normal distance in wall units. Instantaneous visualizations of the flow reveal near-wall low-speed streaks with associated quasi-streamwise vortices, retrograde inverted arch vortices, hairpin vortices and hairpin packets. The hairpin heads are observed as close to the wall as $y^{+}=30$ . Examples of hairpin packet evolution reveal the development of new hairpin vortices, which are created upstream and close to the wall in a manner consistent with the auto-generation model (Zhou et al. , J. Fluid Mech. , vol. 387, 1999, pp. 353–396). The development of the new hairpin appears to be initiated by an approaching sweep event, which perturbs the shear layer associated with the initial packet. The shear layer rolls up, thereby forming the new hairpin head. The head subsequently connects to existing streamwise vortices and develops into a hairpin. The time scale associated with the hairpin auto-generation is 20–30 wall units of time. This demonstrates that hairpins can be created over short distances within a developed turbulent boundary layer, implying that they are not simply remnants of the laminar-to-turbulent transition process far upstream.
External Plate Reinforcement for Concrete Beams (1998)

Strengthening concrete beams for shear forces by means of attaching steel plates to the external surfaces could provide a practical solution to the program of upgrading concrete bridges for carrying heavier loads. The experimental study carried out on three beams with 2, 4, and 6 mm plates attached by bolting to the vertical sides (web) of the beams resulted in considerable enhancement to the shear strength capacity. External plate attachment can also be designed to give simultaneous enhancement to flexural capacity. Although the beams failed in shear, as expected, the mode of failure was ductile, controlled by the yielding and local buckling of the external plates. The experimental study, although limited in terms of number of tests, showed that the method of construction could prove to be both practical and reliable for strengthening the existing in-situ concrete beams.
A 5.5-kOe 60-Hz magnetic hysteresis loop tracer with precise digital readout (1971)

A new hysteresis loop tracer ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">B-H</tex> meter), operating at 60 Hz, has been developed for use in the quality control of magnetic materials for magnetic recording. The instrument is suitable for making hysteresis measurements of hard magnetic materials with coercivities ranging from about 2.5 Oe (200 A/m) to 2.5 kOe (200 kA/m), which can be saturated (or nearly so) in fields up to -5.5 kOe (450 kA/m). Materials may be tapes, rods, or packed tubes. Precise measurements may be made by relatively untrained personnel. The pertinent specifications are as follows : 1) maximum applied field (H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</inf> ) to 5.5 kOe (450 kA/m) ; 2) sample flux range from 50 mMx (0.5 nWb) to 1 kMx (10 μWb) ; 3) direct digital readout of H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</inf> , coercive force (H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ci</inf> ), maximum flux ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\varphi_{mi}</tex> ), remanent flux ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\varphi_{r}</tex> ), and loop squareness ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">box$^b$</tex> ); 4) X-Y plotting of the hysteresis loop, the differentiated loop, or <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">H_{ci}, \varphi_{mi}, \varphi_{r}, box$^b$</tex> , etc., versus H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</inf> ; 5) precision of flux and field measurements to the order of 1 percent. Contributing to the performance is a novel main coil design which generates a field constant to within 0.5 percent in a volume containing the sample and the pickup coils. The electronics package makes extensive use of analog function modules to process the signal information.
How To Get the Most Out of Two Phosphorus Chemistries. Studies on H-Phosphonates (2002)

The biological importance and practical significance of phosphate esters and their analogues have been the major driving forces for research in various areas of synthetic organic phosphorus chemistry. In this Account, the authors' studies on the development of a comprehensive H-phosphonate methodology and the underlying chemistry for the preparation of biologically important phosphate esters and their analogues are briefly discussed.
Policy-driven security management for fog computing: Preliminary framework and a case study (2014)

With the increasing user demand for elastic provisioning of resources coupled with ubiquitous and on-demand access to data, cloud computing has been recognized as an emerging technology to meet such dynamic user demands. In addition, with the introduction and rising use of mobile devices, the Internet of Things (IoT) has recently received considerable attention since the IoT has brought physical devices and connected them to the Internet, enabling each device to share data with surrounding devices and virtualized technologies in real-time. Consequently, the exploding data usage requires a new, innovative computing platform that can provide robust real-time data analytics and resource provisioning to clients. As a result, fog computing has recently been introduced to provide computation, storage and networking services between the end-users and traditional cloud computing data centers. This paper proposes a policy-based management of resources in fog computing, expanding the current fog computing platform to support secure collaboration and interoperability between different user-requested resources in fog computing.
Potent Gene Silencing <i>In Vitro</i> at Physiological pH Using Chitosan Polymers (2012)

Among non-viral cationic polymers, biodegradable chitosan has during the last decade become an attractive carrier for small interference RNA (siRNA) delivery. Currently, degradation of macromolecules in the lysosomes is assumed to be a major barrier for effective siRNA transfection. Hence, transfection protocols are focused toward endosomal release mechanisms. In this work, we have tested 3 novel chitosan polymers and their siRNA delivery properties in vitro. To obtain efficient gene silencing of our model gene, S100A4, various transfection parameters were investigated, such as pH, nitrogen/phosphate ratio, photochemical internalization (PCI), media for complex formation, and cell lines. Our results showed that 2 linear chitosan polymers demonstrated excellent siRNA gene silencing, better than Lipofectamine 2000. The silencing effect was achieved without PCI treatment, under physiological pH, and with no observable reduction in cell viability.
Low-dark-current low-voltage 1.3–1.6 μm avalanche photodiode with high-low electric field profile and separate absorption and multiplication regions by molecular beam epitaxy (1984)

The operation of the recently disclosed heterojunction avalanche photodiode with high-low electric field profile and separate absorption and multiplication regions (HI-LO SAM APD) is demonstrated. This new structure which features a doping spike in the wide gap layer offers several advantages over conventional SAM APDs (lower dark current and excess noise factor, greater gain stability). Low dark currents (≃1 nA), low voltage operation (−26 V) and gains as high as 50 at 1.60 μm are demonstrated in an Al0.48In0.52As/Ga0 47In0 53As prototype grown by molecular beam epitaxy.
RelB/p50 Dimers Are Differentially Regulated by Tumor Necrosis Factor-α and Lymphotoxin-β Receptor Activation (2003)

Tumor necrosis factor-alpha (TNF-alpha) and lymphotoxin-beta receptor (LTbetaR) signaling both play important roles in inflammatory and immune responses through activation of NF-kappaB. Using various deficient mouse embryonic fibroblast cells, we have compared the signaling pathways leading to NF-kappaB induction in response to TNF-alpha and LTbetaR activation. We demonstrate that LTbetaR ligation induces not only RelA/p50 dimers but also RelB/p50 dimers, whereas TNF-alpha induces only RelA/p50 dimers. LTbetaR-induced binding of RelB/p50 requires processing of p100 that is mediated by IKKalpha but is independent of IKKbeta, NEMO/IKKgamma, and RelA. Moreover, we show that RelB, p50, and p100 can associate in the same complex and that TNF-alpha but not LTbeta signaling increases the association of p100 with RelB/p50 dimers in the nucleus, leading to the specific inhibition of RelB DNA binding. These results suggest that the alternative NF-kappaB pathway based on p100 processing may account not only for the activation of RelB/p52 dimers but also for that of RelB/p50 dimers and that p100 regulates the binding activity of RelB/p50 dimers via at least two distinct mechanisms depending on the signaling pathway involved.
3-D Object Tracking in Panoramic Video and LiDAR for Radiological Source–Object Attribution and Improved Source Detection (2020)

Networked detector systems can be deployed in urban environments to aid in the detection and localization of radiological and/or nuclear material. However, effectively responding to and interpreting a radiological alarm using spectroscopic data alone may be hampered by a lack of situational awareness, particularly in complex environments. This study investigates the use of Light Detection and Ranging (LiDAR) and streaming video to enable real-time object detection and tracking, and the fusion of this tracking information with radiological data for the purposes of enhanced situational awareness and increased detection sensitivity. This work presents an object detection, tracking, and novel source-object attribution analysis that is capable of operating in real time. By implementing this analysis pipeline on a custom-developed system that comprises a static 2 in. × 4 in. × 16 in. NaI(Tl) detector colocated with a 64beam LiDAR and four monocular cameras, we demonstrate the ability to accurately correlate trajectories from tracked objects to spectroscopic gamma-ray data in real time and use physics-based models to reliably discriminate between source-carrying and nonsource-carrying objects. In this work, we describe our approach in detail and present a quantitative performance assessment that characterizes the source-object attribution capabilities of both video and LiDAR. Additionally, we demonstrate the ability to simultaneously track pedestrians and vehicles in a mock urban environment and use this tracking information to improve both detection sensitivity and situational awareness using our contextual-radiological data fusion methodology.
Cauliflower mosaic virus (CaMV) aphid transmission factor (ATF) forms para-crystalline structures when expressed both in vitro and upon CaMV plant infection (1993)

*INRA, Centre de Montpellier Diffusion du document : INRA, Centre de Montpellier
Arrestin/Clathrin Interaction (1997)

Previously we demonstrated that nonvisual arrestins exhibit a high affinity interaction with clathrin, consistent with an adaptor function in the internalization of G protein-coupled receptors (Goodman, O. B., Jr., Krupnick, J. G., Santini, F., Gurevich, V. V., Penn, R. B., Gagnon, A. W., Keen, J. H., and Benovic, J. L. (1996) Nature 383, 447-450). In this report we show that a short sequence of highly conserved residues within the globular clathrin terminal domain is responsible for arrestin binding. Limited proteolysis of clathrin cages results in the release of terminal domains and concomitant abrogation of arrestin binding. The nonvisual arrestins, beta-arrestin and arrestin3, but not visual arrestin, bind specifically to a glutathione S-transferase-clathrin terminal domain fusion protein. Deletion analysis and alanine scanning mutagenesis localize the binding site to residues 89-100 of the clathrin heavy chain and indicate that residues 1-100 can function as an independent arrestin binding domain. Site-directed mutagenesis identifies an invariant glutamine (Glu-89) and two highly conserved lysines (Lys-96 and Lys-98) as residues critical for arrestin binding, complementing hydrophobic and acidic residues in arrestin3 which have been implicated in clathrin binding (Krupnick, J. G., Goodman, O. B., Jr., Keen, J. H., and Benovic, J. L. (1997) J. Biol. Chem. 272, 15011-15016). Despite exhibiting high affinity clathrin binding, arrestins do not induce coat assembly. The terminal domain is oriented toward the plasma membrane in coated pits, and its binding of both arrestins and AP-2 suggests that this domain is the anchor responsible for adaptor-receptor recruitment to the coated pit.
Yeasts as Producers of Flavor Precursors during Cocoa Bean Fermentation and Their Relevance as Starter Cultures: A Review (2022)

During the fermentation of cocoa beans, the yeasts produce volatile organic compounds (VOCs). Through reactions associated with amino acid metabolism, yeasts generate important aroma precursors as acetate esters and fatty acid ethyl esters are essential in developing fruity flavors and aromas in the final product (usually chocolate). In addition, some yeasts may have pectinolytic and antifungal activity, which is desirable in the post-harvest process of cocoa. The main yeast species in cocoa fermentation are Saccharomyces cerevisiae, Pichia kudriavzevii, and Hanseniaspora opuntiae. These produce higher alcohols and acetyl-CoA to make acetate–esters, compounds that produce floral and fruity notes. However, there are still controversies in scientific reports because some mention that there are no significant differences in the sensory characteristics of the final product. Others mention that the fermentation of cocoa by yeast has a significant influence on improving the sensory attributes of the final product. However, using yeasts as starter cultures for cocoa bean fermentation is recommended to homogenize sensory attributes such as notes and flavors in chocolate.
Variable antigen genes of the relapsing fever agent <i>Borrelia hermsii</i> are activated by promoter addition (1991)

Borrelia hermsii, an agent of relapsing fever, avoids the host's immune response by means of multiphasic antigenic variation. Serotype specificity is determined by variable antigens called the Vmp lipoproteins. Through recombination between linear plasmids a formerly silent vmp gene replaces another vmp gene at a telomeric expression locus. We examined strain HS1 borreliae before and after a switch from serotype 7 to serotype 21. The nucleotide sequences of 5' regions of silent and expressed vmp7 and vmp21 were determined. Silent and active vmp7 and vmp21 genes shared a block of homologous sequences surrounding their 5' ends. Sequences upstream of silent vmp7 and vmp21 genes lacked the promoter and substantially differed from each other. In this antigenic switch a vmp gene was activated by a recombination that placed it downstream of a promoter.
Ameliorative effects of follistatin‐related protein/TSC‐36/FSTL1 on joint inflammation in a mouse model of arthritis (2004)

These findings from in vivo experiments suggest that FRP could be one of the key molecules in the treatment of inflammatory joint diseases such as RA.
Detection of Necrosis by Release of Lactate Dehydrogenase Activity (2013)

Apoptosis and necrosis are two major forms of cell death observed in normal and disease pathologies. Although there are many assays for detection of apoptosis, relatively few assays are available for measuring necrosis. A key signature for necrotic cells is the permeabilization of the plasma membrane. This event can be quantified in tissue culture settings by measuring the release of the intracellular enzyme lactate dehydrogenase (LDH). When combined with other methods, measuring LDH release is a useful method for the detection of necrosis. In this chapter, we describe the step-by-step procedure for detection of LDH release from necrotic cells using a microtiter plate-based colorimetric absorbance assay.
Field-plate effects on the breakdown voltage of an integrated high-voltage LDMOS transistor (2004)

A 700 V double-resurf LDMOS (DR-LDMOS) with double-metal field plates is successfully integrated monolithically in a 1 /spl mu/ double-level metal (DLM) Bi-CMOS process for use in HV off-line switching applications. The process and device parameters, which determine the best-in-class specific on-resistance of lower than 200 mohm-cm/sup 2/, and a robust breakdown voltage of greater than 700 V, were optimized and addressed in our 1/sup st/ generation DR-LDMOS with single-level metal (SLM) process. It is found, during the DLM process development, that breakdown voltage begins to show significant degradation after stress when a 2/sup nd/ layer of dielectric layer (ILD-1) is added on top of Metal-1, as opposed to no degradation when there was no ILD-1 on top of Metal-1. This paper presents the re-optimization of DR-LDMOS with new Metal-2 field plate designs with respect to Metal-1 and ILD-1 to maintain a stable and robust breakdown voltage (BV) after stress.