gebhart/patrepeval huggingface dataset:
Reovirus Binding to Cell Surface Sialic Acid Potentiates Virus-Induced Apoptosis (2001)

Reovirus induces apoptosis in cultured cells and in vivo. Genetic studies indicate that the efficiency with which reovirus strains induce apoptosis is determined by the viral S1 gene, which encodes attachment protein sigma1. However, the biochemical properties of sigma1 that influence apoptosis induction are unknown. To determine whether the capacity of sigma1 to bind cell surface sialic acid determines the magnitude of the apoptotic response, we used isogenic reovirus mutants that differ in the capacity to engage sialic acid. We found that T3SA+, a virus capable of binding sialic acid, induces high levels of apoptosis in both HeLa cells and L cells. In contrast, non-sialic-acid-binding strain T3SA- induces little or no apoptosis in these cell types. Differences in the capacity of T3SA- and T3SA+ to induce apoptosis are not due to differences in viral protein synthesis or production of viral progeny. Removal of cell surface sialic acid with neuraminidase abolishes the capacity of T3SA+ to induce apoptosis. Similarly, incubation of T3SA+ with sialyllactose, a trisaccharide comprised of lactose and sialic acid, blocks apoptosis. These findings demonstrate that reovirus binding to cell surface sialic acid is a critical requirement for the efficient induction of apoptosis and suggest that virus receptor utilization plays an important role in regulating cell death.
AIFD: A Runtime Solution to Buffer Overflow Attack (2007)

While buffer overflow problem has been known for a long time, it continues to present a serious security threat. Many solutions to the notorious problem were proposed. However, they had their own drawbacks. This paper presents a solution called API invocation fingerprint detection (AIFD) to eliminate overflow vulnerability with very low performance penalty. The solution is API-hook-based, which does not require compiler extensions or operating system kernel patches. Unlike other API-hook-based solutions, which will not discover that system calls are actually invoked by malicious code in certain cases, AIFD works well in those cases. By it, programs protected will not yield control to the exploitation code, but rather enter a fail-safe state. In this paper, we present principle of buffer overflow attacks, implementation details of AIFD, and experimental results of both penetration resistance and the performance impact of this solution.
Leucine and valine supplementation of low-protein diets for broiler chickens from 21 to 42 days of age (2016)

The objective of this study was to determine the requirements and interactions between the standardized ileal digestible (SID) Leu and Val levels in low-protein diets, and their effects on performance, serum characteristics, carcass yield and diameter of muscle fibers of broiler chickens from d 21 to 42 posthatch. A total of 1,500 21-day-old Cobb 500 male broiler chickens were distributed in a completely randomized design in a 5 × 5 factorial arrangement for a total of 25 treatments with 3 replicates of 20 birds each. Treatments consisted of 5 SID Leu levels (1.0, 1.2, 1.4, 1.6, or 1.8%) and 5 SID Val levels (0.52, 0.67, 0.82, 0.97, or 1.12%). At 42 d of age, there was interaction (P < 0.05) between the SID levels of Leu and Val on feed intake and weight gain. There was a quadratic effect (P < 0.05) of Leu and Val levels on feed conversion, with minimal point estimated at the levels of 1.19 and 0.86%, respectively. Dietary Leu supplementation reduced linearly (P < 0.05) serum concentrations of triglycerides and β-hydroxybutyrate. Dietary Leu increased (P ≤ 0.05) the fiber diameters of the pectoralis major muscle and breast yield at the levels of 1.24 and 1.13%, respectively, while the thigh yield was improved with the level of 0.71% Val. Abdominal fat decreased linearly (P < 0.05) with increasing levels of dietary Leu and Val. The SID Leu and Val levels needed to optimize weight gain and feed conversion in low-CP diets for broiler chickens from d 21 to 42 posthatch were estimated at 1.15 and 0.86%, and 1.19 and 0.86%, respectively. The supplementation of Leu and Val can reduce the abdominal fat deposition in birds fed low-CP diets during the grower phase. Leu and Val interactions can influence the performance but not the serum characteristics, carcass yield and diameter of muscle fibers of broilers fed low-protein diets. Therefore, it is necessary to consider the dietary Leu content to estimate the ideal level of Val in low-CP diets for optimum broiler performance.
Poly(<i>N</i>-isopropylacrylamide)-Coated Superparamagnetic Iron Oxide Nanoparticles: Relaxometric and Fluorescence Behavior Correlate to Temperature-Dependent Aggregation (2011)

Magnetic nanoparticles coated with polymers have existing and further potential for applications in medicine, including magnetic resonance imaging (MRI) imaging for diagnostics and assessing biodistribution, and their capacity to remotely generate heat in response to alternating current magnetic fields to elicit biological responses. Advances in such domains rely on developing better understanding of how such materials respond to magnetic fields. This paper reports thermosensitive properties of poly(N-isopropylacrylamide-co-Nile Red)-coated magnetic nanostructures upon passing through the lower critical solution temperature (LCST) of the polymer brush, and correlation of this behavior with formation of aggregates. Discrete magnetite nanoparticles coated with brush layers comprised of terminally attached poly(N-isopropylacrylamide-co-Nile Red) afforded highly water-dispersible nanoparticles (intensity average diameter of 38 nm) with good colloidal stability in phosphate buffers. The nanoparticles displayed enhanced transverse (T2) NMR relaxometric behavior as the temperature was increased through the LCST. Moreover, incorporation of the environmentally sensitive Nile Red dye into the copolymer leads to significant changes in fluorescence emission intensity upon aggregation that present new possibilities for the remote fluorescence detection of aggregated structures.
Three-dimensional orientational order in the bulk and on the surface of polymer films and its effect on liquid-crystal alignment (2004)

The correlation between orientation ordering of polymer chains in the bulk of polymer film and at the polymer-liquid-crystal (LC) interface has been studied to determine it's role in LC alignment. The bulk and surface ordering of polymer were investigated by null ellipsometry and x-ray reflectivity, respectively. Two kinds of liquid-crystalline polymers were used; side-chain azopolymers with azochromophores containing hydrophobic OC4H9 alkyl chain (P1) and strongly polar NO2 group (P2) as the end substituents. The uniaxial tilt orientation of azochromophores in the films of both polymers was induced by the oblique irradiation with unpolarized UV light. The two polymers exhibit similar chain orientation but different ordering of azochromophores on the surface of the films of P1 and P2. Surface ordering of P1 films correlates very well with the order in the bulk of the film, which are essentially determined by the UV exposure. However, orientational order of polymer chains at the surface of P2 films is different from that in its bulk and is not determined by UV exposure. This is explained by strong aggregation of azochromophores during its self-assembling at the polymer-air interface. The LC alignment is determined by the surface ordering of azochromophores. The results imply that ordering tendency can be effectively transferred from polymer bulk to polymer surface and then to LC if it is not lost at the polymer-LC interface.
Characterization and Noncovalent Inhibition of the Deubiquitinase and deISGylase Activity of SARS-CoV-2 Papain-Like Protease (2020)

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent for COVID-19, is a novel human betacoronavirus that is rapidly spreading worldwide. The outbreak currently includes over 3.7 million cases and 260,000 fatalities. As a betacoronavirus, SARS-CoV-2 encodes for a papain-like protease (PLpro) that is likely responsible for cleavage of the coronavirus (CoV) viral polypeptide. The PLpro is also responsible for suppression of host innate immune responses by virtue of its ability to reverse host ubiquitination and ISGylation events. Here, the biochemical activity of SARS-CoV-2 PLpro against ubiquitin (Ub) and interferon-stimulated gene product 15 (ISG15) substrates is evaluated, revealing that the protease has a marked reduction in its ability to process K48 linked Ub substrates compared to its counterpart in SARS-CoV. Additionally, its substrate activity more closely mirrors that of the PLpro from the Middle East respiratory syndrome coronavirus and prefers ISG15s from certain species including humans. Additionally, naphthalene based PLpro inhibitors are shown to be effective at halting SARS-CoV-2 PLpro activity as well as SARS-CoV-2 replication.
Metrics of circadian lighting for clinical investigations (2013)

There are currently no accepted metrics for summarising lighting conditions in studies aimed at investigating effects mediated by the circadian system. The objectives of this paper are to propose a set of metrics for capturing circadian variations in environmental lighting conditions and to compare two different lighting regimes applied to patient rooms. Our metric design emphasises the characterisation of light stimuli over time, e.g. their spread over one or more days. Lighting measurements for comparative assessment were taken in 20 beds in the intensive care unit of the Jeroen Bosch Hospital. Lighting conditions between the intensive care unit beds differed significantly across a number of circadian metrics. The proposed set of metrics offers a simple yet comprehensive approach to characterising lighting conditions from the circadian perspective with direct application in clinical studies investigating the effects of light on health.
First Examples of β‐Diketonate Platinum(<scp>II</scp>) Complexes with Sulfoxide Ligands (2005)

Abstract New platinum( II ) complexes have been prepared as models for explaining the coordination of multiple β‐diketonate li‐gands to give [Pt( O,O′ ‐acac)(γ‐acac)L] species. The new com‐pounds containing both an O,O′ ‐chelated acetylacetonate ligand and a sulfoxide in the platinum coordination sphere, [PtCl( O,O′ ‐acac)(DMSO)] ( 1 ) and [Pt( O,O ′ ‐acac)(γ‐acac)(DMSO)] ( 2 ), have been synthesised and characterised by 1 H, 13 C, 195 Pt 1‐D and 2‐D NMR heteronuclear correlation spectroscopy and, in the case of 2 , by X‐ray crystal structure analysis also. Moreover, a new synthetic pathway to obtain the previously reported complex K[Pt( O,O ′ ‐acac)(γ‐acac) 2 ] ( 3 ) has been developed. The data presented herein are consistent with a reaction mechanism which explains the subsequent steps of the coordination of multiple β‐diketonate li‐gands to platinum( II ) complexes, where the first species formed contains one O,O ′ ‐chelated acac group. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)
A new approach to GPS integrity monitoring using prior probability models and optimal threshold search (2002)

Current methods for GPS receiver autonomous integrity monitoring are limited by the assumptions they make. Using published studies of navigation system reliability, this paper develops a prior probability model for spacecraft and receiver anomalies based on non-ideal failure models and the uncertainty present in their failure distribution parameters. With this model, the thresholds for a residuals test statistic are found to optimize an arbitrary objective function based on relative costs for false alarm and missed detection errors. The outputs of Monte Carlo simulations allow thresholds to be computed for each geometry case using trial-and-error optimization. The simulation outputs suggest that the assumptions of traditional RAIM may be partially invalid. These results are useful for both snapshot RAIM tests as well as multi-step integrity algorithms which use Bayesian updating to generate posterior failure probabilities. Multi-step algorithms may be a valuable addition to the future GIC integrity structure.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Structural organization of the human insulin receptor ectodomain (1992)

To provide an experimental system amenable to a detailed biochemical and structural investigation of the extracellular (ligand binding) domain of the insulin receptor, we developed a mammalian heterologous cell expression system from which tens of milligrams of the soluble secreted ectodomain (the IR921 protein) can be routinely purified using methods that do not require harsh elution conditions. The purified IR921 protein has a Stokes radius of 6.8 nm and a sedimentation coefficient of 9.8 S, from which we calculate a hydro-dynamic mass of 281 kDa. Electron microscopic images, using both rotary shadowing and negative staining techniques, demonstrate a characteristic substructure for the IR921 protein consisting of two elongated arms, with a globular domain at each end, connected to each other at a point somewhat off-center to form a Y structure. Analysis using circular dichroism and fluorescence spectroscopy illustrate that insulin binding results in conformational changes in the ectodomain. Furthermore, fluorescence anisotropy decay data reveal segmental mobility within the IR921 protein that is successively frozen as a result of insulin binding, in contrast to results obtained in a previous study of the epidermal growth factor receptor ectodomain. This result suggests a divergence in hormone-induced signaling mechanisms used by the insulin and epidermal growth factor receptors.
Glymphatic clearance controls state-dependent changes in brain lactate concentration (2016)

Brain lactate concentration is higher during wakefulness than in sleep. However, it is unknown why arousal is linked to an increase in brain lactate and why lactate declines within minutes of sleep. Here, we show that the glymphatic system is responsible for state-dependent changes in brain lactate concentration. Suppression of glymphatic function via acetazolamide treatment, cisterna magna puncture, aquaporin 4 deletion, or changes in body position reduced the decline in brain lactate normally observed when awake mice transition into sleep or anesthesia. Concurrently, the same manipulations diminished accumulation of lactate in cervical, but not in inguinal lymph nodes when mice were anesthetized. Thus, our study suggests that brain lactate is an excellent biomarker of the sleep-wake cycle and increases further during sleep deprivation, because brain lactate is inversely correlated with glymphatic-lymphatic clearance. This analysis provides fundamental new insight into brain energy metabolism by demonstrating that glucose that is not fully oxidized can be exported as lactate via glymphatic-lymphatic fluid transport.
RF Bandpass Delta-Sigma Modulators for highly-efficient Class-S transmitters in SiGe BiCMOS technology (2010)

In this paper an overview of different RF BDSMs at 450 MHz, 900 MHz, and 2.14 GHz is presented. The BDSMs were specifically designed for use in Class-S transmitters. Different BDSM architectures are discussed and implemented with the goal to reduce the BDSM clock frequency and hence the PA switching speed requirements. The BDSMs are realized as continuous-time 1-bit bandpass delta-sigma modulators using modern SiGe BiCMOS technologies.
BRAF Mutations in Melanocytic Lesions and Papillary Thyroid Carcinoma Samples Identified Using Melting Curve Analysis of Polymerase Chain Reaction Products (2007)

Abstract Context. —Mutations of the proto-oncogene B- raf ( BRAF ) have been detected in melanocytic lesions and papillary carcinomas of the thyroid, and identification of these mutations could be useful in resolving some diagnostic problems. Objective. —To develop a method to evaluate mutations of BRAF that could provide results much more rapidly than conventional polymerase chain reaction and DNA sequencing assays. Design. —An assay using a LightCycler was developed to evaluate DNA sequences encoding amino acids within the activation loop of BRAF . Results. —Using this real-time polymerase chain reaction method, we analyzed 55 paraffin-embedded melanoma or nevus samples. The V600E mutation was found in 0 (0%) of 13 samples diagnosed histologically as Spitz nevi, 9 (24.3%) of 37 invasive melanomas, and 5 (100%) of 5 other melanocytic nevi. Two additional mutations, V600K and VK600-1E, also were identified in cases of invasive melanoma. We analyzed 14 paraffin-embedded papillary thyroid cancer (PTC) samples, 6 of which showed the V600E mutation. We found that our test worked efficiently with fine-needle aspirate specimens, and it identified 6 V600E mutations in 10 fine-needle aspirate specimens diagnosed as PTC. We also identified 4 V600E mutations in 6 specimens of PTC metastatic to lymph node. Unlike the melanocytic lesions, the PTC specimens yielded only V600E mutations. Comparison of our real-time polymerase chain reaction results with conventional polymerase chain reaction and DNA sequencing demonstrated 100% concordance. Surprisingly, we did not identify the previously reported VK600-1E or K601E mutations in our PTC specimens. Conclusions. —Our results show that the real-time polymerase chain reaction method is a rapid and accurate method for identifying BRAF mutations, such as V600E, in both paraffin-embedded tissue and fine-needle aspirate specimens.
A Privacy-Preserving Fully Homomorphic Encryption and Parallel Computation Based Biometric Data Matching (2020)

One of the most reliable methods of authentication used today is biometric matching. This authentication process, which is done by using biometrics information such as fingerprint, iris, face, etc. is used in many application areas. Authentication at border gates is one of these areas. However, some restrictions have been introduced to storing and using such data, especially with the General Data Protection Regulation (GDPR). The main goal of this work is to find the practical implementation of fully homomorphic encryption-based biometric matching in border controls. In this paper, we propose a biometric authentication system based on hash expansion and fully homomorphic encryption features, considering these restrictions. One of the most significant drawbacks of the homomorphic encryption method is the long execution time. We solved this problem by executing the matching algorithm in parallel manner. The proposed scheme is implemented as proof-of-concept in the SMILE, and its advantages in privacy preservation has been demonstrated.
Stereoselective SN2 Reactions of the (R)-Pantolactone Ester of Racemic .alpha.-Halo Carboxylic Acids with Aryl Oxides. A Synthesis of (S)-2-Aryloxy and (S)-2-Hydroxy Acids (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereoselective SN2 Reactions of the (R)-Pantolactone Ester of Racemic .alpha.-Halo Carboxylic Acids with Aryl Oxides. A Synthesis of (S)-2-Aryloxy and (S)-2-Hydroxy AcidsKevin Koh and Tony DurstCite this: J. Org. Chem. 1994, 59, 16, 4683–4686Publication Date (Print):August 1, 1994Publication History Published online1 May 2002Published inissue 1 August 1994https://pubs.acs.org/doi/10.1021/jo00095a053https://doi.org/10.1021/jo00095a053research-articleACS PublicationsRequest reuse permissionsArticle Views319Altmetric-Citations46LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Mini ReviewActivin Receptor Signaling (2004)

Activin is a member of the TGF-beta superfamily and has various effects on diverse biological systems. Activins initiate their cellular responses by binding to their receptors with intrinsic serine/threonine kinase activity and activation of specific downstream intracellular effectors termed Smad proteins. Smads relay the signal from the cell membrane to the nucleus, where they affect the transcription of target genes. Negative regulation of activin signal occurs at the extracellular, membrane, cytoplasmic and nuclear levels. The presence of many mechanisms for regulation shows its importance to normal physiology. Here, we review the latest advances in activin signal transduction.
Line shape analysis of electron–hole plasma electroluminescence in fully strained SiGe epitaxial layers (2003)

The electroluminescence of p-i-n diodes with fully strained Si0.80Ge0.20/Si(001) is dominated by radiative recombination in an electron–hole plasma. The recombination mechanisms and the band gap renormalization have been studied experimentally and by modeling. In order to minimize the influence of the SiGe/Si interface regions and thus to study the intrinsic behavior of strained SiGe, electroluminescence diodes with thick layers of SiGe in a metastable strain state have been investigated. To explain the electroluminescence spectra, the band filling model for an electron–hole plasma system and different broadening procedures have been investigated. This line shape analysis allowed the determination of the dependence of the renormalized band gap on carrier density and comparison with theoretical predictions was done. The low-energy tails of the electroluminescence spectra correspond to a broadening of the initial electronic states of the recombination process in electron–hole plasma system. The experimental data obtained from the line shape analysis of the electroluminescence spectra are in good agreement with previous results on spectral photocurrent and quantum efficiency measurements.
Oxidation of GaP in an Aqueous H[sub 2]O[sub 2] Solution (1973)

The oxidation of GaP in aqueous has been accomplished by both galvanic action at ∼100°C and by externally applied anodic reaction at room temperature. Films as thick as 1400 and 3500Aå, respectively, have been prepared using these two approaches. A detailed examination of the kinetics of galvanic oxide growth indicates that: (i) the oxidation mechanism involves predominantly the transfer of holes, (ii) the rate‐controlling step in the growth mechanism involves the diffusion of the oxidant, through the grown oxide, (iii) the index of refraction of the grown oxide is 1.58 ± 0.01, and (iv) a drying procedure to remove the water of hydration is necessary in order that the passivating amorphous oxide required for device use may be obtained. The growth of an oxide by externally applied anodic bias has resulted in the facts that: (i) the oxide thickness is linearly dependent on the applied bias up to about 100V, with the constant of proportionality being , (ii) an upper forming voltage of about 200V has been found for obtaining uniformly colored (i.e., thickness) films, and (iii) the index of refraction of the grown films depends on the forming voltage used, and (iv) a drying procedure to remove the water of hydration is necessary in order to obtain a stable amorphous oxide.