gebhart/patrepeval huggingface dataset:
Rapid N-glycan release from glycoproteins using immobilized PNGase F microcolumns B Analytical technologies in the biomedical and life sciences (2016)

N-glycosylation profiling of glycoprotein biotherapeutics is an essential step in each phase of product development in the biopharmaceutical industry. For example, during clone selection, hundreds of clones should be analyzed quickly from limited amounts of samples. On the other hand, identification of disease related glycosylation alterations can serve as early indicators (glycobiomarkers) for various pathological conditions in the biomedical field. Therefore, there is a growing demand for rapid and easy to automate sample preparation methods for N-glycosylation analysis. In this paper, we report on the design and implementation of immobilized recombinant glutathione-S-transferase (GST) tagged PNGase F enzyme microcolumns for rapid and efficient removal of N-linked carbohydrates from glycoproteins. Digestion speed and efficiency were compared to conventional in-solution based protocols. The use of PNGase F functionalized microcolumns resulted in efficient N-glycan removal in 10min from all major N-linked glycoprotein types of: (i) neutral (IgG), (ii) highly sialylated (fetuin), and (iii) high mannose (ribonuclease B) carbohydrate containing glycoprotein standards. The approach can be readily applied to automated sample preparation systems, such as liquid handling robots.
A framework for the robust estimation of optical flow (2002)

The authors consider the problem of robustly estimating optical flow from a pair of images using a new framework based on robust estimation which addresses violations of the brightness constancy and spatial smoothness assumptions. They also show the relationship between the robust estimation framework and line-process approaches for coping with spatial discontinuities. In doing so, the notion of a line process is generalized to that of an outlier process that can account for violations in both the brightness and smoothness assumptions. A graduated non-convexity algorithm is presented for recovering optical flow and motion discontinuities. The performance of the robust formulation is demonstrated on both synthetic data and natural images.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Microstructure and properties of additively manufactured Al–Ce–Mg alloys (2021)

Additive manufacturing of aluminum alloys is largely dominated by a near-eutectic Al-Si compositions, which are highly weldable, but have mechanical properties that are not competitive with conventional wrought Al alloys. In addition, there is a need for new Al alloys with improved high temperature properties and thermal stability for applications in the automotive and aerospace fields. In this work, we considered laser powder bed fusion additive manufacturing of two alloys in the Al-Ce-Mg system, designed as near-eutectic (Al-11Ce-7Mg) and hyper-eutectic (Al-15Ce-9Mg) compositions with respect to the binary L → Al + Al<sub>11</sub>Ce eutectic reaction. The addition of magnesium is used to promote solid solution strengthening. A custom laser scan pattern was used to reduce the formation of keyhole porosity, which was caused by excessive vaporization due to the high vapor pressure of magnesium. The microstructure and tensile mechanical properties of the alloys were characterized in the as-fabricated condition and following hot isostatic pressing. The two alloys exhibit significant variations in solidification structure morphology. These variations in non-equilibrium solidification structure were rationalized using a combination of thermodynamic and thermal modeling. Both alloys showed higher yield strength than AM Al-10Si-Mg for temperatures up to 350 °C and better strength retention at elevated temperatures than additively manufactured Scalmaloy.
Methodology for the Digital Calibration of Analog Circuits and Systems (2005)

This thesis presents a complete methodology for the digital calibration of analog circuits. It shows how to relax the extreme design constraints in analog circuits, allowing the realization of high-precision systems even with low-performance components. In addition, three applications of the methodology are proposed. To start with, an in-depth analysis of existing compensation techniques for analog circuit imperfections is carried out. The M/2+M sub-binary digital-to-analog converter is thoroughly studied, and the use of this very low-area circuit in conjunction with a successive approximations algorithm for digital compensation is described. A complete methodology based on this compensation circuit and algorithm is then proposed. The detection and correction of analog circuit imperfections is studied, and a simulation tool allowing the transparent simulation of analog circuits with automatic compensation blocks is introduced. An additional up/down converter is suggested for the compensation of continuoustime analog signal processing circuits. The first application shows how the sub-binary M/2+M structure can be employed as a conventional digital-to-analog converter if two calibration and radix conversion algorithms are implemented. The second application, a SOI 1T DRAM, is then presented. An automatic reference current generation for memory reading is described. A digital algorithm chooses a suitable value which compensates several circuit imperfections together, from the sense amplifier offset to the dispersion of the memory read currents. The third application is the calibration of the sensitivity of a current measurement microsystem based on a Hall magnetic field sensor. An integrated reference generates a magnetic field for calibration. Using a variant of the chopper modulation, the spinning current technique, combined with a second modulation of the reference signal, the sensitivity of the complete system is continuously measured without interrupting normal operation. Modulation and demodulation schemes allowing the joint processing of both external and reference magnetic fields are proposed. Additional circuit techniques for extracting the very low reference signal are presented. The implementation of the microsystem is then discussed. The realization of the blocks composing the system is detailed, and circuit issues are presented. Finally, measurements validate the calibration principle. A thermal drift lower than 50 ppm/°C is achieved. This is 6 to 10 times less than in state-ofthe-art implementations. Furthermore, the calibration technique also compensates drifts due to mechanical stresses and ageing.
Epidermal growth factor in mice: changes during circadian and female reproductive cycles (1990)

To clarify the variation of mouse epidermal growth factor production during the 24-h and female reproductive cycles, we measured its concentrations in the plasma, submandibular salivary gland, urine, kidneys and liver of adult male and female mice during consecutive 12-h dark and 12-h light periods, different stages of pregnancy, and lactation. The concentration of epidermal growth factor in the submandibular gland showed no circadian changes. In plasma and in the liver it increased during the dark period, whereas in urine and in the kidneys it peaked in the daytime. In the submandibular gland the concentration decreased during early pregnancy, but it returned to the non-pregnant levels by mid-pregnancy. In plasma it decreased progressively during pregnancy and recovered during lactation. In urine and the kidneys the concentration of epidermal growth factor increased after early pregnancy; with a further great increase in the kidneys during lactation. In the liver the concentration was clearly below the non-pregnant levels during late pregnancy and lactation.
Supplementary File 1 from Integrative Analysis of Genomic Aberrations Associated with Prostate Cancer Progression (2023)

Supplementary File 1 from Integrative Analysis of Genomic Aberrations Associated with Prostate Cancer Progression
Palladium‐Catalyzed Coupling of Pyrazole Triflates with Arylboronic Acids. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
p53 Induces NF-κB Activation by an IκB Kinase-independent Mechanism Involving Phosphorylation of p65 by Ribosomal S6 Kinase 1 (2004)

Apoptosis induced by p53 has been proposed to involve activation of the transcription factor NF-kappaB. Here we describe the novel molecular mechanism through which p53 and DNA-damaging agents activate NF-kappaB. NF-kappaB induction by p53 does not occur through classical activation of the IkappaB kinases and degradation of IkappaBalpha. Rather, p53 expression stimulates the serine/threonine kinase ribosomal S6 kinase 1 (RSK1), which in turn phosphorylates the p65 subunit of NF-kappaB. The lower affinity of RSK1-phosphorylated p65 for its negative regulator, IkappaBalpha, decreases IkappaBalpha-mediated nuclear export of shuttling forms of NF-kappaB, thereby promoting the binding and action of NF-kappaB on cognate kappaB enhancers. These findings highlight a rather unusual pathway of NF-kappaB activation, which is utilized by the p53 tumor suppressor.
Theory of Superconductivity at the LaAlO3/SrTiO3 heterointerface: Electron pairing mediated by deformation of ferroelastic domain walls (2020)

SrTiO$_3$ is a superconducting semiconductor with a pairing mechanism that is not well understood. SrTiO$_3$ undergoes a ferroelastic transition at $T=$ 105 K, leading to the formation of domains with boundaries that can couple to electronic properties. At two-dimensional SrTiO$_3$ interfaces, the orientation of these ferroelastic domains is known to couple to the electron density, leading to electron-rich regions that favor out-of-plane distortions and electron-poor regions that favor in-plane distortion. Here we show that ferroelastic domain walls support low energy excitations that are analogous to capillary waves at the interface of two fluids. We propose that these capillary waves mediate electron pairing at the LaAlO$_3$/SrTiO$_3$ interface, resulting in superconductivity around the edges of electron-rich regions. This mechanism is consistent with recent experimental results reported by Pai et al. [PRL $\bf{120}$, 147001 (2018)]
310 Investigation of Mixing Performance by a Shuttlecock Optical Micro-Rotor (2000)

The shuttlecock optical micro-rotor is one of the micro-actuators and the micro-mixing devices in the micro-systems. To investigate the rotor's mixing performance in the micro-crossed flow field, both general CFD techniques (FVM & SIMPLEC) and visualization method (the marker particles) are used in this paper. The result shows that mixing has been shown in first rotor's revolution, and that the diffusion at the interface between two fluids, which is the remarkable phenomenon in such small or micro scale systems, cannot be negligible. In concluding, we need to both calculate the flow field and investigate the rotor's performance by applying the random walks to the marker particles in addition to changing several parameters.
Limits of maximum-likelihood sequence estimation in chromatic dispersion limited systems (2006)

We experimentally investigated the performance of MLSE in chromatic dispersion-limited 10 Gb/s links, and assessed the limits in terms of the number of states and A/D converter sample rate, up to 40 GSa/s
N-Terminus Urea-Substituted Chemotactic Peptides:  New Potent Agonists and Antagonists toward the Neutrophil fMLF Receptor (1996)

ADVERTISEMENT RETURN TO ISSUELetterNEXTN-Terminus Urea-Substituted Chemotactic Peptides: New Potent Agonists and Antagonists toward the Neutrophil fMLF ReceptorJohn D. Higgins, Gary J. Bridger, Claudia K. Derian, Michael J. Beblavy, Pedro E. Hernandez, Forrest E. Gaul, Michael J. Abrams, Marilyn C. Pike, and Howard F. SolomonView Author Information Johnson Matthey Biomedical Research, 1401 King Road, West Chester, Pennsylvania 19380, The R. W. Johnson Pharmaceutical Research Institute, Welsh and McKean Roads, Spring House, Pennsylvania 19477, and The Massachusetts General Hospital, Arthritis Unit, 55 Fruit Street, Boston, Massachusetts 02114 Cite this: J. Med. Chem. 1996, 39, 5, 1013–1015Publication Date (Web):March 1, 1996Publication History Received11 December 1995Published online1 March 1996Published inissue 1 January 1996https://doi.org/10.1021/jm950908dCopyright © 1996 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views407Altmetric-Citations34LEARN 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 InReddit Read OnlinePDF (83 KB) Get e-AlertsSUBJECTS:Agonists,Antagonists,Peptides and proteins,Receptors,Urea Get e-Alerts
The enzymatic oxidation of phenolic tetrahydroisoquinoline-1-carboxylic acids (1979)

Tetrahydroisoquinoline-1-carboxylic acids with a 6- or 7-hydroxy substituent undergo oxidative decarboxylation on treatment with horseradish peroxidase or fungal laccase to give high yields of the corresponding 3,4-dihydroisoquinolines. Attempts to apply this reaction to the formation of an aporphine were unsuccessful.
TtgV Represses Two Different Promoters by Recognizing Different Sequences (2008)

Expression of the multidrug efflux pump ttgDEF and ttgGHI operons is modulated in vivo mainly by the TtgV repressor. TtgV is a multidrug recognition repressor that exhibits a DNA binding domain with a long interaction helix comprising residues 47 to 64. The pattern of expression of the two pumps is different in Pseudomonas putida: in the absence of effectors, the promoter for the ttgD gene is silent, whereas the ttgG gene is expressed at a high basal level. This correlates with the fact that TtgV exhibits a higher affinity for the ttgD operator (K(D)=10+/-1 nM) than for the ttgG (K(D)=19+/-1 nM) operator. Sequence analysis revealed that both operators are 40% identical, and mutational analysis of the ttgD and ttgG operators combined with electrophoretic mobility shift assays and in vivo expression analysis suggests that TtgV recognizes an inverted repeat with a high degree of palindromicity around the central axis. We generated a collection of alanine substitution mutants with substitutions between residues 47 and 64 of TtgV. The results of extensive combinations of promoter variants with these TtgV alanine substitution mutants revealed that TtgV modulates expression from ttgD and ttgG promoters through the recognition of both common and different sequences in the two promoters. In this regard, we found that TtgV mutants at residues 48, 50, 53, 54, 60, and 61 failed to bind ttgG but recognized the ttgD operator. TtgV residues R47, R52, L57, and T49 are critical for binding to both operators. Based on three-dimensional models, we propose that these residues contact nucleotides within the major groove of DNA.
Differentiation of West Nile and St. Louis Encephalitis Virus Infections by Use of Noninfectious Virus-Like Particles with Reduced Cross-Reactivity (2007)

Differential diagnosis of St. Louis encephalitis virus (SLEV) and West Nile virus (WNV) infections can be complicated due to the high degree of cross-reactivity observed in most serodiagnostic assays. In an effort to provide a more specific diagnostic test, we developed virus-like particle (VLP) antigens with reduced cross-reactivity for both SLEV and WNV by identifying and mutating envelope protein amino acids within the cross-reactive epitopes of VLP expression plasmids. To determine the serodiagnostic discriminatory ability of the antigens with reduced cross-reactivity, a panel of 134 human serum samples collected predominately from North American patients with SLEV or WNV infections was used to evaluate the performance of these novel antigens in imunoglobulin M antibody-capture enzyme-linked immunosorbent assays. Positive/negative ratios and the resulting diagnostic classifications were compared between the mutant and the wild-type (WT) VLPs. The mutant VLP antigens were more specific, with higher positive predictive values and higher likelihood ratios than the WT VLP antigens. Both the SLEV and WNV mutant VLPs greatly reduced the observed cross-reactivity, significantly increasing the specificity and sensitivity of the assay. The use of these novel VLP antigens with reduced cross-reactivity in these serodiagnostic assays and others should lead to more accurate diagnoses of current infections, thereby reducing the need for time-consuming and cumbersome confirmatory plaque-reduction neutralization tests to differentiate between SLEV and WNV infections in North America.
Expérimentations géophysiques sur les dépôts archéologiques peu différenciés. Apport aux stratégies de fouilles des « terres noires ». (2003)

Le manque de lisibilité de l'organisation interne de certains dépôts archéologiques, comme les « terres noires » de l'Antiquité tardive et du haut Moyen Age, constitue un frein puissant à leur étude. Il est possible que seule une fouille très fine de ces niveaux soit capable d'apporter des résultats significatifs mais au prix d'un investissement encore souvent considéré comme excessif. Pour que de telles fouilles soient entreprises sur les secteurs les plus riches de ces dépôts problématiques nous tentons, afin de minimiser les coûts de mise en oeuvre, d'élaborer une aide à la stratégie de fouille. Elle repose sur une prospection géophysique préalable en plan (après un décapage à la pelle mécanique, par exemple) à une maille extrêmement fine adaptée à l'objet d'étude. Notre but est de fournir des images de la résistivité du terrain pour alimenter un diagnostic explicite des potentialités archéologiques afin de définir des choix d'intervention efficaces. Cette expérimentation a été conduite sur les fouilles du Palais de Justice à Besançon (France).
Online Privacy-Preserving Data-Driven Network Anomaly Detection (2022)

We study online privacy-preserving anomaly detection in a setting in which the data are distributed over a network and locally sensitive to each node, and a probabilistic data model is unknown. We design and analyze a data-driven solution scheme where each node observes a high-dimensional data stream for which it computes a local outlierness score. This score is then perturbed, encrypted, and sent to a network operator. The network operator then decrypts an aggregate statistic over the network and performs online network anomaly detection via the proposed generalized cumulative sum (CUSUM) algorithm. We derive an asymptotic lower bound and an asymptotic approximation for the average false alarm period of the proposed algorithm. Additionally, we derive an asymptotic upper bound and asymptotic approximation for the average detection delay of the proposed algorithm under a certain anomaly. We show the analytical tradeoff between the anomaly detection performance and the differential privacy level, controlled via the local perturbation noise. Experiments illustrate that the proposed algorithm offers a good tradeoff between privacy and quick anomaly detection against the UDP flooding and spam attacks in a real Internet of Things (IoT) network.
Lateral epitaxial overgrowth of (0001) AlN on patterned sapphire using hydride vapor phase epitaxy (2009)

Coalesced, crack-free (0001) AlN films were grown on stripe patterned sapphire substrates without AlN seed layers using hydride vapor phase epitaxy. Using templates with stripes oriented in the ⟨112¯0⟩sapphire direction, lateral epitaxial overgrowth AlN films were coalesced over trench regions as wide as 10 μm despite parasitic sidewall and trench growth. Using transmission electron microscopy, a reduction in the dislocation density from 1.6×109 cm−2 in the seed region to less than 1.0×108 cm−2 in the wing region was demonstrated. Atomic force microscopy and cathodoluminescence measurements were also performed to assess the material quality.
ChemInform Abstract: Enantiospecific Total Synthesis of the Protein Phosphatase Inhibitor Motuporin (IX). (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Solution stoichiometry determines crystal stoichiometry in halogen-bonded supramolecular complexes (2007)

The behavior of the methylisonicotinate (MINC) building block as halogen bonding-acceptor module has been investigated in the solid state. Both the N and the O atoms of MINC interact with the iodine atoms of 1,4-diiodotetrafluorobenzene (DITFB) giving rise to N⋯I and O⋯I interactions. Hierarchy between these interactions allows the control of the composition and thus the structure of the supramolecular complex, according to the composition of the reaction mixture. A structure based on an infinite chain and a trimeric supermolecule have been obtained starting from a 1 ∶ 1 MINC/DITFB stoichiometry or by using a large excess of MINC, respectively. While the former structure shows simultaneous N⋯I and O⋯I halogen bonds, only N⋯I interactions are present in the latter one. The results also elicit some general considerations based on the rare chain morphology shown by the 1 ∶ 1 complex.
XUV-laser spectrometer for direct absorption measurements: application to CO in the wavelength range 95–97 nm (1998)

A narrowband and tunable XUV-laser source, based on harmonic generation of visible laser light, is developed for sensitive and direct absorption measurements. A novel method to monitor and eliminate the fluctuating intensity of this source is developed, which increases the sensitivity for absorption by an order of magnitude. This procedure allows for accurate relative cross-section measurements, demonstrated on selected bands of CO in the wavelength range 95–97 nm.
BiDi screen (2009)

We transform an LCD into a display that supports both 2D multi-touch and unencumbered 3D gestures. Our BiDirectional (BiDi) screen, capable of both image capture and display, is inspired by emerging LCDs that use embedded optical sensors to detect multiple points of contact. Our key contribution is to exploit the spatial light modulation capability of LCDs to allow lensless imaging without interfering with display functionality. We switch between a display mode showing traditional graphics and a capture mode in which the backlight is disabled and the LCD displays a pinhole array or an equivalent tiled-broadband code. A large-format image sensor is placed slightly behind the liquid crystal layer. Together, the image sensor and LCD form a mask-based light field camera, capturing an array of images equivalent to that produced by a camera array spanning the display surface. The recovered multi-view orthographic imagery is used to passively estimate the depth of scene points. Two motivating applications are described: a hybrid touch plus gesture interaction and a light-gun mode for interacting with external light-emitting widgets. We show a working prototype that simulates the image sensor with a camera and diffuser, allowing interaction up to 50 cm in front of a modified 20.1 inch LCD.