gebhart/patrepeval huggingface dataset:
Antibody mix-and-read assays based on fluorescence intensity probes (2021)

Antibodies and Fc fusion proteins are a rapidly growing class of pharmaceuticals. Cell culture and purification process development and operation require frequent measurement of product concentrations, commonly by complex enzyme-linked immunosorbent assay and high-performance liquid chromatography methods. Here we report a fast (<30 s), and simple antibody Fc assay based on mix-and-read reporting by fluorescence emission. A soluble fluorescein-labeled Fc-affinity reporter produced by standard peptide synthesis is mixed with an Fc-containing sample to produce an immediate shift in both fluorescence polarization and intensity, compatible with on- and at-line measurements and microbioreactor monitoring. We observed significant shifts in fluorescence intensity in Chinese hamster ovary cell culture fluid spiked with IgG and detected an adalimumab biosimilar down to 100 ng/mL (10<sup>-4</sup> g/L), despite the interferents in the complex sample matrix. Neither the fluorescence polarization nor the fluorescence intensity assay is significantly affected by the addition of clarified lysate of 2 million CHO-k1 cells/mL, suggesting applicability even to cultures of low viability. Biochemical and molecular docking approaches suggest that the fluorescence intensity enhancement is caused by changes in the fluorophore's local microenvironment upon binding to IgG Fc, especially by interactions with Fc His433.<b>Abbreviations:</b> CCF: Cell Culture Fluid; CHO: Chinese Hamster Ovary cells; ELISA: Enzyme Linked Immunosorbent Assay; Fc: Fragment Crystallizable of antibody; HPLC: High-Performance Liquid Chromatography; HPβCD: hydroxypropyl-β-cyclodextrin; IgG: ImmunoglobulinG; mAb: Monoclonal Antibody; PBS: Phosphate-Buffered Saline; PDB: Protein Data Bank; SpA: Staphylococcal protein A; SpG: Staphylococcal protein G.
Diarylpropane‐1,3‐dione Derivatives as TetR‐Inducing Tetracycline Mimetics: Synthesis and Biological Investigations (2009)

Synthesis, biological investigations and molecular docking studies of nonantibiotic and nontetracyclic inducers that feature a minimal key motif of the natural lead tetracycline are presented. The diarylpropane-1,3-dione motif was identified as the minimal substructure responsible for TetR induction by tetracyclines. The first nontetracyclic surrogates of the natural tetracyclines displayed significant inducing effects for TetR(BD)S135L, whereby the chlorohydroxyphenyl-substituted beta-diketone 31 displayed the highest activity. Interestingly, antibiotic activity could not be detected for 31. Homology modeling based on the X-ray structure of 7-chlorotetracycline bound to TetR indicated analogous binding modes for the natural inducer and the synthetic diarylpropane-1,3-dione derivatives.
A Novel Prototype of Duty Cycle Controlled Soft-Switching Half-Bridge DC-DC Converter with Input DC Rail Active Quasi Resonant Snubbers Assisted by High Frequency Planar Transformer (2007)

This paper presents a new circuit topology of active edge resonant snubbers assisted half-bridge soft switching PWM inverter type DC-DC high power converter for DC bus feeding power plants. The proposed DC-DC power converter is composed of a typical voltage source-fed half-bridge high frequency PWM inverter with a high frequency planar transformer link in addition to input DC busline side power semiconductor switching devices for PWM control scheme and parallel capacitive lossless snubbers. The operating principle of the new DC-DC converter treated here is described by using switching mode equivalent circuits, together with its unique features. All the active power switches in the half-bridge arms and input DC buslines can achieve ZCS turn-on and ZVS turn-off commutation transitions. The total turn-off switching losses of the power switches can be significantly reduced. As a result, a high switching frequency IGBTs can be actually selected in the frequency range of 60 kHz under the principle of soft switching. The performance evaluations of the experimental setup are illustrated practically. The effectiveness of this new converter topology is proved for such low voltage and large current DC-DC power supplies as DC bus feeding from a practical point of view.
Room-temperature copper metallization for ultralarge-scale integrated circuits by a low kinetic-energy particle process (1988)

Copper films were epitaxially grown on (100)Si substrates at room temperatures utilizing low kinetic-energy particle bombardment of growing copper film surfaces. The crystallographic structure of the film, such as (100) or (111) orientation, was selected by controlling the energy of incident particles. Low-temperature, damage-free substrate surface cleaning has also been realized by the low kinetic-energy particle process, which has made it possible to form ideal metal-semiconductor contacts without employing any alloying heat cycles.
Engineering Trienoic Fatty Acids into Cottonseed Oil Improves Low-Temperature Seed Germination, Plant Photosynthesis and Cotton Fiber Quality (2020)

Alpha-linolenic acid (ALA, 18:3Δ9,12,15) and γ-linolenic acid \ (GLA, 18:3Δ6,9,12) are important trienoic fatty acids, which are beneficial for human health in their own right, or as precursors for the biosynthesis of long-chain polyunsaturated fatty acids. ALA and GLA in seed oil are synthesized from linoleic acid (LA, 18:2Δ9,12) by the microsomal ω-3 fatty acid desaturase (FAD3) and Δ6 desaturase (D6D), respectively. Cotton (Gossypium hirsutum L.) seed oil composition was modified by transforming with an FAD3 gene from Brassica napus and a D6D gene from Echium plantagineum, resulting in approximately 30% ALA and 20% GLA, respectively. The total oil content in transgenic seeds remained unaltered relative to parental seeds. Despite the use of a seed-specific promoter for transgene expression, low levels of GLA and increased levels of ALA were found in non-seed cotton tissues. At low temperature, the germinating cottonseeds containing the linolenic acid isomers elongated faster than the untransformed controls. ALA-producing lines also showed higher photosynthetic rates at cooler temperature and better fiber quality compared to both untransformed controls and GLA-producing lines. The oxidative stability of the novel cottonseed oils was assessed, providing guidance for potential food, pharmaceutical and industrial applications of these oils.
Asymmetric, reflection mode nonlinear Fabry–Perot modulator using bacteriorhodopsin (1996)

We report on the design, fabrication, and testing of an asymmetric reflection mode Fabry–Perot modulator using bacteriorhodopsin as the nonlinear cavity material. The modulator was fabricated to be impedance matched, resulting in high quality modulator performance. A large contrast ratio of 61:1, a reflectivity of 94%, and a dynamic modulation range of 55.5 at a pump; intensity of 26 mW/cm2 were measured by this modulator.
955: Serum Biomarkers of Endothelial Function and Oxidative Stress after Daily Dosing of Sildenafil in Type 2 Diabetic Men with Erectile Dysfunction (2007)

You have accessJournal of UrologyModerated Poster 28, Monday, May 21, 2007, 1:00 - 3:00 pm1 Apr 2007955: Serum Biomarkers of Endothelial Function and Oxidative Stress after Daily Dosing of Sildenafil in Type 2 Diabetic Men with Erectile Dysfunction Arthur L. Burnett, Travis Strong, Biljana Musicki, Trinity J. Bivalacqua, and Liming Jin Arthur L. BurnettArthur L. Burnett More articles by this author , Travis StrongTravis Strong More articles by this author , Biljana MusickiBiljana Musicki More articles by this author , Trinity J. BivalacquaTrinity J. Bivalacqua More articles by this author , and Liming JinLiming Jin More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)31183-2AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "955: Serum Biomarkers of Endothelial Function and Oxidative Stress after Daily Dosing of Sildenafil in Type 2 Diabetic Men with Erectile Dysfunction." The Journal of Urology, 177(4S), p. 316 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 177Issue 4SApril 2007Page: 316 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Arthur L. Burnett More articles by this author Travis Strong More articles by this author Biljana Musicki More articles by this author Trinity J. Bivalacqua More articles by this author Liming Jin More articles by this author Expand All Advertisement PDF DownloadLoading ...
Analysis of Tree-Algorithms with Multi-Packet Reception (2020)

In this paper, we analyze binary-tree algorithms in a setup in which the receiver can perform multi-packet reception (MPR) of up to and including K packets simultaneously. The analysis addresses both traffic-independent performance as well as performance under Poisson arrivals. For the former case, we show that the throughput, when normalized with respect to the assumed linear increase in resources required to achieve K-MPR capability, tends to the same value that holds for the single-reception setup. However, when coupled with Poisson arrivals in the windowed access scheme, the normalized throughput increases with K, and we present evidence that it asymptotically tends to 1. We also provide performance results for the modified tree algorithm with K-MPR in the clipped access scheme. To the best of our knowledge, this is the first paper that provides an analytical treatment and a number of fundamental insights in the performance of tree-algorithms with MPR.
Identification of a TAL1 Target Gene Reveals a Positive Role for the LIM Domain-Binding Protein Ldb1 in Erythroid Gene Expression and Differentiation (2003)

The TAL1 (or SCL) gene, originally identified from its involvement by a recurrent chromosomal translocation, encodes a basic helix-loop-helix transcription factor essential for erythropoiesis. Although presumed to regulate transcription, its target genes are largely unknown. We show here that a nuclear complex containing TAL1, its DNA-binding partner E47, zinc finger transcription factor GATA-1, LIM domain protein LMO2, and LIM domain-binding protein Ldb1 transactivates the protein 4.2 (P4.2) gene through two E box GATA elements in its proximal promoter. Binding of this complex to DNA was dependent on the integrity of both E box and GATA sites and was demonstrated to occur on the P4.2 promoter in cells. Maximal transcription in transiently transfected cells required both E box GATA elements and expression of all five components of the complex. This complex was shown, in addition, to be capable of linking in solution double-stranded oligonucleotides corresponding to the two P4.2 E box GATA elements. This DNA-linking activity required Ldb1 and increased with dimethyl sulfoxide-induced differentiation of murine erythroleukemia (MEL) cells. In contrast, enforced expression in MEL cells of dimerization-defective mutant Ldb1, as well as wild-type Ldb1, significantly decreased E box GATA DNA-binding activities, P4.2 promoter activity, and accumulation of P4.2 and beta-globin mRNAs. These studies define a physiologic target for a TAL1- and GATA-1-containing ternary complex and reveal a positive role for Ldb1 in erythroid gene expression and differentiation.
[New hemophilia treatment employing a bispecific antibody to factors IXa and X]. (2015)

Unmet needs of current hemophilia A treatment include the requirement for frequent intravenous infusions, inhibitor development, and containment of high medical costs. In order to overcome these issues, we produced FVIII which mimics a bispecific antibody against FIXa/FX. ACE910 demonstrated hemostatic effects on both ongoing and spontaneous joint bleeding in the primate acquired hemophilia A model. Recently, a phase 1 study for PK, PD, and the safety of ACE910 was initiated. The t1/2 was approximately 30 days. There were no severe ACE910 related adverse events. Furthermore, bleeding was remarkably decreased by weekly subcutaneous administration in patients with severe hemophilia A, regardless of whether an inhibitor was used. ACE910 has the remarkable advantages of prophylactic efficacy which can be achieved by convenient subcutaneous administrations at a markedly reduced frequency.
Program Synthesis (2017)

Program synthesis is the task of automatically finding a program in the underlying programming language that satisfies the user intent expressed in the form of some specification. Since the inception of AI in the 1950s, this problem has been considered the holy grail of Computer Science. Despite inherent challenges in the problem such as ambiguity of user intent and a typically enormous search space of programs, the field of program synthesis has developed many different techniques that enable program synthesis in different real-life application domains. It is now used successfully in software engineering, biological discovery, computer-aided education, end-user programming, and data cleaning. In the last decade, several applications of synthesis in the field of programming by examples have been deployed in mass-market industrial products. This survey is a general overview of the state-of-the-art approaches to program synthesis, its applications, and subfields. We discuss the general principles common to all modern synthesis approaches such as syntactic bias, oracle-guided inductive search, and optimization techniques. We then present a literature review covering the four most common state-of-the-art techniques in program synthesis: enumerative search, constraint solving, stochastic search, and deduction-based programming by examples. We conclude with a brief list of future horizons for the field.
INI1/hSNF5-interaction defective HIV-1 IN mutants exhibit impaired particle morphology, reverse transcription and integration in vivo (2013)

Our results demonstrate that a severe defect in IN-INI1 interaction is associated with production of defective particles and a subsequent defect in post-entry events. A partial defect in IN-INI1 interaction leads to production of normal virions that are partially impaired for early events including integration. Our studies suggest that proper interaction of INI1 with IN within Gag-Pol is necessary for proper HIV-1 morphogenesis and integration.
High Resolution Full Wavefield Inversion: Impact on Imaging and Reservoir Characterisation (2013)

Abstract Seismic imaging has been advancing rapidly over the last two decades, transitioning from post-stack time migration to pre-stack depth migration and from ray-theoretic algorithms (Kirchhoff migration) to one-way wave equation solvers (wave equation migration) and recently to two-way wave equation methods like Reverse Time Migration (RTM). The most recent step in this evolving sequence is Full Wavefield Inversion (FWI), which has rapidly become a focal area of research, development, and application within the geophysical community and industry. FWI products, unlike migration results, are not depictions of seismic reflectivity, but rather high resolution images of subsurface properties such as compressional and shear velocities and density. The high resolution velocity models generated with FWI can be used to address challenging imaging problems that are difficult to solve using conventional processing tools. High fidelity velocity models will assist in imaging below fault shadows and shallow channels and may also better identify and quantify overpressured drilling hazards. FWI estimates of other elastic paramters, in particular the Vp/Vs ratio, are promising lithology indicators useful in reservoir characterization applications. In addition to imaging challenges, the broadband nature of FWI is ideally suited to address reservoir monitoring problems with the ability to provide high resolution updates of property changes in the subsurface due to production. FWI products, appropriately integrated into an interpretation strategy, will allow us to better understand subtler subsurface features such as stratigraphic traps or non-DHI plays. In our presentation, we will use FWI examples from several real data studies to explain the nature of the process and illustrate some of the potential applications. Introduction Full Wavefield Inversion (FWI) is the most advanced and ambitious seismic imaging technology ever conceived. This technology produces the dream of every geoscientist: broadband images of sub-surface rock properties ahead of the drill bit. Seismic imaging has advanced rapidly over the last two decades in lockstep with advances in High Performance Computing (HPC). Traditional seismic imaging methods, such as Beam Migration or Reverse Time Migration (RTM), focus seismic reflections from layer interfaces that the geoscientist can use to map structure and amplitudes that relate to the change in rock properties across layer boundaries. By contrast, FWI simultaneously focuses the image of the subsurface and produces amplitudes that represent actual elastic rock properties within the layers (velocity, density, etc).
A lipid-based passivation scheme for nanofluidics (2012)

Stretching DNA in nanochannels allows for direct, visual studies of genomic DNA at the single molecule level. In order to facilitate the study of the interaction of linear DNA with proteins in nanochannels, we have implemented a highly effective passivation scheme based on lipid bilayers. We show long-term passivation of nanochannel surfaces to several relevant reagents and demonstrate that the performance of the lipid bilayer is significantly better compared to standard bovine serum albumin-based passivation. Moreover, we demonstrate how the passivated devices allow us to monitor single DNA cleavage events during enzymatic degradation.
Information Use with Paper and Electronic Nursing Documentation by Nurses Caring for Pediatric Patients (2012)

&lt;p&gt;This dissertation aimed to investigate the use of electronic nursing documentation as a strategy to improve the quality of care provided to hospitalized patients. The literature to support the use of electronic nursing documentation on the quality of care delivered to patients is limited to date. Additionally, the literature describing the use of information for the delivery of care on paper-based nursing documentation is limited. This dissertation reviews the current literature, investigated the knowledge needed for nurses to know their patients and established categories of nurses' information needs as preliminary work to be able to descriptively compare the use of paper with electronic nursing documentation on inpatient care units within a hospital setting. The main study conducted for this investigation used a mixed-methods multiple case study design, to describe the processes of information use on two inpatient care units, while first using paper and subsequently electronic nursing documentation. Findings revealed the importance of the categories of nurses' information needs for both cases in addition to the use of verbal, paper-based and electronic information sources for the collection, communication and temporary storage of information needs. Additionally, the conversion to electronic nursing documentation introduced new challenges related to three quality metrics: efficiency, timeliness and safety. Recommendations are provided for further evaluation of electronic health records with additional consideration for appropriate hardware devices in the context of the care environment.&lt;/p&gt;
Determination of the number of wideband acoustical sources in a reverberant environment (2006)

This paper addresses the problem of determining the number of wideband sources in a reverberant environment. In [1] an Expo-nential Fitting Test (EFT) is proposed based on the exponential profile of the noise only eigenvalues. We consider the performance of this test for the problem in question, and compare it with the results achieved by the well known Akaike Information Criterion (AIC) and Minimum Description Length (MDL). Once reverbera-tion is present in the received signals the EFT is seen to perform much better than the AIC and MDL. 1.
Favipiravir for Treatment of Outpatients With Asymptomatic or Uncomplicated Coronavirus Disease 2019: A Double-Blind, Randomized, Placebo-Controlled, Phase 2 Trial (2022)

NCT04346628.
Asynchrony Detection in Amblyopes (2012)

Amblyopia is a developmental abnormality of visual cortex. Although amblyopes experience perceptual deficits in spatial vision tasks, they have less temporal sensitivity loss. We investigated whether their temporal synchrony sensitivity is impaired. In experiment 1, four Gaussian blobs, located at the top, bottom, left, and right of a presentation screen, were flickering in 3 Hz and one of them was flickering in out-of-phase fashion in time. Participants needed to tell which blob was different from the other three and contrast threshold of the blobs was measured to determine the synchrony detection threshold. We found the thresholds were not correlated with the contrast thresholds for detecting the flickering blobs, suggesting synchrony detection and temporal detection threshold are processed by different mechanisms. In experiment 2, synchrony thresholds were measured as participants' ability to tell if one of the four high contrast Gaussian blobs was flickering asynchronously in time. Three temporal frequencies (1, 2, and 3 Hz) and two element separations (1.25 and 5 deg) were compared. We found that the amblyopic group exhibited a deficit only for the 1.25 deg element separation in amblyopic eye but was normal for the other configurations compared to controlled participants. It suggests amblyopes have deficits in temporal processing but only for foveal vision. We also found the sensitivity for the non-strabismic anismetropia group is reduced for all three temporal frequencies whereas for the strabismic anisometropia group it was reduced at 3Hz only, suggesting the impairment in temporal synchrony might be different for different types of amblyopia.
Mise en oeuvre de la différenciation retardée dans la production de l'aluminium : standardisation de plaques (2003)

International audience
Selective isolation of glycoproteins and glycopeptides for MALDI-TOF MS detection supported by magnetic particles. (2005)

Glycosylation is the most common form of posttranslational modification of proteins (50-80%). The isolation, discovery, and subsequent identification of glycosylated peptides and proteins is becoming more and more important in glycoproteomics and diagnosis. MALDI-TOF mass spectrometry is an ideal technique for identifying peptides and proteins and their corresponding modifications. The enrichment of glycosylated peptides and proteins from different sources can be attained by affinity chromatography supported by functionalized magnetic particles. Covalent coating of magnetic beads with Concanavalin A (ConA) and diboronic acid was performed by carbodiimide and poly-glutaraldehyde methods, respectively. The functionalized beads were employed to establish and optimize protocols for the binding and detection of glycosylated peptides and proteins with respect to an automated workflow and the subsequent detection and identification by MALDI-TOF mass spectrometry. For several model proteins, the capture and identification could be demonstrated by SDS-PAGE and MALDI-TOF mass spectrometry. According to the type of glycosylation (high man-nose, hybrid, or complex type) the different proteins were enriched by ConA or boronic acid-functionalized beads.
ChemInform Abstract: A Reagent for Safe and Efficient Diazo‐Transfer to Primary Amines: 2‐Azido‐1,3‐dimethylimidazolinium Hexafluorophosphate. (2014)

Abstract The title compound, a safe, crystalline, and commercially available substance, is found to be an efficient diazo‐transfer reagent for primary amines, even without the aid of a metal salt such as Cu(II).