gebhart/patrepeval huggingface dataset:
Comprehensive gene expression profile of LPS-stimulated human monocytes by SAGE (2000)

Monocytes play a pivotal role in various human infectious and inflammatory diseases. To reveal a whole picture of pathophysiologic function of activated human monocytes, this study used the serial analysis of gene expression (SAGE) procedure in lipopolysaccharide (LPS)-stimulated human monocytes. A total of 35 874 tags corresponding to more than 12 000 different transcripts were sequenced. Comparison of gene expression profile with that of resting monocytes revealed the LPS-inducible gene expression profile. Many cytokines and chemokines, including interleukin (IL)-6, IL-1α, IL-1β, tumor necrosis factor (TNF)-α, macrophage inflammatory protein (MIP)-1β, MIP-2β, MIP-2α, liver and activation-regulated chemokine (LARC), MIP-1α, thymus and activation-regulated chemokine (TARC), macrophage-derived chemokine (MDC), regulated on activation, normal T cell expressed and secreted (RANTES), growth-regulated oncogene (GRO) α, and IL-8, were observed in the highest inducible transcripts. Other genes encoding plasminogen activator inhibitor type 2 (PAI-2), Hc-gp39, apolipoproteins, malate dehydrogenase, matrix metalloproteinase-9 (MMP-9), and cyclooxygenase (COX2) were also highly elevated in LPS-stimulated monocytes. Moreover, up-regulation of Naf1β, IL-7 receptor, adenosine receptor A2a, and many novel genes was newly identified. These results suggest that the LPS-inducible gene products may be involved in cell activation and migration, angiogenesis, tissue remodeling, and metabolism, and thus may orchestrate the inflammatory reactions. On the other hand, the expression of numerous sets of novel genes was discovered to be down-regulated on LPS stimulation. This study represents the first comprehensive analysis of LPS-inducible gene expression in human monocytes and provides tremendous novel information for the function of LPS-activated monocytes and targets for diagnosing, monitoring, and treating sepsis and various human infectious and inflammatory diseases.
Properties of Waterborne Polyurethane Adhesives: Effect of Chain Extender and Polyol Content (2008)

A series of waterborne polyurethane (WBPU) adhesives were prepared with various ratios of polyol, poly(tetramethylene oxide glycol) (PTMG), and chain extender, ethylene diamine (EDA), at a fixed content of diisocyanate, 4,4-dicyclohexylmethane diisocyanate (H12MDI) and hydrophilic agent, 2,2-dimethylol propionic acid (DMPA). WBPU adhesives were characterized by IR and 1H-NMR spectroscopies, X-ray diffraction (XRD) and gel permeation chromatography (GPC). It was found that the extent of hydrogen bonds between hard–hard segment (i.e., hydrogen bonds between the NH and carbonyl groups) increased with increasing chain extender content (decreasing polyol content). Moreover, the disordered hydrogen bond of carbonyl group (hydrogen bond of urethane groups in the interfacial region) increased with increasing chain extender content (decreasing polyol content). The cyclic urea and allophanate group, which are attributed to the side reaction and cross-linking reaction, respectively, were found above a molar ratio 0.17 of chain extender to diisocyanate. The adhesive strength was maximum with 0.95 wt% and 63.10 wt% chain extender and soft segment (PTMG), respectively (H2 sample) at room temperature for the WBPU adhesive. However, with increasing application temperature the adhesive strength decreased for all samples.
Noninvasive gene transfer to the lung for systemic delivery of therapeutic proteins (2002)

This study evaluates the use of vectors based on adeno-associated viruses (AAVs) to noninvasively deliver genes to airway epithelial cells as a means for achieving systemic administration of therapeutic proteins. We intranasally delivered AAV vectors to mice in which the same AAV2 genome encoding a cellular marker was packaged in capsids from AAV1, 2, or 5 (AAV2/1, AAV2/2, or AAV2/5, respectively). Gene expression levels achieved in both airways and alveoli were higher with AAV2/5 than with AAV2/1 and were undetectable with AAV2/2. The same set of vectors encoding a secreted therapeutic protein, erythropoietin (Epo), under the control of a lung-specific promoter (CC10) was intranasally delivered to mice, resulting in polycythemia with the highest levels of serum Epo obtained with AAV2/5 vectors. After a single intranasal administration of this vector, secretion of Epo was documented for 150 days. Similarly, intranasal administration of an AAV2/5-CC10-factor IX vector resulted in secretion of functional recombinant protein in the bloodstream of hemophiliac, factor IX-deficient mice. In addition, we demonstrate successful readministration of AAV2/5 to the lung 5 months after the first delivery of the same vector. In conclusion, we show that intranasal administration of AAV vectors results in efficient gene transfer to the lung only when the vector contains the AAV5 capsid and that this noninvasive route of administration results in sustained secretion of therapeutic proteins in the bloodstream.
Assessment and Application of the Biotin Switch Technique for Examining Protein S-Nitrosylation under Conditions of Pharmacologically Induced Oxidative Stress (2007)

Protein S-nitrosylation has emerged as a principal mechanism by which nitric oxide exerts biological effects. Among methods for studying protein S-nitrosylation, the biotin switch technique (BST) has rapidly gained popularity because of the ease with which it can detect individual S-nitrosylated (SNO) proteins in biological samples. The identification of SNO sites by the BST relies on the ability of ascorbate to generate a thiol from an S-nitrosothiol, but not from alternatively S-oxidized thiols (e.g. disulfides, sulfenic acids). However, the specificity of this reaction has recently been challenged, prompting several claims that the BST may produce false-positive results and raising concerns about the application of the BST under oxidizing conditions. Here we perform a comparative analysis of the BST using differentially S-oxidized and S-nitrosylated forms of protein tyrosine phosphatase 1B, as well as intact and lysed human embryonic kidney 293 cells treated with S-oxidizing and S-nitrosylating agents, and verify that the assay is highly specific for SNO. Strikingly, exposure of samples to indirect sunlight from a laboratory window resulted in artifactual ascorbate-dependent signals that are likely promoted by the semidehydroascorbate radical; protection from sunlight eliminated the artifact. In contrast, exposure of SNO proteins to a strong ultraviolet light source (SNO photolysis) prior to the BST provided independent verification of assay specificity. By combining BST with photolysis, we have shown that anti-cancer drug-induced oxidative stress facilitates the S-nitrosylation of the major apoptotic effector glyceraldehyde-3-phosphate dehydrogenase. Collectively, these experiments demonstrate that SNO-dependent signaling pathways can be modulated by oxidative conditions and suggest a potential role for S-nitrosylation in antineoplastic drug action.
Postfiltering Using Multichannel Spectral Estimation in Multispeaker Environments (2007)

This paper investigates the problem of enhancing a single desired speech source from a mixture of signals in multispeaker environments. A beamformer structure is proposed which combines a fixed beamformer with postfiltering. In the first stage, the fixed multiobjective optimal beamformer is designed to spatially extract the desired source by suppressing all other undesired sources. In the second stage, a multichannel power spectral estimator is proposed and incorporated in the postfilter, thus enabling further suppression capability. The combined scheme exploits both spatial and spectral characteristics of the signals. Two new multichannel spectral estimation methods are proposed for the postfiltering using, respectively, inner product and joint diagonalization. Evaluations using recordings from a real-room environment show that the proposed beamformer offers a good interference suppression level whilst maintaining a low-distortion level of the desired source.
Abstract 2936: In situ antitumor immunotherapy with pharmacological blockade of MFG-E8 and chemotherapy against solid and hematological tumors (2010)

Abstract The conventional anticancer strategies, such as chemotherapy and radiotherapy, induce the tumor cell death, which would theoretically become the source of tumor antigens to be recognized in situ by the immune system. However, most of the cytotoxic therapies rarely induce the immunological responses potent enough to cause obvious tumor destruction in the actual clinical settings. This discrepancy might be caused by the tumor evasion systems, which restrain the induction of host immune responses. Thus, the therapeutic efficacy of various anticancer agents could be improved if the novel strategies are found to reverse molecular machineries of tumor-mediated immune evasion. Milk-fat globule EGF-8 (MFG-E8) has been known to maintain tissue homeostasis in multiple aspects; regulating the phagocytosis of apoptotic cells, breast tissue morphogenesis, intestinal epithelium homeostasis and angiogenesis. Here we have shown that the therapeutic interference of MFG-E8 synergistically potentiates antitumor activities of various cytotoxic and target therapies, and radiotherapy, against various murine tumors. These antitumor activities relied on the induction of the potent and specific antitumor immune responses in situ. The MFG-E8 blockade triggered infiltration and activation of dendritic cells at the tumor sites, where apoptotic cells were made available with cytotoxic treatments, resulting in the potent antitumor effector T cell activation and inhibition of Foxp3+Treg cell function. Furthermore, the administration of anti-MFG-E8 antibodies switches the receptor for MFG-E8-mediated tumor cell ingestion from integrins αvβ3 to activating FcγRI/III receptors in dendritic cell recognition of tumor cells, augmenting dendritic cell-mediated cross-priming of tumor-specific T cells. These findings demonstrated that the blockade of MFG-E8, one of the key negative regulators to restrain immune responses against the dying cells, would be a novel strategy to improve durable antitumor responses by various anticancer therapeutic agents. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2936.
Kinetics of Histone Endocytosis in Chinese Hamster Ovary Cells (1982)

~LM chloroquine and remeasured. This provides a method for measuring the kinetics of entry of a fluorescent probe into lysosomes. Internalization into lysosomes began almost immediately upon addition of histone, but stable nonlysosomal fluorescence appeared only after a lag of 1 h. Using suspension cultures, the short term binding and internalization kinetics were also measured. In pulse-chase experiments, lysosomal fluorescence decreased with a half-time of 30 min, but nonlysosomal fluorescence decreased with a half-time of almost 12 h, probably as a result of cell division. These results demonstrate the usefulness of flow cytometry for the quantitation and characterization of endocytosis in cultured cells.
A Game-Theoretic Framework for Controlled Islanding in the Presence of Adversaries (2021)

Controlled islanding effectively mitigates cascading failures by partitioning the power system into a set of disjoint islands. In this paper, we study the controlled islanding problem of a power system under disturbances introduced by a malicious adversary. We formulate the interaction between the grid operator and adversary using a game-theoretic framework. The grid operator first computes a controlled islanding strategy, along with the power generation for the post-islanding system to guarantee stability. The adversary observes the strategies of the grid operator. The adversary then identifies critical substations of the power system to compromise and trips the transmission lines that are connected with compromised substations. For our game formulation, we propose a double oracle algorithm based approach that solves the best response for each player. We show that the best responses for the grid operator and adversary can be formulated as mixed integer linear programs. In addition, the best response of the adversary is equivalent to a submodular maximization problem under a cardinality constraint, which can be approximated up to a $(1-\frac{1}{e})$ optimality bound in polynomial time. We compare the proposed approach with a baseline where the grid operator computes an islanding strategy by minimizing the power flow disruption without considering the possible response from the adversary. We evaluate both approaches using IEEE 9-bus, 14-bus, 30-bus, 39-bus, 57-bus, and 118-bus power system case study data. Our proposed approach achieves better performance than the baseline in about $44\%$ of test cases, and on average it incurs about 12.27 MW less power flow disruption.
Development of selective agonists and antagonists of P2Y receptors (2020)

Although elucidation of the medicinal chemistry of agonists and antagonists of the P2Y receptors has lagged behind that of many other members of group A G protein-coupled receptors, detailed qualitative and quantitative structure–activity relationships (SARs) were recently constructed for several of the subtypes. Agonists selective for P2Y1, P2Y2, and P2Y6 receptors and nucleotide antagonists selective for P2Y1 and P2Y12 receptors are now known. Selective nonnucleotide antagonists were reported for P2Y1, P2Y2, P2Y6, P2Y11, P2Y12, and P2Y13 receptors. At the P2Y1 and P2Y12 receptors, nucleotide agonists (5′-diphosphate derivatives) were converted into antagonists of nanomolar affinity by altering the phosphate moieties, with a focus particularly on the ribose conformation and substitution pattern. Nucleotide analogues with conformationally constrained ribose-like rings were introduced as selective receptor probes for P2Y1 and P2Y6 receptors. Screening chemically diverse compound libraries has begun to yield new lead compounds for the development of P2Y receptor antagonists, such as competitive P2Y12 receptor antagonists with antithrombotic activity. Selective agonists for the P2Y4, P2Y11, and P2Y13 receptors and selective antagonists for P2Y4 and P2Y14 receptors have not yet been identified. The P2Y14 receptor appears to be the most restrictive of the class with respect to modification of the nucleobase, ribose, and phosphate moieties. The continuing process of ligand design for the P2Y receptors will aid in the identification of new clinical targets.
Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): Overview (2008)

INTRODUCTIONT7-based linear amplification of DNA (TLAD) was designed primarily to overcome the shortcomings of exponential amplification approaches. TLAD uses a linear amplification method based on the in vitro transcription (IVT) of template DNA by RNA polymerase from the T7 phage, a common strategy used in RNA amplification protocols. The TLAD protocol introduced here successfully addresses amplification fidelity issues encountered with use of random PCR (R-PCR) with the ChIP-chip method (whereby DNA recovered from chromatin immunoprecipitation [ChIP] of cell lysate is used for subsequent analysis on DNA microarrays). Thus, optimizations have been done with this particular application in mind. For other applications that require DNA instead of RNA to be the end point, reverse transcription is a necessary step that increases the cost and complexity of necessary molecular biological manipulations to the sample, when compared with PCR. However, IVT amplification does offer improved fidelity and a much higher maximum yield per single reaction. Thus, other techniques that require amplification of complex mixtures of randomly fragmented genomic DNA can also benefit from this method.
Figure S2 from PP2A Inactivation Mediated by <i>PPP2R4</i> Haploinsufficiency Promotes Cancer Development (2023)

&lt;p&gt;Phosphatase assays in immunoprecipitates of several endogenous PP2A B-type subunits: time courses.&lt;/p&gt;
Fused silica capillary column gas chromatography of derivatized thyroid hormone standards with electron capture detection (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFused silica capillary column gas chromatography of derivatized thyroid hormone standards with electron capture detectionJeffrey A. Corkill and Roger W. GieseCite this: Anal. Chem. 1981, 53, 11, 1667–1672Publication Date (Print):September 1, 1981Publication History Published online1 May 2002Published inissue 1 September 1981https://pubs.acs.org/doi/10.1021/ac00234a027https://doi.org/10.1021/ac00234a027research-articleACS PublicationsRequest reuse permissionsArticle Views61Altmetric-Citations9LEARN 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-Alertsclose Get e-Alerts
Requirements for systemic risk management in the financial sector (2009)

The subprime financial crisis of 2008 exposed systemic weaknesses in the financial sector. Emergency liquidity on an enormous scale was required to prevent a collapse of the banking system. There is much discussion now concerning how to monitor and manage the risk of such systemic events.
Face Recognition from Correspondence Maps (2022)

This chapter presents several algorithms that have proved useful in the task of recognizing human faces from gray-value images without additional information. Their common feature is the extraction of correspondence maps between an image to be analyzed and several stored views of known objects, which are called models. The processing of a retinal gray-level image in simple cells of the primary visual cortex can be modeled by a wavelet transform based on complex-valued Gabor functions. The major drawback of correspondence-based recognition systems is that the computationally expensive procedure of creating a correspondence map must be carried out for each of the stored models. Humans do very poorly in recognizing faces from photographic negatives. One recognition system has no problem with this, because Gabor amplitudes are identical for positive and negative images. There is now increasing evidence that the human brain employs different modules for the recognition of faces and general objects.
Band Dispersion in Lab-on-a chip for protein separation (2008)

Ampholyte based isoelectric focusing (IEF) simulation was conducted to study dispersion of proteins in a horse shoe microchannel. Four model proteins (pls= 6.49, 7.1, 7.93 and 8.6) are focused in a 1 ㎝ long horse shoe channel under an electric field of 300 V/㎝. The pH gradient is formed in the presence of 25 biprotic carrier ampholytes (?pK = 3.0) within a pH range of 6 to 9. The proteins are focused at 380 sec in a nominal electric field of 300 V/㎝. Our numerical results show that the band dispersions of a protein are large during the gradient formation stage, but the dispersions are significantly reduced when the double peaks start to merge. This rearrangement of spreading band isvery unique compared to linear electrokinetic phenomena (capillary zone electrophoresis) and is independent of channel position and channel shape. Hence, one can perform IEF and other self-sharpening electrokinetic methods, such as, isotachophoresis (ITP), in complex geometries without incorporating hyperturns.
Phase Change Memory Reliability: A Signal Processing and Coding Perspective (2015)

Phase change memory (PCM) is a new solid-state memory technology that promises disruptive changes in the way servers and enterprise storage systems are built. Multilevel-cell (MLC) storage is highly desirable for increasing capacity and thus lowering cost-per-bit in memory technologies. In PCM, MLC storage is hampered by noise and resistance drift. In this paper, the issue of reliability in MLC PCM is addressed. A statistical model is developed that captures the main impairments in MLC PCM cell-arrays. A signal processing and coding framework is then introduced that provides robustness to drift and noise, improving reliability and prolonging data retention. Several examples of codes are provided and practical detection schemes are described.
Li3N-Modified Garnet Electrolyte for All-Solid-State Lithium Metal Batteries Operated at 40 °C (2018)

Lithium carbonate on the surface of garnet blocks Li<sup>+</sup> conduction and causes a huge interfacial resistance between the garnet and electrode. To solve this problem, this study presents an effective strategy to reduce significantly the interfacial resistance by replacing Li<sub>2</sub>CO<sub>3</sub> with Li ion conducting Li<sub>3</sub>N. Compared to the surface Li<sub>2</sub>CO<sub>3</sub> on garnet, Li<sub>3</sub>N is not only a good Li<sup>+</sup> conductor but also offers a good wettability with both the garnet surface and a lithium metal anode. In addition, the introduction of a Li<sub>3</sub>N layer not only enables a stable contact between the Li anode and garnet electrolyte but also prevents the direct reduction of garnet by Li metal over a long cycle life. As a result, a symmetric lithium cell with this Li<sub>3</sub>N-modified garnet exhibits an ultralow overpotential and stable plating/stripping cyclability without lithium dendrite growth at room temperature. Moreover, an all-solid-state Li/LiFePO<sub>4</sub> battery with a Li<sub>3</sub>N-modified garnet also displays high cycling efficiency and stability over 300 cycles even at a temperature of 40 °C.