gebhart/patrepeval huggingface dataset:
Solid-phase Proximity Ligation Assays : High-performance and multiplex protein analyses (2011)

Protein biomarkers circulating in blood hold the promise of improved diagnosis, prognosis and follow-up of treatment of disease via minimally invasive procedures. For the discovery and validation of such biomarkers, methods are needed that can facilitate parallel, highly specific and in-depth analysis of the blood proteome. The work presented in this thesis intends to develop and apply such assays, building on the concept of the proximity ligation assay (PLA). In paper I, I present an easy and non-expensive alternative for the conjugation of oligonucleotides to antibodies via biotin-streptavidin-biotin interaction. This approach can be used when large sets of antibodies and/or oligos need to be validated for their performance as probes in PLA reactions. In paper II, a solid-phase variant of PLA (SP-PLA) for the detection and quantification of proteins in blood is presented. SP-PLA exhibited an improved limit of detection compared to commercial ELISA assays by two orders of magnitude. In addition SP-PLA exhibited a broader dynamic range by at least one order of magnitude and required only 5 μl of sample, rendering the method very well suited for analyses of precious bio-banked material. Last but not least, SP-PLA was used to validate the diagnostic potential of GDF-15 as a biomarker for cardiovascular disease in a set of cardiovascular disease patients and healthy controls. Paper III discusses the development of a multiplex SP-PLA (MultiPLAy) for the simultaneous detection of 36 proteins in just 5 μl of sample. MultiPLAy exhibited an improved LOD when compared to state-of-the-art bead-based sandwich assays. Most importantly, we observed only a minimal tendency to increased background with multiplexing, compared to a sandwich assay, suggesting that much higher levels of multiplexing will be possible. The assay was used to identify putative biomarkers in sample cohorts of colorectal cancer (CRC) and cardiovascular disease (CVD). Subsequent multivariate analysis revealed previously known diagnostic biomarkers. Furthermore, we successfully applied next-generation sequencing as a readout for the protein assays, allowing for the first time digital recording of protein profiles in blood. In paper IV, we investigated the suitability of prostasomes as blood biomarkers in patients with prostate cancer using a newly developed PLA assay (4PLA) that utilizes five binders for the detection of complex target molecules. The assay successfully detected significantly elevated levels of prostasomes in blood samples from prostate cancer patients prior to radical prostatectomy, compared to controls and men with benign biopsy results.
COX-2 Selectivity and Inflammatory Processes (2000)

Increasing amounts of experimental and clinical data support the role of selective cyclooxygenase (COX)-2 inhibition in anti-inflammatory processes and the involvement of COX-1 inhibition in the side effects associated with non steroidal anti-inflammatory drug use. This review will focus on the differences in the structure of the COX-1 and COX-2 molecules, particularly the active site and how they are bound by various NSAIDs to achieve COX-2 selectivity. This COX-2 selectivity will then be characterized in pharmacological assays in vitro and in animal models in vivo. Finally, clinical information available for this new class of selective inhibitors will be discussed.
Anti‐arrhythmic activities of opioid agonists and antagonists and their stereoisomers (1991)

1. A series of opioid agonists, antagonists and their (+)-stereoisomers were tested for antiarrhythmic activity in the rat coronary artery occlusion model. 2. Naloxone (0.01-2 mg kg-1) significantly reduced the incidence and severity of cardiac arrhythmias, in accordance with previous published studies. 3. The non-opioid stereoisomer, (+)-naloxone, was equipotent with naloxone against occlusion-induced arrhythmia. 4. Similar non-stereospecific antiarrhythmic effects were induced by another opioid antagonist, Win 44,441-3 and its stereoisomer Win 44,441-2. 5. The opioid agonists, morphine and levorphanol, protected against occlusion-induced arrhythmia as did the opioid antagonists, and the (+)-stereoisomer, dextrorphan, was equipotent to levorphanol. 6. It is concluded that the antiarrhythmic effects of opioid drugs are not mediated by opioid receptors. A direct effect on ionic currents in cardiac muscle is suggested as the mechanism of opioid antiarrhythmic activity.
Simple methods for detecting zero crossing (2004)

Affects of noise, harmonics, and multi-frequency signal make frequency and period measurements difficult for synchronizing control events. Various methods are presented to minimize errors in period and phase measurements. Both frequency and amplitude domain approaches are analyzed. Post detection processing allows greater accuracy. Static and dynamic hystereses as well as interpolation methods of zero-crossing detection are investigated.
Efficient GPU-based implementation of the median filter based on a multi-pixel-per-thread framework (2018)

Median filtering has become a ubiquitous smoothing tool for image denoising tasks, with its complexity generally determined by the median algorithm used (usually on the order of O(n log(n)) when computing the median of n elements). Most algorithms were formulated for scalar single processor computers, with few of them successfully adapted and implemented for computers with a parallel architecture. However, the redundancy for processing neighboring pixels has not yet been fully exploited for parallel implementations. Additionally, most of the implementations are only suitable for fixed point images, but not for floating point.In this paper we propose an efficient parallel implementation of the 2D median filter, based on a multiple pixel-per-thread framework, and test its implementation on a CUDA-capable GPU either for fixed point or floating point data. Our computational results show that our proposed methods outperforms state-of the art implementations, with the difference increasing significantly as the filter size grows.
Rapid and Long-Term Disappearance of CD4+ T Lymphocyte Responses Specific for <i>Anaplasma Marginale</i> Major Surface Protein-2 (MSP2) in MSP2 Vaccinates following Challenge with Live <i>A. marginale</i> (2005)

In humans and ruminants infected with Anaplasma, the major surface protein 2 (MSP2) is immunodominant. Numerous CD4(+) T cell epitopes in the hypervariable and conserved regions of MSP2 contribute to this immunodominance. Antigenic variation in MSP2 occurs throughout acute and persistent infection, and sequentially emerging variants are thought to be controlled by variant-specific Ab. This study tested the hypothesis that challenge of cattle with Anaplasma marginale expressing MSP2 variants to which the animals had been immunized, would stimulate variant epitope-specific recall CD4(+) T cell and IgG responses and organism clearance. MSP2-specific T lymphocyte responses, determined by IFN-gamma ELISPOT and proliferation assays, were strong before and for 3 wk postchallenge. Surprisingly, these responses became undetectable by the peak of rickettsemia, composed predominantly of organisms expressing the same MSP2 variants used for immunization. Immune responsiveness remained insignificant during subsequent persistent A. marginale infection up to 1 year. The suppressed response was specific for A. marginale, as responses to Clostridium vaccine Ag were consistently observed. CD4(+)CD25(+) T cells and cytokines IL-10 and TGF-beta1 did not increase after challenge. Furthermore, a suppressive effect of nonresponding cells was not observed. Lymphocyte proliferation and viability were lost in vitro in the presence of physiologically relevant numbers of A. marginale organisms. These results suggest that loss of memory T cell responses following A. marginale infection is due to a mechanism other than induction of T regulatory cells, such as peripheral deletion of MSP2-specific T cells.
Oxide Charge Reduction by Chemical Gettering with Trichloroethylene During Thermal Oxidation of Silicon (1972)

Silicon dioxide was thermally grown in an oxygen atmosphere containing a small percentage of trichloroethylene vapor. As a result of this process, it was possible to fabricate metal‐oxide‐semiconductor (MOS) diodes with greatly reduced oxide space charge. This reduction in oxide charge was accompanied by improved electrical stability under bias‐temperature stress. It is believed that the pyrolysis product, chlorine, acts as a getter to continuously remove mobile impurity cations such as Na+ during the oxidation process. Also described are various charge phenomena under bias‐temperature stress conditions.
Algorithmic analysis of complex semantics for timed and hybrid automata (2006)

In the field of formal verification of real-time systems, major developments have been recorded in the last fifteen years. It is about logics, automata, process algebra, programming languages, etc. From the beginning, a formalism has played an important role: timed automata and their natural extension,hybrid automata. Those models allow the definition of real-time constraints using real-valued clocks, or more generally analog variables whose evolution is governed by differential equations. They generalize finite automata in that their semantics defines timed words where each symbol is associated with an occurrence timestamp. The decidability and algorithmic analysis of timed and hybrid automata have been intensively studied in the literature. The central result for timed automata is that they are positively decidable. This is not the case for hybrid automata, but semi-algorithmic methods are known when the dynamics is relatively simple, namely a linear relation between the derivatives of the variables. With the increasing complexity of nowadays systems, those models are however limited in their classical semantics, for modelling realistic implementations or dynamical systems. In this thesis, we study the algorithmics of complex semantics for timed and hybrid automata. On the one hand, we propose implementable semantics for timed automata and we study their computational properties: by contrast with other works, we identify a semantics that is implementable and that has decidable properties. On the other hand, we give new algorithmic approaches to the analysis of hybrid automata whose dynamics is given by an affine function of its variables.
Studies in Mixed Ester Condensations. IV. Acylations with Methyl Dimethoxyacetate<sup>1</sup> (1956)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies in Mixed Ester Condensations. IV. Acylations with Methyl Dimethoxyacetate1E. Earl Royals and A. G. Robinson IIICite this: J. Am. Chem. Soc. 1956, 78, 16, 4161–4164Publication Date (Print):August 1, 1956Publication History Published online1 May 2002Published inissue 1 August 1956https://pubs.acs.org/doi/10.1021/ja01597a083https://doi.org/10.1021/ja01597a083research-articleACS PublicationsRequest reuse permissionsArticle Views466Altmetric-Citations18LEARN 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
Effects of sample size on robustness and prediction accuracy of a prognostic gene signature (2009)

Increasing sample sizes generated a gene signature with better stability, better concordance in outcome prediction, and better prediction accuracy. However, the degree of performance improvement by the increased sample size was different between the degree of overlap and the degree of concordance in outcome prediction, suggesting that the sample size required for a study should be determined according to the specific aims of the study.
Stathmo-apoptosis: Arresting apoptosis by fluorochrome-labeled inhibitor of caspases (2001)

Apoptosis, like mitosis, is a kinetic event. The entire duration of apoptosis, from its onset to total disintegration of the cell, is often short and may be of variable duration. The time-window through which individual apoptotic cells display their characteristic features that serve to identify them varies depending on: a) the assay that is used, b) the cell type, c) the nature of the inducer of apoptosis, and d) the environmental factors the cell is exposed to that may shorten or prolong apoptosis. Thus, because the apoptotic index (AI) does not accurately represent incidence of apoptosis it is desirable to estimate the rate of cell death in analogy to the cell birth rate which is assessed by the stathmo-kinetic approach by arresting cells in mitosis. In this study the fluorescent caspase inhibitor FAM-VAD-FMK was used for dual purposes: a) to arrest the process of apoptosis (stathmo-apoptosis), and b) to have the arrested cells labeled with fluorochrome. Apoptosis of HL-60 and MCF-7 cells was induced by DNA topoisomerase I inhibitor camptothecin (CPT) and FAM-VAD-FMK was added at the same time as the inducer. While the cells become progressively labeled with FAM-VAD-FMK, their disintegration, loss of the phase-contrast and loss of the capability to bind the inhibitor, and in the case of MCF-7 cells, detachment from the slides, all were prevented for up to 48 h. The percentage of FAM-VAD-FMK labeled HL-60 cells was plotted as a function of time after addition of CPT and the rate of cell entrance to apoptosis was estimated from the slopes of the stathmo-apoptotic plot at different time after administration of CPT. The plot revealed the presence of two distinct subpopulations: during the initial 8 h of the treatment with CPT the cells of the first subpopulation, predominantly the S-phase cells, were entering apoptosis at a rate of about 7% of cells per hour. The remaining cells were stochastically entering apoptosis between 8 and 48 h at a rate 1% of cells per hour. The present approach offers a unique capability to accurately estimate the kinetics of cell transition to apoptosis, revealing the unbiased cumulative apoptotic index over a long time span after induction of apoptosis.
Expression of VLA-alpha 2, VLA-alpha 6, and VLA-beta 1 chains in normal mucosa and adenomas of the colon, and in colon carcinomas and their liver metastases. (1991)

'Very late antigen' (VLA) proteins are members of the integrin superfamily with cell-surface receptor function and are involved in the cell-cell matrix interaction. They are heterodimers with a common beta 1 chain and different alpha chains counted through VLA-1 to VLA-6. The VLA-2 complex (alpha 2/beta 1) was found to act as collagen receptor on platelets and the VLA-6 complex (alpha 6/beta 1) as laminin receptor. Using monoclonal antibodies and an indirect immunoperoxidase method, we investigated the expression of VLA-alpha 2, VLA-alpha 6, and VLA-beta 1 chains in 20 normal colonic mucosa samples, in 20 colonic adenomas, and in 96 carcinomas together with 10 accompanying liver metastases. All three proteins were expressed throughout the colonic epithelium, except for VLA-alpha 2, which was present in the cryptic gland but was absent on the mucosal surface in some cases. In general, adenomas were strongly positive for the VLA proteins but 3 of 20 cases showed focal VLA-alpha 2-negative areas. The carcinomas revealed considerable heterogeneity of VLA-alpha 2 expression; ie, 59 tumors were completely positive, 35 tumors revealed a focal loss of antigen, and 2 cases were negative. This reduced antigen expression was statistically associated with Dukes' stage C/D (P = 0.003). VLA-alpha 6 was expressed throughout in all tumors. VLA-beta 1 was found extensively expressed in 77 carcinomas, partially expressed in 17 carcinomas, and was absent in 2 carcinomas. As compared to their primary tumors, liver metastases showed roughly corresponding patterns of antigen expression. The down regulation/loss of VLA proteins in a subset of epithelial colon tumors might cause a disturbed cell-cell/cell-matrix interaction that might augment the invasive property of their cells.
On the Importance of the Work Function and Electron Carrier Density of Oxide Electrodes for the Functional Properties of Ferroelectric Capacitors (2019)

It is important to understand the effect of the interfaces between the oxide electrode layers and the ferroelectric layer on the polarization response for optimizing the device performance of all‐oxide ferroelectric devices. Herein, the effects of the oxide La 0.07 Ba 0.93 SnO 3 (LBSO) as an electrode material in an PbZr 0.52 Ti 0.48 O 3 (PZT) ferroelectric capacitor are compared with those of the more commonly used SrRuO 3 (SRO) electrode. SRO (top)/PZT/SRO (bottom), SRO/PZT/LBSO, and SRO/PZT/2 nm SRO/LBSO devices are fabricated. Only marginal differences in crystalline properties, determined by X‐ray diffraction and scanning transmission electron microscopy, are found. High‐quality polarization loops are obtained, but with a much larger coercive field for the SRO/PZT/LBSO device. In contrast to the SRO/PZT/SRO device, the polarization decreases strongly with increasing field cycling. This fatigue problem can be remedied by inserting a 2 nm SRO layer between PZT and LBSO. It is argued that strongly increased charge injection into the PZT occurs at the bottom interface, because of the low PZT/LBSO interfacial barrier and the much lower carrier density in LBSO, as compared with that in SRO, causing a low dielectric constant, depleted layer in LBSO. The charge injection creates a trapped space charge in the PZT, causing the difference in fatigue behavior.
C (1987)

LA CARAVANE DU CAIRE Opéra en trois actes du comte de Provence et de Morel de Chédeville. Musique d’André-Ernest-Modeste Grétry. Ballets de Pierre Gardel. Création à Fontainebleau le 30 octobre 1783. Première au Théâtre de l’Opéra (salle de la Porte Saint-Martin) le 15 janvier 1784 A. I : Campagne sur les bords du Nil. A. II, t. 1 : Un appartement du pacha au Caire. A. II, t. 2 : Le bazar. A. III, t. 1 : Appartement intérieur du pacha. A. III, t. 2 : Jardin préparé pour une fête. Reprise fin ...
In Vitro Reconstitution of Mycobacterial Ergothioneine Biosynthesis (2010)

Ergothioneine is a histidine-derived thiol of bacterial and fungal origin that has also been isolated from animal and human tissue. Recent findings point to critical functions of ergothioneine in human physiology, but its role in microbial life is poorly understood. This report describes the identification of the ergothioneine biosynthetic gene cluster from mycobacteria and in vitro reconstitution of this process using recombinant proteins from Mycobacterium smegmatis. The key reactions are catalyzed by a methyltransferase that transfers three methyl groups to the alpha-amino moiety of histidine and an iron(II)-dependent enzyme that catalyzes oxidative sulfurization of trimethylhistidine. A search for homologous genes indicated that ergothioneine production is a frequent trait among fungi, actinobacteria, and cyanobacteria but also occurs in numerous bacteroidetes and proteobacteria.
Biodiesel generation from oleaginous yeast Rhodotorula glutinis with xylose assimilating capacity (2007)

  This study explored a strategy to convert agricultural and forestry residues into microbial lipid, which could be further transformed into biodiesel. Among the 250 yeast strains screened for xylose assimilating capacity, eight oleaginous yeasts were selected by Sudan Black B test. The lipid content of these 8 strains was determined by soxhlet extraction method. One strain (T216) was found to produce lipids up to 36.6%, and it was identified as Rhodotorula glutinis. The optimal fermentation conditions were obtained as follows: glucose as carbon source 100 g/L; yeast extract and peptone as nitrogen sources at, respectively, 8 and 3 g/L; initial pH of 5.0; inoculation volume of 5%; temperature at 28oC, shaking speed of 180 r/min, cultivated for 96 h. Under these conditions, R. glutinis accumulated lipids up to 49.25% on a cellular biomass basis and the corresponding lipid productivity reached 14.66 g/L. Experiments with a 5-L bioreactor under the optimal culture conditions showed that R. glutinis accumulated lipids up to 60.69%, resulting in 23.41 g/L in lipid productivity. More encouraging results were observed for the lipid production with alternative carbon sources. Corn stalk and Populus euramevicana leaves hydrolysate could be used to substitute glucose. Chemical analysis indicated that biodiesel obtained by transesterification possessed similar composition to that from vegetable oil, one of the widely used feedstock for biodiesel.   Key words: Oleaginous yeast, Rhodotorula glutinis, culture optimization biodiesel.
Toward a Unified Nomenclature System for Highly Pathogenic Avian Influenza Virus (H5N1) (2008)

Highly pathogenic avian influenza (HPAI) virus (H5N1) has appeared in >60 countries and continues to evolve and diversify at a concerning rate. Because different names have been used to describe emerging lineages of the virus, this study describes a unified nomenclature system to facilitate discussion and comparison of subtype H5N1 lineages.
Incorporation of nisin in micro‐particles of calcium alginate (1997)

Nisin was successfully incorporated into a matrix of calcium alginate and ground into micro-particles smaller than 150 microns. Formation of micro-particles and incorporation of nisin was verified by scanning electron microscopy and by the reduction in the inactivation of nisin activity with proteolytic enzymes. Incorporation efficiency was 87-93% and the nisin in the alginate-incorporated form was 100% active against an indicator culture of Lactobacillus curvatus both in MRS broth and reconstituted skim milk.
An analysis of VI Architecture primitives in support of parallel and distributed communication (2002)

Abstract We present the results of a detailed study of the Virtual Interface (VI) paradigm as a communication foundation for a distributed computing environment. Using Active Messages and the Split‐C global memory model, we analyze the inherent costs of using VI primitives to implement these high‐level communication abstractions. We demonstrate a minimum mapping cost (i.e. the host processing required to map one abstraction to a lower abstraction) of 5.4 μs for both Active Messages and Split‐C using four‐way 550 MHz Pentium III SMPs and the Myrinet network. We break down this cost to the use of individual VI primitives in supporting flow control, buffer management and event processing and identify the completion queue as the source of the highest overhead. Bulk transfer performance plateaus at 44 Mbytes/s for both implementations are due to the addition of fragmentation requirements. Based on this analysis, we present the implications for the VI successor, Infiniband. Copyright © 2002 John Wiley & Sons, Ltd.