gebhart/patrepeval huggingface dataset:
Development of Azo‐Based Fluorescent Probes to Detect Different Levels of Hypoxia (2013)

Let it shine: New hypoxia-sensitive fluorescent probes were developed; they consist of a rhodamine moiety with an azo group directly conjugated to the fluorophore. Because of an ultrafast conformational change around the NN bond, the compounds are nonfluorescent under normoxia. However, under hypoxia, the azo group is reduced, and a strongly fluorescent rhodamine derivative is released.
A mutant of Escherichia coli showing constitutive expression of the lysogenic induction and error-prone DNA repair pathways. (1977)

A mutant of E. coli (designated the STS mutant) has been isolated in which the phage induction and error-prone DNA repair pathways appear to be expressed constitutively without the cells having received an inducing signal. Phage lambda was not able to lysogenize this mutant, whereas a noninducible mutant of lambda, lambdacIind-, known to synthesize a repressor that is insensitive to the induction mechanism, lysogenized it normally. This result suggested that normal phage repressor was synthesized in the STS mutant but was then inactivated by the induction mechanism. The STS strain also had mutator characteristics, and showed spontaneous, error-prone repair of UV-damaged phage lambda. Derived from a lexA tif sfiA parent strain, the STS mutant carried an additional mutation spr at the lexA locus that resulted in a high level of expression of the induction pathways. The properties of this and related strains provide additional evidence that induction of phage and induction of error-prone DNA repair occur by a similar mechanism, and further suggest a model for the regulation of these pathways.
Antibodies to Hmg Proteins in Patients with Drug‐Induced Autoimmunity (1994)

The high prevalence of antibodies to the nucleosomal core HMGs (HMG-14 and HMG-17) in DIL patients adds evidence implicating nucleosomes as immunogens in drug-induced autoimmunity.
Long‐term treatment of systemic lupus erythematosus with cyclosporin A (1997)

CSA represents a helpful second-choice treatment for patients with active SLE. Administration of CSA necessitates expert and careful followup of patients.
A Distributed Algorithmfor Weighted Shortest Path Problem (1999)

Consider the situation that informations necessary to solve a certain problem are distributed among processors on a network. It is called a distributed algorithm that in this situation each processor exchanges the message with adjacent processors to solve the problems. This paper proposes a distributed algorithm to solve the problem that constructs the weighted shortest path tree in an asynchronous network system. In general, a distributed algorithm is estimated by the number of messages(message complexity of the distributed algorithm proposed in this paper are O(n53) and O(nln) respectively. where n is the number of processors on the network.
Immunohistochemical characterization of gastrinomas with antibodies specific to different fragments of progastrin. (1989)

The characterization of the tumors and their metastasis in patients with the Zollinger-Ellison syndrome is currently based on the immunohistochemical identification of gastrin cells. However, sometimes tumoral cells fail to react with common C-terminal gastrin antibodies. In order to clarify this failure, we carried out morphologic, morphometric and immunocytochemical analyses performed on light and electron microscope levels of 6 pancreatic and 1 metastatic gastrinomas, using antibodies raised against various sequences of human progastrin. On the basis, in light microscopy, of qualitative analysis of immunostaining within cells and of immunostained cell numbers, gastrin 34 residue seemed to be the prominent form in 2 of the tumor tissues, G-17 in 1 tumor which was not responsive with C terminus progastrin and N terminus G-34 antisera, and progastrin in the metastatic tissue that did not contain typical gastrin (G-like) cells. Two tumors failed to react with all antisera used. At the electron microscope level, immunogold staining revealed that progastrin was present only in the progranules and gastrin 34 in both progranules and intermediate granules. Quantitative studies performed on 3 tumors showed that, within a given tumoral cell, about 25 percent of progranules contained progastrin while 75 percent contained gastrin 34. We concluded that different forms of gastrin can be immunodetected in a gastrinoma tissue, depending on the regions, and that the distribution of progastrin fragments is variable from tumor to tumor. So, specific antibodies to different fragments of progastrin may help to the characterization of gastrinomas.
Exacerbation of psoriasis by chrysotherapy (1991)

<h3>To the Editor.—</h3> Psoriatic arthritis typically consists of psoriatic skin and nail changes concomitant with asymmetrical, pauciarticular joint disease. The primary therapeutic modality advocated for joint involvement is the administration of an anti-inflammatory medication. Many patients with moderate to severe psoriatic arthritis receive a disease-modifying agent such as injectable gold (chrysotherapy). Although dermatitis occurs in 15% to 25% of patients receiving gold therapy,<sup>1</sup>the ability of chrysotherapy to exacerbate psoriasis has not been proven; neither a major review of drug-induced psoriasis<sup>2</sup>nor a standard textbook of dermatology<sup>3</sup>lists gold as a precipitant. We describe a patient with sparsely distributed, long-standing psoriasis who developed diffuse psoriasis shortly after the initiation of intramuscular gold sodium thiomalate, and review the English literature from 1969 to 1990 for reports of possible gold-induced psoriasis, aided by a Medline search. <h3>Report of a Case.—</h3> A 54-year-old white man was seen with a 14-year
Platelet-Activating Factor Acetylhydrolases:  Broad Substrate Specificity and Lipoprotein Binding Does Not Modulate the Catalytic Properties of the Plasma Enzyme (2001)

Platelet-activating factor acetylhydrolases (PAF-AHs) are a group of enzymes that hydrolyze the sn-2 acetyl ester of PAF (phospholipase A(2) activity) but not phospholipids with two long fatty acyl groups. Our previous studies showed that membrane-bound human plasma PAF-AH (pPAF-AH) accesses its substrate only from the aqueous phase, which raises the possibility that this enzyme can hydrolyze a variety of lipid esters that are partially soluble in the aqueous phase. Here we show that pPAF-AH has broad substrate specificity in that it hydrolyzes short-chain diacylglycerols, triacylglycerols, and acetylated alkanols, and displays phospholipase A(1) activity. On the basis of all of the substrate specificity results, it appears that the minimal structural requirement for a good pPAF-AH substrate is the portion of a glyceride derivative that includes an sn-2 ester and a reasonably hydrophobic chain in the position occupied by the sn-1 chain. In vivo, pPAF-AH is bound to high and low density lipoproteins, and we show that the apparent maximal velocity for this enzyme is not influenced by lipoprotein binding and that the enzyme hydrolyzes tributyroylglycerol as well as the recombinant pPAF-AH does. Broad substrate specificity is also observed for the structurally homologous PAF-AH which occurs intracellularly [PAF-AH(II)] as well as for the PAF-AH from the lower eukaryote Physarum polycephalum although pPAF-AH and PAF-AH(II) tolerate the removal of the sn-3 headgroup better than the PAF-AH from P. polycephalum does. In contrast, the intracellular PAF-AH found in mammalian brain [PAF-AH(Ib) alpha 1/alpha 1 and alpha 2/alpha 2 homodimers] is more selectively operative on compounds with a short acetyl chain although this enzyme also displays significant phospholipase A(1) activity.
Human Galectin 3 Binding Protein Interacts with Recombinant Adeno-Associated Virus Type 6 (2012)

Recombinant adeno-associated viruses (rAAVs) hold enormous potential for human gene therapy. Despite the well-established safety and efficacy of rAAVs for in vivo gene transfer, there is still little information concerning the fate of vectors in blood following systemic delivery. We screened for serum proteins interacting with different AAV serotypes in humans, macaques, dogs, and mice. We report that serotypes rAAV-1, -5, and -6 but not serotypes rAAV-2, -7, -8, -9, and -10 interact in human sera with galectin 3 binding protein (hu-G3BP), a soluble scavenger receptor. Among the three serotypes, rAAV-6 has the most important capacities for binding to G3BP. rAAV-6 also bound G3BP in dog sera but not in macaque and mouse sera. In mice, rAAV-6 interacted with another protein of the innate immune system, C-reactive protein (CRP). Furthermore, interaction of hu-G3BP with rAAV-6 led to the formation of aggregates and hampered transduction when the two were codelivered into the mouse. Based on these data, we propose that species-specific interactions of AAVs with blood proteins may differentially impact vector distribution and efficacy in different animal models.
Discovering Motifs in Ranked Lists of DNA Sequences (2007)

Computational methods for discovery of sequence elements that are enriched in a target set compared with a background set are fundamental in molecular biology research. One example is the discovery of transcription factor binding motifs that are inferred from ChIP-chip (chromatin immuno-precipitation on a microarray) measurements. Several major challenges in sequence motif discovery still require consideration: (i) the need for a principled approach to partitioning the data into target and background sets; (ii) the lack of rigorous models and of an exact p-value for measuring motif enrichment; (iii) the need for an appropriate framework for accounting for motif multiplicity; (iv) the tendency, in many of the existing methods, to report presumably significant motifs even when applied to randomly generated data. In this paper we present a statistical framework for discovering enriched sequence elements in ranked lists that resolves these four issues. We demonstrate the implementation of this framework in a software application, termed DRIM (discovery of rank imbalanced motifs), which identifies sequence motifs in lists of ranked DNA sequences. We applied DRIM to ChIP-chip and CpG methylation data and obtained the following results. (i) Identification of 50 novel putative transcription factor (TF) binding sites in yeast ChIP-chip data. The biological function of some of them was further investigated to gain new insights on transcription regulation networks in yeast. For example, our discoveries enable the elucidation of the network of the TF ARO80. Another finding concerns a systematic TF binding enhancement to sequences containing CA repeats. (ii) Discovery of novel motifs in human cancer CpG methylation data. Remarkably, most of these motifs are similar to DNA sequence elements bound by the Polycomb complex that promotes histone methylation. Our findings thus support a model in which histone methylation and CpG methylation are mechanistically linked. Overall, we demonstrate that the statistical framework embodied in the DRIM software tool is highly effective for identifying regulatory sequence elements in a variety of applications ranging from expression and ChIP-chip to CpG methylation data. DRIM is publicly available at http://bioinfo.cs.technion.ac.il/drim.
Muscle Delivery of Human Kallikrein Gene Reduces Blood Pressure in Hypertensive Rats (1995)

We recently found that transgenic mice expressing human tissue kallikrein develop sustained hypotension. The result suggests that a continuous supply of human tissue kallikrein could have a prolonged effect on blood pressure reduction. In the present study, we investigated the potential of using human tissue kallikrein for gene therapy by injecting a kallikrein gene construct into the skeletal muscle of spontaneously hypertensive rats. Expression of the human tissue kallikrein messenger RNA in spontaneously hypertensive rats was identified by reverse transcription-polymerase chain reaction with Southern blot. Human tissue kallikrein was detected in the injected animals by an enzyme-linked immunosorbent assay. Injection of the human kallikrein gene into spontaneously hypertensive rats caused a significant reduction of systemic blood pressure, ranging from 15 to 26 mm Hg, compared with the control group. The differences were significant 1 week after the injection and continued for more than 2 months. Blood pressure reduction could be reversed after the administration of the bradykinin antagonist Hoe 140. The results indicate that somatic delivery of the human tissue kallikrein gene induces a sustained reduction of systemic blood pressure in spontaneously hypertensive rats. The present study raises the possibility of applying kallikrein gene therapy to the treatment of human hypertensive diseases.
Efficacy of a protein kinase C inhibitor (tamoxifen) in the treatment of acute mania: a pilot study (2007)

Antimanic effects resulted from a protein kinase C inhibitor; onset occurred within five days. Large, controlled studies with selective protein kinase C inhibitors in acute mania are warranted.
ELISA To Detect Proteolysis of Ultrahigh-Temperature Milk upon Storage (2007)

Casein proteolysis can occur in milk during storage leading to its gelation. The two main proteolytic systems suspected to be involved are the plasmin and the proteases produced by psychrotrophic bacteria. The latter have been shown to cleave kappa-casein at the Phe105-Met106 bond. Although several techniques allow the determination of plasmin in milk, few rapid and easy-to-perform analytical techniques are available to check for bacterial proteolytic activity. This study presents the development of an inhibition ELISA allowing for the quantification of the kappa-casein intact at the Phe105-Met106 bond. It uses a monoclonal antibody specifically directed against this peptide bond that binds to the protein as long as the molecule's cleavage site is intact but not when it is cleaved. This simple technique allows for the rapid analysis of more than 20 samples within 3 h. Applied to commercial milks, this assay allowed for the detection of unstable milk.
Maintaining evolving domain models (2016)

When engineering an automated planning model, domain authors typically assume a static, unchanging ground-truth world. Unfortunately, this assumption can clash with reality, where domain changes often rapidly occur in best practices, effectors, or known conditions. In these cases, remodeling the domain causes domain experts to ensure newly captured requirements integrate well with the current model. In this work, we address this model maintenance problem in a system called Marshal. Marshal assists model maintainers by reasoning about their model as a (hidden) stochastic process. It issues queries, and learns models by observing query answers, plan solutions, and direct changes to the model. Our results indicate that anticipating model evolution leads to more accurate models over naive approaches.
Teratogenic effect of hydroxyethylrutoside, a flavonoid derivate drug – a population-based case–control study (2013)

Oral HER treatment during early pregnancy associates with a higher risk for ocular coloboma and for a newly delineated congenital abnormality syndrome.
Measuring the Parallelism Available for Very Long Instruction Word Architectures (1984)

Long instruction word architectures, such as attached scientific processors and horizontally microcoded CPU's, are a popular means of obtaining code speedup via fine-grained parallelism. The falling cost of hardware holds out the hope of using these architectures for much more parallelism. But this hope has been diminished by experiments measuring how much parallelism is available in the code to start with. These experiments implied that even if we had infinite hardware, long instruction word architectures could not provide a speedup of more than a factor of 2 or 3 on real programs.
Protease‐Activated Receptors: A Means of Converting Extracellular Proteolysis into Intracellular Signals (2002)

Protease-activated receptors (PARs) mediate cellular responses to a variety of extracellular proteases. The four known PARs constitute a subgroup of the family of seven-transmembrane domain G protein-coupled receptors and activate intracellular signalling pathways typical for this family of receptors. Activation of PARs involves proteolytic cleavage of the extracellular domain, resulting in formation of a new N terminus, which acts as a tethered ligand. PAR-1, -3, and -4 are relatively selective for activation by thrombin whereas PAR-2 is activated by a variety of proteases, including trypsin and tryptase. Recent studies in mice genetically incapable of expressing specific PARs have defined roles for PAR-1 in vascular development, and for PAR-3 and -4 in platelet activation, which plays a fundamental role in blood coagulation. PAR-1 has also been implicated in a variety of other biological processes including inflammation, and brain and muscle development. Responses mediated by PAR-2 include contraction of intestinal smooth muscle, epithelium-dependent smooth muscle relaxation in the airways and vasculature, and potentiation of inflammatory responses. The area of PAR research is rapidly expanding our understanding of how cells communicate and control biological functions, in turn increasing our knowledge of disease processes and providing potential targets for therapeutic intervention.
Identification of BIME as a Subunit of the Anaphase-Promoting Complex (1996)

The initiation of anaphase and exit from mitosis require the activation of a proteolytic system that ubiquitinates and degrades cyclin B. The regulated component of this system is a large ubiquitin ligase complex, termed the anaphase-promoting complex (APC) or cyclosome. Purified Xenopus laevis APC was found to be composed of eight major subunits, at least four of which became phosphorylated in mitosis. In addition to CDC27, CDC16, and CDC23, APC contained a homolog of Aspergillus nidulans BIME, a protein essential for anaphase. Because mutation of bimE can bypass the interphase arrest induced by either nimA mutation or unreplicated DNA, it appears that ubiquitination catalyzed by APC may also negatively regulate entry into mitosis.
Echo decorrelation from displacement gradients in elasticity and velocity estimation (1999)

Several ultrasonic techniques for the estimation of blood velocity, tissue motion and elasticity are based on the estimation of displacement through echo time-delay analysis. A common assumption is that tissue displacement is constant within a short observation time used for time delay estimation (TDE). The precision of TDE is mainly limited by noise sources corrupting the echo signals. In addition to electronic and quantization noise, a substantial source of TDE error is the decorrelation of echo signals because of displacement gradients within the observation time. The authors present a theoretical model that describes the mean changes of the crosscorrelation function as a function of observation time and displacement gradient. The gradient is assumed to be small and uniform within the observation time; the decorrelation introduced by the lateral and elevational displacement components is assumed to be small compared with the decorrelation caused by the axial component. The decorrelation model predicts that the expected value of the crosscorrelation function is a low-pass filtered version of the autocorrelation function (i.e., the crosscorrelation obtained without gradients). The filter is a function of the axial gradient and the observation time. This theoretical finding is corroborated experimentally. Limitations imposed by decorrelation in displacement estimation and potential uses of decorrelation in medical ultrasound are discussed.
High-power laser source with spectrally beam-combined diode laser bars (2004)

Aculight has demonstrated spectral beam combining of four diode laser bars in a single optical cavity; each 1 cm wide diode bar included 200 individual single mode laser emitters. The beam combining was accomplished in the plane of the diode bar -- slow direction. In earlier work, Aculight has reported near diffraction limited performance from single diode laser bars where we have spectrally beam combined 200 laser emitters while maintaining a beam quality near the diffraction limit. Without spectral beam combination these diode laser bars will have a beam quality, in the plane of the bar, corresponding to an M<sup>2</sup> of 1000. In current work, Aculight is extending this technology to demonstrate a spectrally beam combined, diode laser system of 50 Watts, with near diffraction limited beam quality. To accommodate multiple diode laser bars, optical modeling was used to design and complete sensitivity analysis of a unique optical cavity based on the Schmidt telescope principal to remove off-axis aberrations. Error trees have been developed for beam quality and efficiency that illustrates just how the efficiency and beam quality have been maintained within this system.
rhBMP-2 (ACS and CRM Formulations) Overcomes Pseudarthrosis in a New Zealand White Rabbit Posterolateral Fusion Model (2007)

The 2 rhBMP-2 formulations led to significantly higher fusion rates and histologic bone formation than no graft and autograft controls in this pseudarthrosis repair model.
Complexing nickel(II) by cysteine, tyrosine, and related ligands and evidence for zwitterion reactivity (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTComplexing nickel(II) by cysteine, tyrosine, and related ligands and evidence for zwitterion reactivityJ. E. Letter Jr. and Robert B. JordanCite this: J. Am. Chem. Soc. 1975, 97, 9, 2381–2390Publication Date (Print):April 1, 1975Publication History Published online1 May 2002Published inissue 1 April 1975https://pubs.acs.org/doi/10.1021/ja00842a013https://doi.org/10.1021/ja00842a013research-articleACS PublicationsRequest reuse permissionsArticle Views177Altmetric-Citations13LEARN 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