gebhart/patrepeval huggingface dataset:
Current therapeutic paradigm for the treatment of non-Hodgkin's lymphoma. (2000)

Patients with indolent non-Hodgkin's lymphoma may be treated with various approaches ranging from deferred initial therapy (watch and wait) to single-agent alkylating agents, radiation therapy, or combination chemotherapy. None of these approaches have produced curative results. Clearly, innovative treatment strategies are needed. The use of interferon, monoclonal antibodies with or without radioisotopes, purine analogues, and even high-dose therapy with stem-cell rescue are under investigation. Based on the fact that fewer than 40% of advanced-stage, aggressive non-Hodgkin's lymphoma patients are cured with cyclophosphamide/doxorubicin/vincristine/prednisone chemotherapy, the best approach for any patient is an experimental one. Examples include: (1) increasing the dose intensity of drugs used in standard regimens; (2) preventing the development of drug resistance; (3) combining monoclonal antibodies with chemotherapy; or (4) autologous stem-cell transplantation as a rescue from marrow-ablative chemotherapy. If a patient is not eligible or does not wish to participate in a clinical trial, cyclophosphamide/doxorubicin/vincristine/prednisone, as inadequate as it is, remains the gold standard.
Automatic construction of an effective training set for prioritizing static analysis warnings (2010)

In order to improve ineffective warning prioritization of static analysis tools, various approaches have been proposed to compute a ranking score for each warning. In these approaches, an effective training set is vital in exploring which factors impact the ranking score and how. While manual approaches to build a training set can achieve high effectiveness but suffer from low efficiency (i.e., high cost), existing automatic approaches suffer from low effectiveness. In this paper, we propose an automatic approach for constructing an effective training set. In our approach, we select three categories of impact factors as input attributes of the training set, and propose a new heuristic for identifying actionable warnings to automatically label the training set. Our empirical evaluations show that the precision of the top 22 warnings for Lucene, 20 for ANT, and 6 for Spring can achieve 100% with the help of our constructed training set.
Human acetylcholine receptor presentation in myasthenia gravis. DR restriction of autoimmune T epitopes and binding of synthetic receptor sequences to DR molecules. (1994)

Autoimmune Th cells in myasthenia gravis recognize several sequence regions of the human muscle acetylcholine receptor (AChR). Most AChR Th epitopes are presented by HLA class II DR molecules (DR). Four sequence regions of the AChR alpha-subunit form Th epitopes recognized by most myasthenic patients, irrespective of their DR haplotype. In this study we first identified in five myasthenic patients the DR molecule(s) likely to be involved in presentation of T immunodominant AChR sequences. We then investigated the binding to the affinity purified DR molecules thus identified (DR2/w51, DR4/w53, and DR7/w53) and to the DR1 molecule, of a panel of overlapping synthetic peptides screening the human alpha-subunit sequence, previously used to identify AChR Th epitopes in myasthenic patients. The AChR peptides that stimulated anti-AChR autoimmune Th cells all bound the relevant DR molecules. Some AChR peptides never recognized by Th cells of myasthenic patients also bound well to one or more DR molecules. The relative ability to bind to DR molecules of different sequence regions of the AChR, i.e., an autoantigen, agrees well with the results of previous studies on the DR binding of synthetic sequences of exogenous antigens. Some peptide sequences uniquely bound one DR molecule, others bound several DR molecules, and others did not bind any of the DR molecules tested.
PCR primer: a laboratory manual. (2003)

Introduction to PCR sample preparation RNA PCR methods detection of PCR products - specialized applications analysis of differential gene expression by PCR cloning by PCR cloning of PCR products mutagenesis by PCR.
RTP Payload for Text Conversation (2000)

This memo describes how to carry text conversation session contents in RTP packets. Text conversation session contents are specified in ITU-T Recommendation T.140 [1].
Phylogenetic analysis of a highly specific association between ectosymbiotic, sulfur-oxidizing bacteria and a marine nematode (1994)

The phylogenetic relationship of chemoautotrophic, sulfur-oxidizing, ectosymbiotic bacteria growing on a marine nematode, a Laxus sp. (formerly a Catanema sp.), to known endosymbionts and free-living bacteria was determined. Comparative 16S rRNA sequencing was used to investigate the unculturable nematode epibionts, and rRNA-targeted oligonucleotide hybridization probes were used to identify the ectosymbionts in situ. Both analyses revealed a remarkably specific and stable symbiosis. Unique hybridization of a specific probe to the ectosymbionts indicated that only one species of bacteria was present and growing on the cuticle of the nematode. Distance and parsimony methods used to infer phylogenetic trees both placed the nematode ectosymbionts at the base of a branch containing chemoautotrophic, sulfur-oxidizing endosymbionts of three bivalve families and of the tube worm Riftia pachyptila. The most closely related free-living bacteria were chemoautotrophic sulfur oxidizers belonging to the genus Thiomicrospira. Furthermore, our results suggested that a second, only distantly related group of thioautotrophic endosymbionts has as its deepest branch surface-colonizing bacteria belonging to the genus Thiothrix, some of which are capable of sulfur-oxidizing chemoautotrophic growth.
Methods used in the structure determination of bovine mitochondrial F1 ATPase (1996)

With a size of 372 kDa, the F(1) ATPase particle is the largest asymmetric structure solved to date. Isomorphous differences arising from reacting the crystals with methyl-mercury nitrate at two concentrations allowed the structure determination. Careful data collection and data processing were essential in this process as well as a new form of electron-density modification, 'solvent flipping'. The most important feature of this new procedure is that the electron density in the solvent region is inverted rather than set to a constant value, as in conventional solvent flattening. All non-standard techniques and variations on new techniques which were employed in the structure determination are described.
Norovirus Gastroenteritis (2009)

Noroviruses are now recognized as the leading cause of epidemics of gastroenteritis and an important cause of sporadic gastroenteritis among both children and adults. In the United States, more than 90% of the outbreaks of gastroenteritis for which the cause could not previously be identified can now be attributed to this virus. Understanding the nature of immunity to the norovirus is a key determinant for future improvements in the control and prevention of this viral infection.
<title>Unique symbol for marking and tracking very small semiconductor products</title> (1991)

The problem of tracking very small semiconductor products with a bar code is easily overcome by the use of the matrix symbol, which is a unique two-dimensional symbol that is the most space efficient method of packing binary data. It is both machine written and machine read to provide the utmost in accuracy and repeatability. The number of data cells can either be expanded or contracted to handle the required information and in addition can contain parity and error correcting codes. Semiconductor chips, wafers, substrates, modules and even masks can all be laser marked with this symbol and quickly read at any later stage of the manufacturing process. This unique symbol is computer generated by a software algorithm which creates the data cells and data frame which are laser etched on the product. On-line product identification yields immediate benefits in manufacturing such as inventory control, proper mating of parts, proper selection of test programs, quality control, etc. Use of a very small unique machine readable symbol now permits these benefits to be extended to miniature parts in an automated high speed manufacturing line.
ASR error detection using recurrent neural network language model and complementary ASR (2014)

Detecting automatic speech recognition (ASR) errors can play an important role for effective human-computer spoken dialogue system, as recognition errors can hinder accurate system understanding of user intents. Our goal is to locate errors in an utterance so that the dialogue manager can pose appropriate clarification questions to the users. We propose two approaches to improve ASR error detection: (1) using recurrent neural network language models to capture long-distance word context within and across previous utterances; (2) using a complementary ASR system. The intuition is that when two complementary ASR systems disagree on a region in an utterance, this region is most likely an error. We train a neural network predictor of errors using a variety of features. We performed experiments on both English and Iraqi Arabic ASR and observed significant improvement in error detection using the proposed methods.
Nucleolin Is a Matrix Attachment Region DNA-Binding Protein That Specifically Recognizes a Region with High Base-Unpairing Potential (1995)

A DNA affinity column containing a synthetic double-stranded nuclear matrix attachment region (MAR) was used to purify a 100-kDa protein from human erythroleukemia K562 cells. This protein was identified as nucleolin, the key nucleolar protein of dividing cells, which is thought to control rRNA gene transcription and ribosome assembly. Nucleolin is known to bind RNA and single-stranded DNA. We report here that nucleolin is also a MAR-binding protein. It binds double-stranded MARs from different species with high affinity. Nucleolin effectively distinguishes between a double-stranded wild-type synthetic MAR sequence with a high base-unpairing potential and its mutated version that has lost the unpairing capability but is still A+T rich. Thus, nucleolin is not merely an A+T-rich sequence-binding protein but specifically binds the base-unpairing region of MARs. This binding specificity is similar to that of the previously cloned tissue-specific MAR-binding protein SATB1. Unlike SATB1, which binds only double-stranded MARs, nucleolin binds the single-stranded T-rich strand of the synthetic MAR probe approximately 45-fold more efficiently than its complementary A-rich strand, which has an affinity comparable to that of the double-stranded form of the MAR. In contrast to the high selectivity of binding to double-stranded MARs, nucleolin shows only a small but distinct sequence preference for the T-rich strand of the wild-type synthetic MAR over the T-rich strand of its mutated version. The affinity to the T-rich synthetic MAR is severalfold higher than to its corresponding RNA and human telomere DNA. Quantitative cellular fractionation and extraction experiments indicate that nucleolin is present both as a soluble protein and tightly bound to the matrix, similar to other known MAR-binding proteins.
Prolonged treatment with the specific 5-HT-uptake inhibitor citalopram: effect on dopaminergic and serotonergic functions. (1984)

The effect of prolonged administration of the clinically effective and specific serotonin (5-HT)-uptake-inhibitor, citalopram, has been studied in rats on behavioural measures of dopaminergic (DA) and serotonergic activity and on DA D-2, 5-HT2, alpha 1- and beta-adrenergic receptor number and affinity in vitro. Thirteen days treatment with citalopram in the diet (40 mg/kg/day) did not change receptor binding for either of the ligands studied, although citalopram was detected in high concentrations in brain and plasma and induced a 75% depletion of 5-HT in whole blood. This citalopram dose-regimen was followed by a potentiated hypermotility response to d-amphetamine. Also DA-dependent hypermotility induced by methylphenidate and (+)-3-PPP was increased. In contrast, the 5-HT2-receptor mediated head shake syndrome induced by 1-5-HTP or quipazine was decreased after prolonged citalopram treatment. Two weeks oral bolus treatment (10 mg/kg once or twice daily) with the 5-HT-uptake-inhibitors citalopram, fluoxetine, zimelidine, cyanimipramine or paroxetine induced d-amphetamine potentiation, whereas amitriptyline, nortriptyline, imipramine, iprindole, and mianserin treatment showed no effect. It is suggested that d-amphetamine potentiation induced by citalopram is mainly dependent on DA mechanisms, and that this profile is characteristic for preferential 5-HT-uptake-inhibitors. The lack of correlation between behavioural effect and receptor changes was important. Since citalopram has been shown to have clinical antidepressant activity, it is concluded that down-regulation of beta-adrenoceptors is not a prerequisite for antidepressant action.
Comparison of mobile host protocols for IP (1993)

Host mobility is becoming an increasingly important feature with the recent arrival of notebook and palm top computers, the development of wireless network interfaces and the implementation of the global network. This paper describes and compares three proposals from Sony, IBM and Columbia University for mobile host protocols (MHP) that are compatible with the TCP/IP protocol suite. A set of basic requirements for a MHP are also suggested and it is observed that none of the three proposals entirely satisfies these requirements. Each proposal has faults in their implementation of mobile network layer functionality. Moreover, it is noted they do not address problems that must be solved in both higher and lower layers. Key Words: Mobile Protocols, Wireless Networks, Networks, IP 1 Introduction Computers are no longer large, expensive, and nonportable. Recent developments make it possible to buy inexpensive notebook and palm top computers that are both portable and extremely powerful. As a...
Size-Dependent Catalytic Activity of Zeolite-Supported Iridium Clusters (2006)

Iridium carbonyl clusters approximated as Ir2(CO)8, Ir4(CO)12, and Ir6(CO)16 were synthesized by carbonylation under various conditions of Ir(CO)2(acac) sorbed in the cages of zeolite NaY. These supported clusters were decarbonylated by treatment in helium and used to catalyze ethene hydrogenation at atmospheric pressure and temperatures up to 80 °C. Extended X-ray absorption fine structure (EXAFS) spectroscopy was used to characterize the decarbonylated clusters, which are approximated as Ir2, Ir4, and Ir6, respectively. The data are consistent with the inference that these clusters are the catalytically active species. The catalytic activities and apparent activation energies for ethene hydrogenation depend significantly on the cluster size, with the identity of the most active of the three catalysts depending on the temperature. There appears to be no simple explanation for the variation in catalytic performance with cluster size.
Irreversible Inactivation of Trypanothione Reductase by Unsaturated Mannich Bases:  A Divinyl Ketone as Key Intermediate (2005)

Trypanothione reductase is a flavoenzyme unique to trypanosomatid parasites. Here we show that unsaturated Mannich bases irreversibly inactivate trypanothione reductase from Trypanosoma cruzi, the causative agent of Chagas' disease. The inhibitory potency of the compounds strongly increased upon storage of the DMSO stock solutions. HPLC, NMR, and mass spectrometry data of potential intermediates revealed a divinyl ketone as the active compound inactivating the enzyme. ESI- and MALDI-TOF mass spectrometry of trypanothione reductase modified by the Mannich base or the divinyl ketone showed specific alkylation of the active site Cys52 by a 5-(2'chlorophenyl)-3-oxo-4-pentenyl substituent. The reaction mechanism and the site of alkylation differ from those in Plasmodium falciparum thioredoxin reductase where the C-terminal redox active dithiol is modified. After deamination, unsaturated Mannich bases are highly reactive in polycondensation with trypanothione. Interaction of these compounds with both trypanothione and trypanothione reductase could account for their potent trypanocidal effect against Trypanosoma brucei.
Structure and Biosynthesis of Staphyloxanthin from Staphylococcus aureus (2005)

Most Staphylococcus aureus strains produce the orange carotenoid staphyloxanthin. The staphyloxanthin biosynthesis genes are organized in an operon, crtOPQMN, with a sigma(B)-dependent promoter upstream of crtO and a termination region downstream of crtN. The functions of the five encoded enzymes were predicted on the basis of their sequence similarity to known enzymes and by product analysis of gene deletion mutants. The first step in staphyloxanthin biosynthesis is the head-to-head condensation of two molecules of farnesyl diphosphate to form dehydrosqualene (4,4'-diapophytoene), catalyzed by the dehydrosqualene synthase CrtM. The dehydrosqualene desaturase CrtN dehydrogenates dehydrosqualene to form the yellow, main intermediate 4,4'-diaponeurosporene. CrtP, very likely a mixed function oxidase, oxidizes the terminal methyl group of 4,4'-diaponeurosporene to form 4,4'-diaponeurosporenic acid. CrtQ, a glycosyltransferase, esterifies glucose at the C(1)'' position with the carboxyl group of 4,4'-diaponeurosporenic acid to yield glycosyl 4,4'-diaponeurosporenoate; this compound was the major product in the clone expressing crtPQMN. In the final step, the acyltransferase CrtO esterifies glucose at the C(6)'' position with the carboxyl group of 12-methyltetradecanoic acid to yield staphyloxanthin. Staphyloxanthin overexpressed in Staphylococcus carnosus (pTX-crtOPQMN) and purified was analyzed by high pressure liquid chromatography-mass spectroscopy and NMR spectroscopy. Staphyloxanthin was identified as beta-D-glucopyranosyl 1-O-(4,4'-diaponeurosporen-4-oate)-6-O-(12-methyltetradecanoate).
Polymers at Interfaces J. Am. Chem. Soc. 1996, 118, 297 (1996)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTPolymers at Interfaces J. Am. Chem. Soc. 1996, 118, 297G. J. Fleer and Cite this: J. Am. Chem. Soc. 1996, 118, 43, 10678Publication Date (Web):October 30, 1996Publication History Published online30 October 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ja965442ihttps://doi.org/10.1021/ja965442icorrectionACS PublicationsCopyright © 1996 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views303Altmetric-Citations1LEARN 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 PDF (20 KB) Get e-Alertsclose Get e-Alerts
The Plant-Growth-Promoting Rhizobacterium Paenibacillus polymyxa Induces Changes in Arabidopsis thaliana Gene Expression: A Possible Connection Between Biotic and Abiotic Stress Responses (1999)

This paper addresses changes in plant gene expression induced by inoculation with plant-growth-promoting rhizobacteria (PGPR). A gnotobiotic system was established with Arabidopsis thaliana as model plant, and isolates of Paenibacillus polymyxa as PGPR. Subsequent challenge by either the pathogen Erwinia carotovora (biotic stress) or induction of drought (abiotic stress) indicated that inoculated plants were more resistant than control plants. With RNA differential display on parallel RNA preparations from P. polymyxa-treated or untreated plants, changes in gene expression were investigated. From a small number of candidate sequences obtained by this approach, one mRNA segment showed a strong inoculation-dependent increase in abundance. The corresponding gene was identified as ERD15, previously identified to be drought stress responsive. Quantification of mRNA levels of several stress-responsive genes indicated that P. polymyxa induced mild biotic stress. This suggests that genes and/or gene classes associated with plant defenses against abiotic and biotic stress may be co-regulated. Implications of the effects of PGPR on the induction of plant defense pathways are discussed.
Regulation of urokinase receptors in monocytelike U937 cells by phorbol ester phorbol myristate acetate. (1989)

A specific surface receptor for urokinase plasminogen activator (uPA) recognizes the amino-terminal growth factor-like sequence of uPA, a region independent from and not required for the catalytic activity of this enzyme. The properties of the uPA receptor (uPAR) and the localization and distribution of uPA in tumor cells and tissues suggest that the uPA/uPAR interaction may be important in regulating extracellular proteolysis-dependent processes (e.g., invasion, tissue destruction). Phorbol myristate acetate (PMA), an inducer of U937 cell differentiation to macrophage-like cells, elicits a time- and concentration-dependent increase in the number of uPAR molecules as shown by binding, cross-linking, and immunoprecipitation studies. The effect of PMA is blocked by cycloheximide. Overall, the data indicate that PMA increases the synthesis of uPA. PMA treatment also causes a decrease in the affinity of the uPAR for uPA, thus uncovering another way of regulating the interaction between uPA and uPAR. In addition, the PMA treatment causes a modification of migration of the cross-linked receptor in mono- and bidimensional gel electrophoresis.
3‐Iodothyronamine: a modulator of the hypothalamus‐pancreas‐thyroid axes in mice (2012)

BACKGROUND AND PURPOSE Preclinical pharmacology of 3-iodothyronamine (T1AM), an endogenous derivative of thyroid hormones, indicates that it is a rapid modulator of rodent metabolism and behaviour. Since T1AM undergoes rapid enzymatic degradation, particularly by MAO, we hypothesized that the effects of T1AM might be altered by inhibition of MAO. EXPERIMENTAL APPROACH We investigated the effects of injecting T1AM (i.c.v.) on (i) feeding behaviour, hyperglycaemia and plasma levels of thyroid hormones and (ii) T1AM systemic bioavailability, in overnight fasted mice, under control conditions and after pretreatment with the MAO inhibitor clorgyline. T1AM (1.3, 6.6, 13, 20 and 26 µg·kg(-1) ) or vehicle were injected i.c.v. in fasted male mice not pretreated or pretreated i.p. with clorgyline (2.5 mg·kg(-1) ). Glycaemia was measured by a glucorefractometer, plasma triiodothyronine (fT3) by a chemiluminescent immunometric assay, c-fos activation immunohistochemically and plasma T1AM by HPLC coupled to tandem-MS. KEY RESULTS T1AM, 1.3 µg·kg(-1) , produced a hypophagic effect (-24% vs. control) and reduced c-fos activation. This dose showed systemic bioavailability (0.12% of injected dose), raised plasma glucose levels and reduced peripheral insulin sensitivity (-33% vs. control) and plasma fT3 levels. These effects were not linearly related to the dose injected. Clorgyline pretreatment strongly increased the systemic bioavailability of T1AM and prevented the hyperglycaemia and reduction in fT3 induced by T1AM. CONCLUSIONS AND IMPLICATIONS T1AM induces central and peripheral effects including hyperglycaemia and a reduction in plasma fT3 levels in fasted mice. These effects critically depend on the concentration of T1AM or its metabolites in target organs.