gebhart/patrepeval huggingface dataset:
Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines (2007)

An epitope conservancy analysis tool was developed to analyze the variability or conservation of epitopes. The tool is user friendly, and is expected to aid in the design of epitope-based vaccines and diagnostics.
Direct Detection of Low-Concentration NO in Physiological Solutions by a New GaAs-Based Sensor (2001)

Nitric oxide (NO) acts as a signal molecule in the nervous system, as a defense against infections, as a regulator of blood pressure, and as a gate keeper of blood flow to different organs. In vivo, it is thought to have a lifetime of a few seconds. Therefore, its direct detection at low concentrations is difficult. We report on a new type of hybrid, organic-semiconductor, electronic sensor that makes detection of nitric oxide in physiological solution possible. The mode of action of the device is described to explain how its electrical resistivity changes as a result of NO binding to a layer of native hemin molecules. These molecules are self-assembled on a GaAs surface to which they are attached through a carboxylate binding group. The new sensor provides a fast and simple method for directly detecting NO at concentrations down to 1 microM in physiological aqueous (pH=7.4) solution at room temperature.
A Cost-effectiveness Analysis of Prophylaxis Against Deep-Vein Thrombosis in Major Orthopedic Surgery (1987)

A number of methods of prophylaxis can reduce the likelihood of postoperative deep-vein thrombosis in patients undergoing major orthopedic surgery. Using techniques of decision analysis, we examine the cost-effectiveness of several of these--warfarin sodium, low-dose subcutaneous heparin sodium, graduated compression stockings, intermittent pneumatic compression, heparin plus dihydroergotamine mesylate, and heparin plus stockings--compared with clinical diagnosis and treatment only. Our results show that 153 deaths per 10 000 patients occur when no prophylaxis is used; with most prophylaxis, this number is at least halved, and the most effective methods may reduce the number of deaths by three fourths. In addition, all of the prophylaxis considered are cost saving: average costs of care (including prophylaxis costs) are reduced by +19.40 to +181.60 per patient. Prophylaxis against deep-vein thrombosis in major orthopedic surgery therefore saves both lives and health care dollars.
CHEMISTRY OF SULFONYLMETHYL ISOCYANDES. 39. GENERATION OF 2,3-DIMETHYLENE-2,3-DIHYDROPYRROLE DERIVATIVES - INTERMEDIATES IN INTRAMOLECULAR AND INTERMOLECULAR DIELS-ALDER REACTIONS (1992)

Three different approaches are described for the generation of derivatives of 2,3-dimethylene-2,3-dihydropyrro 2, which are reactive intermediates in Diels-Alder cycloaddition reactions; one of the intramolecular cycloadditions provides a new tricyclo[3.2.1.0(2.7)]octane compound B.
Computerized Scanning Erbiumi:YAG Laser for Skin Resurfacing (1998)

Laser skin resurfacing has become increasingly popular as a method of facial rejuvenation. Although carbon dioxide (CO2) laser resurfacing is extremely effective, there is considerable morbidity associated with this procedure. Erbium (Er):YAG lasers, like CO2 lasers, are highly absorbed by water, and are absorbed superficially in skin. In our study of 141 patients using the computerized scanning Er:YAG laser, we found that it was possible to precisely ablate skin with less thermal injury than the currently available scanning CO2 lasers. The scanning system allowed very precise and homogeneous skin ablation. It was possible to ablate epidermis and superficial dermis, although deeper resurfacing led to pinpoint bleeding. Furthermore, healing was more rapid than generally experienced using CO2 lasers. Erythema was less marked, and disappeared usually within 3-4 weeks. Histological studies confirmed the minimal degree of thermal injury, as was evident clinically. Fluences of at least 20 J/cm2 were necessary to produce new collagen formation.
Reflexives and blocking effects in Iron Range English (2011)

In some, but not all, languages with long-distance reflexives, coreference with a higher nominal expression is “blocked” when an intervening expression does not match a lower expression for person. It is suggested that only languages without subject/verb agreement exhibit Blocking Effects. The fact that languages differ in terms of Blocking Effects suggests that binding and Blocking are separate processes (Cole &amp;amp; Sung 1994). I present new data from Iron Range English which challenges the generalization that blocking only occurs in languages without subject/verb agreement, but at the same time provides further evidence that binding and blocking are separate processes.
p-Bis(o-methylstyryl)benzene as a power-squared sensor for two-photon absorption measurements between 537 and 694 nm (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTp-Bis(o-methylstyryl)benzene as a power-squared sensor for two-photon absorption measurements between 537 and 694 nmS. M. Kennedy and F. E. LytleCite this: Anal. Chem. 1986, 58, 13, 2643–2647Publication Date (Print):November 1, 1986Publication History Published online1 May 2002Published inissue 1 November 1986https://pubs.acs.org/doi/10.1021/ac00126a014https://doi.org/10.1021/ac00126a014research-articleACS PublicationsRequest reuse permissionsArticle Views321Altmetric-Citations78LEARN 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
Relaxin modulates synthesis and secretion of procollagenase and collagen by human dermal fibroblasts. (1990)

Relaxin is believed to play a role in connective tissue remodeling during pregnancy (Bell, R.J., Eddie, L. W., Lester, A. R., Wood, E. C., Johnston, P.D., and Niall, H. D. (1987) Obstet. Gynecol. 69, 585-589; MacLennan, A. H. (1983) Clin. Reprod. Fertil. 2, 77-95). In the present study, normal human fibroblasts exposed to concentrations of a synthetic bioactive relaxin peptide from 0.1 to 10 ng/ml synthesized and secreted the metalloproteinase procollagenase, which was immunoprecipitable as a doublet of 52 and 57 kDa by a monoclonal antibody to human collagenase. The stimulation in procollagenase protein expression was reflected in an elevation in procollagenase mRNA levels. Media conditioned for 48 h by relaxin-treated fibroblasts (0.1 ng/ml) contained 1.7 units/ml activatable collagenase compared with 0.2 units/ml by untreated fibroblasts. In addition, relaxin caused a modest decrease in the levels of tissue inhibitor of metalloproteinases, as detected by reverse zymography and Northern analysis. Relaxin was also a potent modulator of the collagen secretory phenotype of these fibroblasts. Relaxin at 100 ng/ml down-regulated collagen secretion by 40%. When fibroblasts were treated simultaneously with cytokines such as transforming growth factor beta or interleukin 1 beta, which stimulated collagen synthesis to at least 9-fold of basal levels, relaxin at 100 ng/ml was able to down-regulate collagen expression by up to 88%. This decrease was reflected by changes at the mRNA level. These results indicate that relaxin can cause significant collagen turnover both by stimulating collagenase expression and by down-modulating collagen synthesis and secretion.
Pertussis vaccine inhibits immune insulitis induced with streptozotocin. (1982)

Normally, the injection of streptozotocin (STZ) at a lower dose (60 mg/kg body weight) to young (45 days old) CD-1 male mice produces a sustained hyperglycemia with the concomitant development of hypoinsulinemia and immune insulitis in the pancreas, both of which lead to insulin-dependent diabetes (IDD). In an effort to abort the development of IDD, pertussis vaccine (PV) was administered either intraperitoneally (n = 12) or intravenously (n = 12) 3 days prior to STZ injection. In contrast to the control group (n = 12) which received only STZ resulting in the subsequent development of IDD after 16 weeks, none of the vaccinated group developed IDD. The complete protective effect was evidenced by normal insulin values, normoglycemia, the lack of the development of nucleic acid antibody and the absence of insulitis in the vaccinated animals. Under these experimental conditions, PV appeared to offer satisfactory protection of the beta cells of islets in pancreas against the inflammatory effect of STZ.
Novel Potent Ligands for the Central Nicotinic Acetylcholine Receptor:  Synthesis, Receptor Binding, and 3D-QSAR Analysis (2000)

In the past few years the focus on central acetylcholine receptors has shifted from compounds with affinity for muscarinic acetylcholine receptors (mAChR) to compounds with affinity for nicotinic acetylcholine receptors (nAChR). The therapeutic potential includes treatment of a variety of diseases, e.g., Alzheimer's disease, Parkinson's disease, and Tourette's syndrome. This work describes the synthesis of six novel series of potent ligands with nanomolar affinity for the alpha4beta2 nAChR subtype. Structure-activity relationship (SAR) was evaluated by the calculation of a 3D-QSAR model. 3D-QSAR analysis of the compounds using the GRID/GOLPE methodology resulted in a model of high quality (R(2) = 0.97, Q(2) = 0.81). The coefficient plots reveal that the steric interactions between the target and our compounds are of major importance for the affinity. Bulky substituents in the 6-position of the pyridine ring will reduce the affinity of the compounds, whereas bulky ring systems including a sp(3)-nitrogen will increase the affinity of the compounds.
EXCRETION OF KYNURENIC ACID AND XANTHURENIC ACID DURING INFECTION (1971)

Urinary excretion of diazotizable amines in acute febrile disease was demonstrated 90 years ago. These substances were subsequently identified as metabolites of tryptophan via the kynurenine pathway and the hepatic enzyme tryptophan pyrrolase (TP) was established as a regulator of this pathway. Animal studies have previously shown that TP has a circadian periodicity of activity and can be induced by gram-negative infections in the intact animal. Steroid administration also can enhance TP activity whereas endotoxin inhibits TP. This study measured urinary excretion of kynurenic acid (KA) and xanthurenic acid (XA), two tryptophan metabolites via the kynurenine pathway, in 26 hospitalized children with a variety of febrile disorders and 10 age-matched control subjects. Increased excretion of these metabolites was noted in the febrile patients and was unrelated to etiology of the fever. Circadian periodicity in the excretion of these metabolites was observed in both normal and febrile individuals. Significant group periodicity was not noted for minimal and maximal excretory values did not occur synchronously in patients within any group. Two patients with endotoxic shock failed to exhibit an increased excretion of kynuremic acid and xanthurenic acid presumably because of inhibition of TP. A biochemical basis for the therapeutic use of exogenous corticosteroids in endotoxic shock is postulated.
ANTIGENIC STREPTOCOCCAL HEMOLYSIN (1932)

1. Normal serum, used in cultures for preparation of the streptolysin, modifies the properties of the streptolysin, causing delayed hemolysis, increased filterability, resistance to oxidation or reduction, and absence of antigenicity. 1. Streptolysin prepared without serum is an active antigen. 3. Similar temperatures are required to destroy the antigenic activity of serum-free streptolysin and the skin reactivity of Dick toxin. 4. Scarlet fever antitoxin contains antistreptolysin which does not neutralise serum streptolysin and which can be detected only by titration against serum-free streptolysin. 5. The antihemolysin which neutralises serum-free streptolysin is species-specific but not type-specific.
Design of a Partial Peptide Mimetic of Anginex with Antiangiogenic and Anticancer Activity (2003)

Based on structure-activity relationships of the angiostatic beta-sheet-forming peptide anginex, we have designed a mimetic, 6DBF7, which inhibits angiogenesis and tumor growth in mice. 6DBF7 is composed of a beta-sheet-inducing dibenzofuran (DBF)-turn mimetic and two short key amino acid sequences from anginex. This novel antiangiogenic molecule is more effective in vivo than parent anginex. In a mouse xenograft model for ovarian carcinoma, 6DBF7 is observed to reduce tumor growth by up to 80%. It is suggested that the activity is based on antiangiogenesis, because in vitro tube formation is inhibited, and because treatment of tumor-bearing mice led to a significant reduction in microvessel density within the tumor. This partial peptide mimetic is the first endothelial cell-specific molecule designed as a substitute for an angiostatic inhibitory peptide.
Human astrocyte production of tumour necrosis factor-α, interleukin-1β, and interleukin-6 following exposure to lipopolysaccharide endotoxin (1993)

The cytokines, tumour necrosis factor (TNF)-alpha, interleukin (IL)-1 beta, and IL-6, have been found in the human central nervous system. Recent studies have demonstrated that murine astrocytes produce these cytokines when induced with lipopolysaccharide endotoxin (LPS). The present study investigates the kinetics of TNF-alpha, IL-1 beta, and IL-6 production by normal adult human astrocytes when exposed to LPS.
Nanocomposite Hydrogels: A Unique Organic–Inorganic Network Structure with Extraordinary Mechanical, Optical, and Swelling/De-swelling Properties (2002)

Novel nanocomposite hydrogels (NC gels) with a unique organic–inorganic (clay) network structure (see Figure) have been synthesized by in-situ free radical polymerization. The resulting NC gels exhibit high structural homogeneity, superior elongation with near-complete recovery, good swellability, and rapid de-swelling in response to temperature changes.
Assessing total body and extracellular water from bioelectrical response spectroscopy (1997)

We developed and validated assessments for total body water (TBW) and extracellular water (ECW) by using two resistance values of a new electric circuit model (CM) (two resistors; a capacitor and an inductor) with or without body mass. Fluid shifts occurring after 40 min of supine rest did not increase the validity of either estimate. CM estimates were valid; r = 0.941 to 0.969, low SE of estimates of 1.15-2.28 kg, nonsignificant mean differences (CM - dilution; %delta = -0.4 to 1.3%) that were close to the expected measurement errors for TBW (+/- 1%) and ECW (+/- 5%), and Bland-Altman pairwise comparisons that showed equivalence between methods. The CM estimates of TBW and ECW had marginally better validity than the previously published bioimpedance models. The advantage of the CM model is its assessments of multiple fluid spaces and that it does not require gender-specific equations. We conclude that CM estimate of TBW is acceptable, whereas further validation is needed before the ECW estimate should be used in a clinical or research setting.
Recovery of a Fully Viable Chimeric Human Parainfluenza Virus (PIV) Type 3 in Which the Hemagglutinin-Neuraminidase and Fusion Glycoproteins Have Been Replaced by Those of PIV Type 1 (1998)

The recent recovery of human parainfluenza virus type 3 (PIV3) from cDNA, together with the availability of a promising, highly characterized live attenuated PIV3 vaccine virus, suggested a novel strategy for the rapid development of comparable recombinant vaccine viruses for human PIV1 and PIV2. The strategy, illustrated here for PIV1, is to create chimeric viruses in which the two protective antigens, the hemagglutinin-neuraminidase (HN) and fusion (F) envelope glycoproteins, of an attenuated PIV3 variant are replaced by those of PIV1 or PIV2. As a first step, this has been achieved by using recombinant wild-type (wt) PIV3 as the recipient for PIV1 HN and F, engineered so that each PIV1 open reading frame is flanked by the existing PIV3 nontranslated regions and transcription signals. This yielded a viable chimeric recombinant virus, designated rPIV3-1, that encodes the PIV1 HN and F glycoproteins in the background of the wt PIV3 internal proteins. There were three noteworthy findings. First, in contrast to recently reported glycoprotein replacement chimeras of vesicular somatitis virus or measles virus, the PIV3-1 chimera replicates in LLC-MK2 cells and in the respiratory tract of hamsters as efficiently as its PIV1 and PIV3 parents. This is remarkable because the HN and F glycoproteins share only 43 and 47%, respectively, overall amino acid sequence identity between serotypes. In particular, the cytoplasmic tails share only 9 to 11% identity, suggesting that their presumed role in virion morphogenesis does not involve sequence-specific contacts. Second, rPIV3-1 was found to possess biological properties derived from each of its parent viruses. Specifically, it requires trypsin for efficient plaque formation in tissue culture, like its PIV1 parent but unlike PIV3. On the other hand, it causes an extensive cytopathic effect (CPE) in LLC-MK2 cultures which resembles that of its PIV3 parent but differs from that of its noncytopathic PIV1 parent. This latter finding indicates that the genetic basis for the CPE of PIV3 in tissue culture lies outside regions encoding the HN or F glycoprotein. Third, it should now be possible to rapidly develop a live attenuated PIV1 vaccine by the staged introduction of known, characterized attenuating mutations present in a live attenuated PIV3 vaccine candidate into the PIV3-1 cDNA followed by recovery of attenuated derivatives of rPIV3-1.
Copper-Mediated Cross-Coupling of Aryl Boronic Acids and Alkyl Thiols (2000)

[reaction: see text] The cross-coupling of aryl boronic acids and alkanethiols mediated by copper(II) acetate and pyridine in anhydrous dimethylformamide affords aryl alkyl sulfides in good yield with a wide variety of substituted aryl boronic acids. The method is applicable to the synthesis of aryl sulfides of cysteine.
Lipoproteins inhibit macrophage activation by lipoteichoic acid (1999)

Regulation of lipid metabolism during infection is thought to be part of host defense, as lipoproteins neutralize endotoxin (LPS) and viruses. Gram-positive infections also induce disturbances in lipid metabolism. Therefore, we investigated whether lipoproteins could inhibit the toxic effects of lipoteichoic acid (LTA), a fragment of gram-positive bacteria. LTA activated RAW264.7 macrophage cells, stimulating production of tumor necrosis factor (TNF) in a dose-dependent matter, but produced less TNF than that seen after LPS activation. High density (HDL) or low density lipoprotein (LDL) alone inhibited the ability of LPS to stimulate TNF production, but had little effect on the activation by LTA. When a maximally effective dose of LTA was mixed with lipoproteins and 10% lipoprotein-depleted plasma (LPDP), the ability of LTA to stimulate macrophage production of TNF was inhibited. HDL, LDL, and the synthetic particle, Soyacal, when mixed with LPDP, were able to inhibit the ability of LTA to activate macrophages. Lipopolysaccharide-binding protein (LBP) substituted for LPDP in catalyzing lipoprotein neutralization of LTA by HDL. Antibody to LBP inhibited the ability of LPDP to induce LTA neutralization by HDL.Thus, lipoproteins can prevent macrophage activation by fragments from both gram-positive and gram-negative microorganisms.-Grunfeld, C., M. Marshall, J. K. Shigenaga, A. H. Moser, P. Tobias, and K. R. Feingold. Lipoproteins inhibit macrophage activation by lipoteichoic acid.
Characterization of a cDNA Encoding a Novel Human Golgi α1,2-Mannosidase (IC) Involved in N-Glycan Biosynthesis (2000)

A human cDNA encoding a 70.9-kDa type II membrane protein with sequence similarity to class I alpha1,2-mannosidases was isolated. The enzymatic properties of the novel alpha1,2-mannosidase IC were studied by expressing its catalytic domain in Pichia pastoris as a secreted glycoprotein. alpha1,2-Mannosidase IC sequentially hydrolyzes the alpha1,2-linked mannose residues of [(3)H]mannose-labeled Man(9)GlcNAc to form [(3)H]Man(6)GlcNAc and a small amount of [(3)H]Man(5)GlcNAc. The enzyme requires calcium for activity and is inhibited by both 1-deoxymannojirimycin and kifunensine. The order of mannose removal was determined by separating oligosaccharide isomers formed from pyridylaminated Man(9)GlcNAc(2) by high performance liquid chromatography. The terminal alpha1,2-linked mannose residue from the middle branch is the last mannose removed by the enzyme. This residue is the mannose cleaved from Man(9)GlcNAc(2) by the endoplasmic reticulum alpha1, 2-mannosidase I to form Man(8)GlcNAc(2) isomer B. The order of mannose hydrolysis from either pyridylaminated Man(9)GlcNAc(2) or Man(8)GlcNAc(2) isomer B differs from that previously reported for mammalian Golgi alpha1,2-mannosidases IA and IB. The full-length alpha1,2-mannosidase IC was localized to the Golgi of MDBK and MDCK cells by indirect immunofluorescence. Northern blot analysis showed tissue-specific expression of a major transcript of 3.8 kilobase pairs. The expression pattern is different from that of human Golgi alpha1,2-mannosidases IA and IB. Therefore, the human genome contains at least three differentially regulated Golgi alpha1, 2-mannosidase genes encoding enzymes with similar, but not identical specificities.
The Jak Kinases Differentially Associate with the α and β (Accessory Factor) Chains of the Interferon γ Receptor to Form a Functional Receptor Unit Capable of Activating STAT Transcription Factors (1995)

Interferon gamma (IFN gamma) induces the expression of early response genes by tyrosine phosphorylation of Jak kinases and transcription factors referred to as STAT proteins. The topology of the IFN gamma receptor is partially understood and the relationship between the alpha chain that binds the ligand and the beta chain that is required for signal transduction is undefined. In a cell line which expresses only the human alpha chain, we show that these cells did not activate Jak kinases or STAT proteins with human IFN gamma, even though Jak1 co-immunoprecipitated with the alpha chain. In cells unexposed to IFN gamma, Jak1 preferentially associated with the alpha chain, while Jak2 associated with the beta chain. There was evidence for Jak1 kinase activity in untreated cells. For Jak2, kinase activity was IFN gamma-dependent. Although the alpha chain was tyrosine-phosphorylated in response to ligand, we found no evidence for tyrosine phosphorylation of the beta chain. These data are consistent with a model of the IFN gamma receptor in which Jak1 associates with the alpha chain, whereas Jak2 associates with the beta chain. IFN gamma clusters at least two receptor units which results in the tyrosine phosphorylation of Jak1 and Jak2, the activation of Jak2 kinase activity, and the recruitment of STAT1 alpha resulting in its activation by tyrosine phosphorylation.