gebhart/patrepeval huggingface dataset:
Attempts to locate residues in complementarity-determining regions of antibody combining sites that make contact with antigen. (1976)

From collected data on variable region sequences of heavy chains of immunoglobulins, the probability of random associations of any two amino-acid residues in the complementarity-determining segments was computed, and pairs of residues occurring significantly more frequently than expected were selected by computer. Significant associations between Phe 32 and Tyr 33, Phe 32 and Glu 35, and Tyr 33 and Glu 35 were found in six proteins, all of which were mouse myeloma proteins which bound phosphorylcholine (= phosphocholine). From the x-ray structure of McPC603, Tyr 33 and Glu 35 are contacting residues; a seventh phosphorylcholine-binding mouse myeloma protein also contained Phe 32 and Tyr 33 but position 35 had only been determined as Glx and thus this position had not been selected. Met 34 occurred in all seven phosphorylcholine-binding myeoma proteins but was also present at this position in 29 other proteins and thus was not selected; it is seen in the x-ray structure not to be a contacting residue. The role of Phe 32 is not obvious but it could have some conformational influence. A human phosphorylcholine-binding myeloma protien also had Phe, Tyr, and Met at positions 32, 33, and 34, but had Asp instead of Glu at position 35 and showed a lower binding constant. The ability to use sequence data to locate residues in complementarity-determing segments making contact with antigenic determinants and those playing essentially a structural role would contribute substantially to the understanding of antibody specificity.
Demethylation of ITGAL (CD11a) regulatory sequences in systemic lupus erythematosus (2002)

DNA methylation changes occur in specific sequences that regulate LFA-1 expression in lupus T cells and in the hypomethylation model, indicating that altered methylation of specific genes may play a role in the pathogenesis of lupus.
Migraine: A Chronic Sympathetic Nervous System Disorder (2004)

The major finding of the present study is that migraine is a disorder of chronic sympathetic dysfunction, sharing many diagnostic and clinical characteristics with pure autonomic failure and multiple system atrophy. However, the sympathetic nervous system dysfunction in migraine differs from pure autonomic failure and multiple system atrophy in that occurs in an anatomically intact system. It is proposed that the sympathetic dysfunction in migraine relates to an imbalance of sympathetic co-transmitters. Specifically, it is suggested that a migraine attack is characterized by a relative depletion of sympathetic norepinephrine stores in conjunction with an increase in the release of other sympathetic cotransmitters such as dopamine, prostaglandins, adenosine triphosphate, and adenosine. An enhanced understanding of the sympathetic dysfunction in migraine may help to more effectively diagnose, prevent, and/or treat migraine and other types of headache.
Mutagenesis of the supF Gene of pSP189 Replicating in AD293 Cells Cocultivated with Activated Macrophages:  Roles of Nitric Oxide and Reactive Oxygen Species (2006)

Dysregulated production of nitric oxide (NO*) and reactive oxygen species by inflammatory cells contributes to mutagenesis and carcinogenesis. We have characterized mutagenesis in the target supF gene of pSP189 replicating in AD293 cells cocultivated with mouse macrophage-like RAW264.7 cells activated with interferon-gamma (IFN-gamma) and lipopolysaccharide (LPS). Activated macrophages produced substantial amounts of NO*, superoxide anion (O2*-), and hydrogen peroxide (H2O2) over 12-72 h periods. A time-dependent decrease in total cell number and a 3.7-fold increase in supF mutation frequency (MF), compared with unstimulated controls, were observed at 72 h. The increase in MF was effectively suppressed by N-methyl-L-arginine monoacetate (NMA), an NO* synthase inhibitor, and also by superoxide dismutase (SOD) and catalase (CAT); cotreatment with NMA and SOD/CAT suppressed mutagenesis by 87% at 72 h. Mutations in supF were mainly multiple sequence changes (47%) and single base pair substitutions (51%) following IFN-gammaLPS activation. Following cotreatment with NMA alone or together with SOD/CAT, however, single base pair substitutions were prevalent (70 and 85%); decreased multiple mutations were observed (24 and 11%). Almost all single base pair substitutions induced under all exposure conditions occurred at G:C base pairs (87.8-94.6%). Whereas those induced by all treatments consisted predominantly of G:C to T:A transversions, G:C to T:A and A:T to T:A transversions were less frequent following treatment with NMA alone or with SOD/CAT compared to those induced by activated macrophages without additional treatment. Our results strongly suggest that ONOO- or its derivatives generated by reaction of NO* with O2*- may have been a major contributor to the observed mutagenesis by the activated macrophages, and mitigating their effects might serve a preventive function in ameliorating cancer risks associated with prolonged inflammation.
Psoralen Photochemotherapy of Cutaneous Disorders (1980)

Due to the massive data sets available for drug candidates, modern drug discovery has advanced to the big data era. Central to this shift is the development of artificial intelligence approaches to implementing innovative modeling based on the dynamic, ...Read More
Systematic identification of immunodominant CD8+T-cell responses to influenza A virus in HLA-A2 individuals (2011)

Immunodominant T-cell responses are important for virus clearance. However, the identification of immunodominant T-cell peptide + HLA glycoprotein epitopes has been hindered by the extent of HLA polymorphism and the limitations of predictive algorithms. A simple, systematic approach has been used here to screen for immunodominant CD8(+) T-cell specificities. The analysis targeted healthy HLA-A2(+) donors to allow comparison with responses to the well-studied influenza matrix protein 1 epitope. Although influenza matrix protein 1 was consistently detected in all individual samples in our study, the response to this epitope was only immunodominant in three of eight, whereas for the other five, prominent CD8(+) T-cell responses tended to focus on various peptides from the influenza nucleoprotein that were not presented by HLA-A2. Importantly, with the four immunodominant T-cell epitopes identified here, only one would have been detected by the current prediction programs. The other three peptides would have been either considered too long or classified as not containing typical HLA binding motifs. Our data stress the importance of systematic analysis for discovering HLA-dependent, immunodominant CD8(+) T-cell epitopes derived from viruses and tumors. Focusing on HLA-A2 and predictive algorithms may be too limiting as we seek to develop targeted immunotherapy and vaccine strategies that depend on T cell-mediated immunity.
Parametric investigation of latch-up sensitivity in 1.25 μm CMOS technology (1987)

The dependence of latch-up sensitivity in 1.25 μm p-well, CMOS devices on layout parameters, backside contacts, and thickness of epitaxial layers has been investigated by analysis and testing using a specially designed test chip. Retrograde wells and small source-to-substrate/well contact spacings play a critical role in suppressing latch-up, especially in non-epitaxial devices, by reducing the gains of vertical transistors. The backside contact directs high currents to the n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> source without developing large IR drops underneath the p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> source, thereby increasing the holding current. The epitaxial layer devices exhibit the holding voltages substantially higher than the ones for the non-epitaxial devices. Analyses and measurements have shown that the vertical transistors are in the-active mode at latch-up in the epitaxial devices in contrast with the saturation mode in the non-epitaxial devices. There exists an optimum epitaxial layer thickness, at which the holding voltage is a maximum. The optimum spacing is primarily determined by the n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> to p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> source spacing.
Proteins of the Rpf Family: Immune Cell Reactivity and Vaccination Efficacy against Tuberculosis in Mice (2003)

It was shown recently that Mycobacterium tuberculosis expresses five proteins that are homologous to Rpf (resuscitation promoting factor), which is secreted by growing cells of Micrococcus luteus. Rpf is required to resuscitate the growth of dormant Micrococcus luteus organisms, and its homologues may be involved in mycobacterial reactivation. Mycobacterial Rpf-like products are secreted proteins, which makes them candidates for recognition by the host immune system and anti-Rpf immune responses potentially protective against reactivated tuberculosis. Here we report that the Rpf protein itself and four out of five of its mycobacterial homologues, which were administered as subunit vaccines to C57BL/6 mice, are highly immunogenic. Rpf-like proteins elicit immunoglobulin G1 (IgG1) and IgG2a responses and T-cell proliferation and stimulate production of gamma interferon, interleukin-10 (IL-10), and IL-12 but not IL-4 or IL-5. Both humoral and T-cell responses against these antigens show a high degree of cross-reactivity. Vaccination of mice with Rpf-like proteins results in a significant level of protection against a subsequent high-dose challenge with virulent M. tuberculosis H37Rv, both in terms of survival times and mycobacterial multiplication in lungs and spleens.
Total Synthesis of Taxol. 1. Retrosynthesis, Degradation, and Reconstitution (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTotal Synthesis of Taxol. 1. Retrosynthesis, Degradation, and ReconstitutionK. C. Nicolaou, P. G. Nantermet, H. Ueno, R. K. Guy, E. A. Couladouros, and E. J. SorensenCite this: J. Am. Chem. Soc. 1995, 117, 2, 624–633Publication Date (Print):January 1, 1995Publication History Published online1 May 2002Published inissue 1 January 1995https://pubs.acs.org/doi/10.1021/ja00107a006https://doi.org/10.1021/ja00107a006research-articleACS PublicationsRequest reuse permissionsArticle Views5570Altmetric-Citations156LEARN 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-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
γ-γ Cross-linking sites in human and bovine fibrin (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTγ-γ Cross-linking sites in human and bovine fibrinRenne Chen and Russell F. DoolittleCite this: Biochemistry 1971, 10, 24, 4486–4491Publication Date (Print):November 1, 1971Publication History Published online1 May 2002Published inissue 1 November 1971https://pubs.acs.org/doi/10.1021/bi00800a021https://doi.org/10.1021/bi00800a021research-articleACS PublicationsRequest reuse permissionsArticle Views261Altmetric-Citations223LEARN 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
A Subset of Human Dendritic Cells Expresses IgA Fc Receptor (CD89), Which Mediates Internalization and Activation Upon Cross-Linking by IgA Complexes (2001)

Immature dendritic cells (DC) sample Ags within nonlymphoid tissues and acquire exogenous proteins/pathogens via scavenger receptors or Ig FcR such as Fc gamma R and Fc epsilon R. IgA is present in a significant proportion among serum Ig and is the main isotype in mucosae, where DC are numerous. We found that a functional Fc alpha R (CD89) was expressed in situ and in vitro on interstitial-type DC but not on Langerhans cell-type DC. Interstitial-type DC expressed CD89 as a 50- to 75-kDa glycoprotein with a 32-kDa protein core, which was down-regulated upon addition of TGF-beta 1. DC, Fc alpha R specifically, bound IgA1 and IgA2. Cross-linking of CD89 on DC triggered endocytosis in time-dependent manner. In addition, internalization of polymeric IgA complexes induced the production of IL-10 and DC activation, as reflected by up-regulation of CD86 costimulatory molecules, class II MHC expression, and increased allostimulatory activity. Therefore, interstitial-type DC may use Fc alpha R-mediated Ag sampling in the subepithelium to check tissue integrity while Langerhans cells inside epithelial layers may neglect IgA immune complexes.
Synthesis of 3-Epi-6,7-dideoxyxestobergsterol A. (2000)

3-Epi-6,7-dideoxyxestobergsterol A (2), an analogue of xestobergsterol A, has been synthesized from dehydroepiandrosterone (3) in 15 steps. The key synthetic intermediate, 15beta,16alpha-dioxypregn-17(20)E-ene derivative 8, was prepared from the corresponding 15beta,16beta-epoxide 6 by treating with acetic acid and titanium tetraisopropoxide. The 23-oxo side chain was constructed stereoselectively by orthoester Claisen rearrangement of 8 followed by introduction of an isobutyl group. Basic treatment of the 15,23-diketone 12 followed by deprotection gave the title compound 2.
A serum-derived hyaluronan-associated protein (SHAP) is the heavy chain of the inter alpha-trypsin inhibitor. (1993)

We showed previously that hyaluronan (HA) synthesized by cultured fibroblasts firmly bound 85-kDa proteins. The proteins were derived from serum used for the culture and appeared to be covalently linked to HA (Yoneda, M., Suzuki, S., and Kimata, K. (1990) J. Biol. Chem. 265, 5247-5257). In these regards, we named this molecule SHAP (serum-derived HA associated proteins). Incubation of serum with exogenous HA under physiological conditions enabled us to prepare SHAP.HA complex without cell cultivation. The complex thus obtained from bovine or human serum was served for the characterization of SHAP. Digestion with HA-lyase and subsequent separation on SDS-polyacrylamide gel electrophoresis yielded two components, X and Y. Because of the block of their NH2 termini, peptides were obtained by the digestion of X and Y with V8 protease, separated on SDS-polyacryl-amide gel electrophoresis and then subjected to the analysis. Peptides from X and Y showed a high degree of sequence similarity to the two heavy chains, HC2 and HC1, of human inter-alpha-trypsin inhibitor (ITI), respectively (over 80% with bovine SHAP and essentially 100% with human SHAP). Cross-reactivity with antibodies against ITI supported the findings. Direct digestion of the complex with V8 protease and the subsequent purification of the HA-resistant fragment complex were performed to identify the HA-binding domains. NH2-terminal sequences of the fragments suggested the participation of the COOH-terminal half of ITI with an amphipathic alpha helix structure in the HA binding.
Phosphodiesterase 4 Inhibitors in Inflammatory Bowel Disease: A Comprehensive Review (2010)

Inflammatory bowel disease (IBD) is known as a chronic inflammation of gastrointestinal tract that its pathogenesis still is not completely understood. Several drug categories are used for management of IBD but there is no exact cure for the disease, however biological drugs targeting the inflammation of gut are on the center of attention. In investigation into the anti-inflammatory drugs, phosphodiesterase inhibitors were found to be effective in different inflammatory disorders. Of them phosphodiesterase 4 (PDE4) inhibitors are considered for treatment of asthma and chronic obstructive pulmonary disease (COPD). Some of PDE4 inhibitors showed promising efficacy in animal studies, however to date no phase III clinical study showed their effectiveness in IBD. The present study has the most relevant studies in this field. PDE4 inhibitors affect IBD in different ways including anti-inflammatory, anti-depressant, and anti-fibrotic effects. Unfortunately, the most common side effect of PDE4 inhibitors is nausea which limits its use. Tetomilast the second generation of PDE4 inhibitors showed promising effects in phase II studies with better safety profile. Other drugs in this class are ongoing phase II and III trials.
Stabilization of Osteochondral Fragments Using Limited Placement of Cyanoacrylate in Rabbits (1988)

The higher homologues of the alkyl-2-cyanoacrylates appear to possess properties useful for an osseous adhesive. Considering currently available bonding strengths, the most reasonable potential application of an osseous adhesive would appear to involve the stabilization of relatively small osteochondral fragments. If used as a means of temporary internal fixation, such an adhesive would need to be used in limited amounts in limited areas to allow for normal healing processes to occur between areas of adhesive placement. An animal study was therefore conducted utilizing the viscous isoamyl-2-cyanoacrylate monomer to evaluate its ability to maintain the reduction of an unstable osteochondral fragment while allowing for healing around the sites of adhesive placement. Used in limited quantities, this monomer appeared to allow adjacent healing to occur unimpeded and to be nontoxic to adjacent viable bone and cartilage. This adhesive also appeared to lend significant stability to the reduction of an osteochondral fragment in the knees of a series of rabbits.
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes (2005)

We have conducted a comprehensive search for conserved elements in vertebrate genomes, using genome-wide multiple alignments of five vertebrate species (human, mouse, rat, chicken, and Fugu rubripes). Parallel searches have been performed with multiple alignments of four insect species (three species of Drosophila and Anopheles gambiae), two species of Caenorhabditis, and seven species of Saccharomyces. Conserved elements were identified with a computer program called phastCons, which is based on a two-state phylogenetic hidden Markov model (phylo-HMM). PhastCons works by fitting a phylo-HMM to the data by maximum likelihood, subject to constraints designed to calibrate the model across species groups, and then predicting conserved elements based on this model. The predicted elements cover roughly 3%-8% of the human genome (depending on the details of the calibration procedure) and substantially higher fractions of the more compact Drosophila melanogaster (37%-53%), Caenorhabditis elegans (18%-37%), and Saccharaomyces cerevisiae (47%-68%) genomes. From yeasts to vertebrates, in order of increasing genome size and general biological complexity, increasing fractions of conserved bases are found to lie outside of the exons of known protein-coding genes. In all groups, the most highly conserved elements (HCEs), by log-odds score, are hundreds or thousands of bases long. These elements share certain properties with ultraconserved elements, but they tend to be longer and less perfectly conserved, and they overlap genes of somewhat different functional categories. In vertebrates, HCEs are associated with the 3' UTRs of regulatory genes, stable gene deserts, and megabase-sized regions rich in moderately conserved noncoding sequences. Noncoding HCEs also show strong statistical evidence of an enrichment for RNA secondary structure.
Selective reduction of T cells bearing invariant V alpha 24J alpha Q antigen receptor in patients with systemic sclerosis. (1995)

A novel subset of T cells characterized by the expression of an invariant T cell antigen receptor (TCR) encoded by V alpha 24J alpha Q gene segments was investigated in patients with systemic sclerosis (SSc). Polymerase chain reaction analysis demonstrated that the V alpha 24 TCR repertoire was selectively used in CD4-CD8- double-negative T cells both in patients and in healthy individuals, while almost all families of TCR V alpha were expressed in single-positive T cell fractions. The V alpha 24+ double-negative T cells were increased by approximately fivefold in patients. However, sequence analysis clearly showed significant differences in the V alpha 24 TCR repertoire dominating in patients and healthy donors. In healthy individuals, the invariant V alpha 24J alpha Q was expanded and comprised 20-50% of the total TCR-alpha, while their selective reduction was observed in SSc patients who also showed expansion of invariant V alpha 24 TCR other than V alpha 24J alpha Q. Analogous to murine invariant V alpha 14J alpha 281 TCR, these results suggest that T cells with invariant V alpha 24J alpha Q TCR would function as regulatory T cells, whereas T cells bearing other invariant V alpha 24 TCR in SSc patients could be autoaggressive T cells in nature.
BAFF Augments Certain Th1-Associated Inflammatory Responses (2005)

B cell-activating factor belonging to the TNF family (BAFF; BLyS) is a critical regulator of B cell maturation and survival, and its overexpression in BAFF transgenic (Tg) mice results in the development of autoimmune disorders. BAFF also affects T cell function through binding to one of the BAFF receptors, BAFF-R. Using BAFF Tg mice, we examined a typical Th1-mediated response, the cutaneous delayed-type hypersensitivity reaction, and found a much greater degree of paw swelling and inflammation than in control mice. Importantly, delayed-type hypersensitivity scores correlated directly with BAFF levels in serum. Conversely, in a Th2-mediated model of allergic airway inflammation, BAFF Tg mice were largely protected and showed markedly reduced Ag-specific T cell proliferation and eosinophil infiltration associated with the airways. Thus, local and/or systemically distributed BAFF affects Th1 and Th2 responses and impacts on the course of some T cell-mediated inflammatory reactions. Our results are consistent with the idea that BAFF augments T cell as well as B cell responses, particularly Th1-type responses. Results in BAFF Tg mice may reflect the situation in certain autoimmune patients or virally infected individuals, because BAFF levels in blood are comparable.