gebhart/patrepeval huggingface dataset:
The lectin‐complement pathway – its role in innate immunity and evolution (2004)

Innate immunity was formerly thought to be a non-specific immune response characterized by phagocytosis. However, innate immunity has considerable specificity and is capable of discriminating between pathogens and self. Recognition of pathogens is mediated by a set of pattern recognition receptors, which recognize conserved pathogen-associated molecular patterns (PAMPs) shared by broad classes of microorganisms, thereby successfully defending invertebrates and vertebrates against infection. Lectins, carbohydrate-binding proteins, play an important role in innate immunity by recognizing a wide range of pathogens. Mannose-binding lectin (MBL) and ficolin are lectins composed of a lectin domain attached to collagenous region. However, they use a different lectin domain: a carbohydrate recognition domain (CRD) is responsible for MBL and a fibrinogen-like domain for ficolin. These two collagenous lectins are pattern recognition receptors, and upon recognition of the infectious agent, they trigger the activation of the lectin-complement pathway through attached serine proteases, MBL-associated serine proteases (MASPs). A similar lectin-based complement system, consisting of the lectin-protease complex and C3, is present in ascidians, our closest invertebrate relatives, and functions in an opsonic manner. We isolated several lectins homologous to MBLs and ficolins and several MASPs in invertebrates and lower vertebrates, and herein we discuss the molecular evolution of these molecules. Based on these findings, it seems likely that the complement system played a pivotal role in innate immunity before the evolution of an acquired immune system in jawed vertebrates.
MMDB: annotating protein sequences with Entrez's 3D-structure database (2006)

Three-dimensional (3D) structure is now known for a large fraction of all protein families. Thus, it has become rather likely that one will find a homolog with known 3D structure when searching a sequence database with an arbitrary query sequence. Depending on the extent of similarity, such neighbor relationships may allow one to infer biological function and to identify functional sites such as binding motifs or catalytic centers. Entrez's 3D-structure database, the Molecular Modeling Database (MMDB), provides easy access to the richness of 3D structure data and its large potential for functional annotation. Entrez's search engine offers several tools to assist biologist users: (i) links between databases, such as between protein sequences and structures, (ii) pre-computed sequence and structure neighbors, (iii) visualization of structure and sequence/structure alignment. Here, we describe an annotation service that combines some of these tools automatically, Entrez's 'Related Structure' links. For all proteins in Entrez, similar sequences with known 3D structure are detected by BLAST and alignments are recorded. The 'Related Structure' service summarizes this information and presents 3D views mapping sequence residues onto all 3D structures available in MMDB (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=structure).
17 beta-estradiol-induced increases in glucose-regulated protein 78kD and 94kD protect human breast cancer T47-D cells from thermal injury. (1997)

Heat shock alters the susceptibility of tumor cells to chemotherapeutic agents. We conducted experiments to study the regulation of expression of heat shock proteins (HSP) in 17 beta-estradiol-treated T47-D cells, a human breast cancer cell line. Cells exposed to 17 beta-estradiol for 24-48 h displayed increased expression of glucose regulated protein 78kD (GRP-78) and 94kD (GRP-94), as shown by [35S]methionine incorporation and Western blotting experiments. The increase was time (5 h to 48 h)-dependent at 1 nM and 1 microM 17 beta-estradiol. Cells overexpressing GRP-78 and -94 after treatment with 17 beta-estradiol displayed resistance against heat shock (47 degrees C for 50 min)-induced death. Removal of external Ca2+ or treatment of cells with BAPTA (a Ca2+ chelator) did not alter the synthesis of GRP-78 and -94, suggesting that the 17 beta-estradiol effect on the synthesis of GRP-78 and -94 is Ca(2+)-independent. In addition, exposure of cells to 17 beta-estradiol up to 100 microM did not increase [Ca2+]i, which further supports the view that the estrogen-induced GRPs are not regulated by [Ca2+]i. Treatment with H89 (a protein kinase A inhibitor, 1 microM, 30 min) or GF-109203X (a protein kinase C inhibitor, 1 microM, 30 min) also did not change the GRP synthesis, indicating that protein kinase A and C are not involved in regulation of GRP synthesis.
Preliminary report of a clinical trial supporting the sequential use of an attenuated E39 peptide (E39') to optimize the immunologic response to the FBP (E39+GM-CSF) vaccine (2015)

Meeting abstracts Folate Binding Protein (FBP) is overexpressed in breast, endometrial, and ovarian cancers. E39 (FBP191-199, EIWTHSYKV) is an HLA-A2 restricted FBP peptide vaccine already shown to generate significant in vivo immunologic response (IR) in a Phase I/IIa trial in endometrial and
Effect of Topical PPARβ/δ and PPARγ Agonists on Plaque Psoriasis (2003)

With the reservations due to the limited nature of this pilot trial, it seems that these topical PPARbeta/delta and gamma agonists do not exert a strong antipsoriatic effect when used alone at 0.5%.
Periodontal regeneration Current status and directions (1994)

The challenge of periodontal regeneration has become a central issue in periodontal research and practice. The objective, of course, is to reconstitute the biologic complex of cementum, periodontal ligament, and alveolar bone onto the root surfaces associated with marginal periodontitis. In this book, premier investigators and clinicians, contending that standard treatment techniques do not result in periodontal regeneration, approach the problem from a biologic perspective
Critiquing Physician Decision Making Using Data from Automated Medical Records: Assessing the Limitations. (1990)

Abstract
This paper describes the evaluation of a critiquing system, HYPERCRITIC, that relies on automated medical records for its data input. The purpose of HYPERCRITIC is to offer comments to general practitioners on their treatment of hypertension. HYPERCRITIC has access to the data stored in a primary-care information system that supports a fully automated medical record. Medical records of 20 patients with hypertension were submitted to both physicians and HYPERCRITIC. The critique generated by the physicians was subsequently compared to the critique generated by HYPERCRITIC. Of the 260 comments made by the majority of the physicians, 118 were also made by HYPERCRITIC. The reasons why HYPERCRITIC failed to reproduce the remaining 142 comments are evaluated.
Nuclear Transplantation in the Mouse Embryo by Microsurgery and Cell Fusion (1983)

Nuclear transplantation in the mouse embryo was achieved by using a method that combines microsurgical removal of the zygote pronuclei with the introduction of a donor nucleus by a virus-mediated cell fusion technique. Survival of embryos was greater than 90 per cent in tests of this procedure. The embryos developed to term at a frequency not significantly different from that of nonmanipulated control embryos. Because nuclei and cytoplasm from genetically distinct inbred mouse strains can be efficiently interchanged, this procedure may be useful in characterizing possible cytoplasmic contributions to the embryonic and adult phenotype.
Selective Inhibition of Tumor Growth by Clonal NK Cells Expressing an ErbB2/HER2-Specific Chimeric Antigen Receptor (2014)

Natural killer (NK) cells are an important effector cell type for adoptive cancer immunotherapy. Similar to T cells, NK cells can be modified to express chimeric antigen receptors (CARs) to enhance antitumor activity, but experience with CAR-engineered NK cells and their clinical development is still limited. Here, we redirected continuously expanding and clinically usable established human NK-92 cells to the tumor-associated ErbB2 (HER2) antigen. Following GMP-compliant procedures, we generated a stable clonal cell line expressing a humanized CAR based on ErbB2-specific antibody FRP5 harboring CD28 and CD3ζ signaling domains (CAR 5.28.z). These NK-92/5.28.z cells efficiently lysed ErbB2-expressing tumor cells in vitro and exhibited serial target cell killing. Specific recognition of tumor cells and antitumor activity were retained in vivo, resulting in selective enrichment of NK-92/5.28.z cells in orthotopic breast carcinoma xenografts, and reduction of pulmonary metastasis in a renal cell carcinoma model, respectively. γ-irradiation as a potential safety measure for clinical application prevented NK cell replication, while antitumor activity was preserved. Our data demonstrate that it is feasible to engineer CAR-expressing NK cells as a clonal, molecularly and functionally well-defined and continuously expandable cell therapeutic agent, and suggest NK-92/5.28.z cells as a promising candidate for use in adoptive cancer immunotherapy.
Identification of Multiple HLA-DR-Restricted Epitopes of the Tumor-Associated Antigen CAMEL by CD4+ Th1/Th2 Lymphocytes (2004)

CD4(+) Th cells play an important role in the induction and maintenance of adequate CD8(+) T cell-mediated antitumor responses. Therefore, identification of MHC class II-restricted tumor antigenic epitopes is of major importance for the development of effective immunotherapies with synthetic peptides. CAMEL and NY-ESO-ORF2 are tumor Ags translated in an alternative open reading frame from the highly homologous LAGE-1 and NY-ESO-1 genes, respectively. In this study, we investigated whether CD4(+) T cell responses could be induced in vitro by autologous, mature dendritic cells pulsed with recombinant CAMEL protein. The data show efficient induction of CAMEL-specific CD4(+) T cells with mixed Th1/Th2 phenotype in two healthy donors. Isolation of CD4(+) T cell clones from the T cell cultures of both donors led to the identification of four naturally processed HLA-DR-binding CAMEL epitopes: CAMEL(1-20), CAMEL(14-33), CAMEL(46-65), and CAMEL(81-102). Two peptides (CAMEL(1-20) and CAMEL(14-33)) also contain previously identified HLA class I-binding CD8(+) T cell epitopes shared by CAMEL and NY-ESO-ORF2 and are therefore interesting tools to explore for immunotherapy. Furthermore, two CD4(+) T cell clones that recognized the CAMEL(14-33) peptide with similar affinities were shown to differ in recognition of tumor cells. These CD4(+) T cell clones recognized the same minimal epitope and expressed similar levels of adhesion, costimulatory, and inhibitory molecules. TCR analysis demonstrated that these clones expressed identical TCR beta-chains, but different complementarity-determining region 3 loops of the TCR alpha-chains. Introduction of the TCRs into proper recipient cells should reveal whether the different complementarity-determining region 3 alpha loops are important for tumor cell recognition.
Identification of the sensory neuron specific regulatory region for the mouse gene encoding the voltage‐gated sodium channel NaV1.8 (2008)

Voltage-gated sodium channels (VGSC) are critical membrane components that participate in the electrical activity of excitable cells. The type one VGSC family includes the tetrodotoxin insensitive sodium channel, Na(V)1.8, encoded by the Scn10a gene. Na(V)1.8 expression is restricted to small and medium diameter nociceptive sensory neurons of the dorsal root ganglia and cranial sensory ganglia. To understand the stringent transcriptional regulation of the Scn10a gene, the sensory neuron specific promoter was functionally identified. While identifying the mRNA 5'-end, alternative splicing within the 5'-UTR was observed to create heterogeneity in the RNA transcript. Four kilobases of upstream genomic DNA was cloned and the presence of tissue specific promoter activity was tested by microinjection and adenoviral infection of fluorescent protein reporter constructs into primary mouse and rat neurons, and cell lines. The region contained many putative transcription factor-binding sites and strong homology with the predicted rat ortholog. Homology to the predicted human ortholog was limited to the proximal end and several conserved cis elements were noted. Two regulatory modules were identified by microinjection of reporter constructs into dorsal root ganglia and superior cervical ganglia neurons: a neuron specific proximal promoter region between -1.6 and -0.2 kb of the transcription start site cluster, and a distal sensory neuron switch region beyond -1.6 kb that restricted fluorescent protein expression to a subset of primary sensory neurons.
Induction of Human T Lymphocyte Cytotoxicity and Inhibition of Tumor Growth by Tumor-Specific Diabody-Based Molecules Secreted from Gene-Modified Bystander Cells (2003)

Infiltrating T cells are found in many malignancies, but they appear to be mostly anergic and do not attack the tumor, presumably because of the absence of activation and/or costimulatory signals. We describe a strategy for cellular antitumor immunotherapy by the in situ production of soluble bifunctional Ab-based molecules that activate and retarget T cells to the tumor. We genetically modified cells to simultaneously secrete two bifunctional molecules, a bispecific diabody directed against the carcinoembryonic Ag (CEA) and the CD3 epsilon chain of the TCR (alphaCEA x alphaCD3), and a fusion protein comprising the extracellular portion of B7-1 fused to a bivalent anti-CEA diabody (B7-alphaCEA). Together, alphaCEA x alphaCD3 and B7-alphaCEA proved potent at inducing the activation, proliferation, and survival of primary human T cells. When producer cells were cocultured with primary T cells and CEA(+) cancer cells, alphaCEA x alphaCD3 and B7-alphaCEA acted in combination to activate and retarget T cell cytotoxicity and completely abrogate tumor growth in the coculture. Furthermore, the introduction of just a few such producer cells at the tumor site efficiently inhibited the growth of established human colon carcinoma xenografts. Despite a cumbersome generation process, the use of autologous gene-modified producer cells opens the way for a new diabody-based gene therapy strategy of cancer.
Attacks on WebView in the Android system (2011)

WebView is an essential component in both Android and iOS platforms, enabling smartphone and tablet apps to embed a simple but powerful browser inside them. To achieve a better interaction between apps and their embedded "browsers", WebView provides a number of APIs, allowing code in apps to invoke and be invoked by the JavaScript code within the web pages, intercept their events, and modify those events. Using these features, apps can become customized "browsers" for their intended web applications. Currently, in the Android market, 86 percent of the top 20 most downloaded apps in 10 diverse categories use WebView.
Global data association for multi-object tracking using network flows (2008)

We propose a network flow based optimization method for data association needed for multiple object tracking. The maximum-a-posteriori (MAP) data association problem is mapped into a cost-flow network with a non-overlap constraint on trajectories. The optimal data association is found by a min-cost flow algorithm in the network. The network is augmented to include an Explicit Occlusion Model(EOM) to track with long-term inter-object occlusions. A solution to the EOM-based network is found by an iterative approach built upon the original algorithm. Initialization and termination of trajectories and potential false observations are modeled by the formulation intrinsically. The method is efficient and does not require hypotheses pruning. Performance is compared with previous results on two public pedestrian datasets to show its improvement.
Nivolumab plus Ipilimumab versus Sunitinib in Advanced Renal-Cell Carcinoma (2018)

Overall survival and objective response rates were significantly higher with nivolumab plus ipilimumab than with sunitinib among intermediate- and poor-risk patients with previously untreated advanced renal-cell carcinoma. (Funded by Bristol-Myers Squibb and Ono Pharmaceutical; CheckMate 214 ClinicalTrials.gov number, NCT02231749 .).
Operation Characteristics of a Side-Light-Injection Multiple-Quantum-Well Bistable Laser for All-Optical Switching (1994)

An InGaAs/InAlAs side-light-injection multiple-quantum-well bistable laser for all-optical switching has been developed. It consists of one main bistable laser and two waveguides perpendicular to the main laser. Saturable absorption and gain quenching are used for set and reset operations. The voltages applied to the gain quenching and saturable absorption regions, which are located at the intersections of the main laser and the waveguide regions, are +1.00 and +0.29 V, respectively. As the input light intensity ( 1.55 µm range) increases, the turn-on and turn-off times decrease. The turn-on time is 200 ps when the input light peak intensity is 1 mW and the turn-off time is 2 ns when the input light peak intensity is 200 mW. The experimental results are supported by numerical simulation. Higher differential gain material is expected to enable faster switching speed.
Lymphocyte transformation and the number of antigen-responsive cells in humans. (1981)

The lymphocyte transformation response of normal human subjects to the antigen streptokinase/streptodornase (SK/SD) was analyzed by quantitating antigen-responsive cells (ARC), estimating the first generation lymphocyte response (FGLR), and performing standard lymphocyte transformation assays at different time points. Unlike the results obtained with the nonspecific mitogen phytohemagglutinin (PHA), the response to SK/SD appeared to depend almost entirely on the participation of progeny lymphocytes derived from a small number (mean of 21.3 +/- 5.8 per 100,000 mononuclear cells) of cells initially sensitive to the antigen. Similar peak lymphocyte transformation responses were obtained for the 2 stimuli, although those to SK/SD occurred later. Lymphocyte transformation data obtained after a shorter than optimal culture period (6 days) appeared to be a better estimate of ARC than the data obtained at the peak of the response of ARC than the data obtained at the peak of the responses did. However, ARC were best estimated by determining the FGLR or the number of days required for the lymphocyte transformation response to reach its peak.
Induction of semantic classes from natural language text (2001)

Many applications dealing with textual information require classification of words into semantic classes (or concepts). However, manually constructing semantic classes is a tedious task. In this paper, we present an algorithm, UNICON, for UNsupervised Induction of CONcepts. Some advantages of UNICON over previous approaches include the ability to classify words with low frequency counts, the ability to cluster a large number of elements in a high-dimensional space, and the ability to classify previously unknown words into existing clusters. Furthermore, since the algorithm is unsupervised, a set of concepts may be constructed for any corpus.
Protective antigenic determinant of streptococcal M protein shared with sarcolemmal membrane protein of human heart. (1982)

We present definitive evidence that at least one protective antigenic determinant on type 5 M protein of group A streptococci evokes antibody that is cross-reactive with human heart tissue. One of nine rabbits immunized with a peptide fragment of type 5 M protein (pep M5) produced antibody that cross-reacted by immunofluorescence with sarcolemmal membranes of human heart. The cross-reactive antibody could be removed by absorbing the antiserum with sarcolemmal membranes, types 5 and 19 streptococci, or their pepsin-extracted M proteins, but with no other serotypes tested. Although each of the pep M5 immune sera was opsonic for type 5 streptococci, only the heart-reactive antiserum opsonized type 19 streptococci. The opsonization of type 19 streptococci was abolished by absorbing the antiserum with sarcolemmal membranes isolated from human heart tissue. Purified heart-reactive antibodies eluted from sarcolemmal membranes opsonized both types 5 and 19 streptococci, indicating that the heart cross-reactive determinant of type 5 M protein is cross-protective. The cross-reactive antigen was purified by affinity chromatography from detergent extracts of sarcolemmal membranes and determined to be a complex protein composed of four subunits apparently linked by disulfide bonds.
Myocardial infarction redefined—A consensus document of The Joint European Society of Cardiology/American College of Cardiology Committee for the Redefinition of Myocardial Infarction (2000)

This document was developed by a consensus conference initiated by Kristian Thygesen, MD, and Joseph S. Alpert, MD, after formal approval by Lars Rydén, MD, President of the European Society of Cardiology (ESC), and Arthur Garson, MD, President of the American College of Cardiology (ACC). All of the participants were selected for their expertise in the field they represented, with approximately one-half of the participants selected from each organization. Participants were instructed to review the scientific evidence in their area of expertise and to attend the consensus conference with prepared remarks. The first draft of the document was prepared during the consensus conference itself. Sources of funding appear in Appendix A. The recommendations made in this document represent the attitudes and opinions of the participants at the time of the conference, and these recommendations were revised subsequently. The conclusions reached will undoubtedly need to be revised as new scientific evidence becomes available. This document has been reviewed by members of the ESC Committee for Scientific and Clinical Initiatives and by members of the Board of the ESC who approved the document on April 15, 2000.*
Parahydrogen and synthesis allow dramatically enhanced nuclear alignment (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTParahydrogen and synthesis allow dramatically enhanced nuclear alignmentC. Russell Bowers and D. P. WeitekampCite this: J. Am. Chem. Soc. 1987, 109, 18, 5541–5542Publication Date (Print):September 1, 1987Publication History Published online1 May 2002Published inissue 1 September 1987https://pubs.acs.org/doi/10.1021/ja00252a049https://doi.org/10.1021/ja00252a049research-articleACS PublicationsRequest reuse permissionsArticle Views2698Altmetric-Citations830LEARN 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