gebhart/patrepeval huggingface dataset:
Prediction of the Coding Sequences of Unidentified Human Genes. III. The Coding Sequences of 40 New Genes (KIAA0081-KIAA0120) Deduced by Analysis of cDNA Clones from Human Cell Line KG-1 (1995)

We isolated full-length cDNA clones from size-fractionated cDNA libraries of human immature myeloid cell line KG-1, and the coding sequences of 40 genes were newly predicted. A computer search of the GenBank/EMBL databases indicated that the sequences of 14 genes were unrelated to any reported genes, while the remaining 26 genes carried some sequences with similarities to known genes. Significant transmembrane domains were identified in 17 genes, and protein motifs that matched those in the PROSITE motif database were identified in 11 genes. Northern hybridization analysis with 18 different cells and tissues demonstrated that 10 genes were apparently expressed in a cell-specific or tissue-specific manner. Among the genes predicted, half were isolated from the medium-sized cDNA library and the other half from the small-sized cDNA library, and their average sizes were 4 kb and 1.4 kb, respectively. As judged by Northern hybridization profiles, small-sized cDNAs appeared to be expressed more ubiquitously and abundantly in various tissues, compared with that of medium-sized cDNAs.
Drug Interactions Involving Immunologic Agents Part I. Vaccine–Vaccine, Vaccine–Immunoglobulin, and Vaccine–Drug Interactions (1990)

Information about immunologic drug interactions is needed by pharmacists to make rational drug-use decisions. Previously, reports of interactions involving vaccines, immune globulins, and immunodiagnostic reagents were widely dispersed. In this two-part review article, over 50 individual and categorical interactions are described, as are dozens of vaccine-vaccine and vaccine-immunoglobulin, and vaccine-drug interactions are reviewed in this first part. Vigilance by all pharmacists is needed to detect previously unreported immunologic drug interactions and to further assess known interactions.
EZH2 is a marker of aggressive breast cancer and promotes neoplastic transformation of breast epithelial cells (2003)

The Polycomb Group Protein EZH2 is a transcriptional repressor involved in controlling cellular memory and has been linked to aggressive prostate cancer. Here we investigate the functional role of EZH2 in cancer cell invasion and breast cancer progression. EZH2 transcript and protein were consistently elevated in invasive breast carcinoma compared with normal breast epithelia. Tissue microarray analysis, which included 917 samples from 280 patients, demonstrated that EZH2 protein levels were strongly associated with breast cancer aggressiveness. Overexpression of EZH2 in immortalized human mammary epithelial cell lines promotes anchorage-independent growth and cell invasion. EZH2-mediated cell invasion required an intact SET domain and histone deacetylase activity. This study provides compelling evidence for a functional link between dysregulated cellular memory, transcriptional repression, and neoplastic transformation.
Left-Right Asymmetry and Kinesin Superfamily Protein KIF3A: New Insights in Determination of Laterality and Mesoderm Induction by kif3A−/− Mice Analysis (1999)

KIF3A is a classical member of the kinesin superfamily proteins (KIFs), ubiquitously expressed although predominantly in neural tissues, and which forms a heterotrimeric KIF3 complex with KIF3B or KIF3C and an associated protein, KAP3. To elucidate the function of the kif3A gene in vivo, we made kif3A knockout mice. kif3A-/- embryos displayed severe developmental abnormalities characterized by neural tube degeneration and mesodermal and caudal dysgenesis and died during the midgestational period at approximately 10.5 dpc (days post coitum), possibly resulting from cardiovascular insufficiency. Whole mount in situ hybridization of Pax6 revealed a normal pattern while staining by sonic hedgehog (shh) and Brachyury (T) exhibited abnormal patterns in the anterior-posterior (A-P) direction at both mesencephalic and thoracic levels. These results suggest that KIF3A might be involved in mesodermal patterning and in turn neurogenesis.
Identification and induction of keratinocyte-derived IL-10 (1992)

It has previously been demonstrated that the epidermis is a rich source of proinflammatory cytokines and growth factors and that complex interactions between these factors may affect inflammatory responses in skin. To investigate whether IL-10 (cytokine synthesis inhibitory factor) is part of this complex process, RNA was extracted from normal epidermis at various times after application of various chemicals to murine skin and mRNA signals for IL-10 were sought using a quantitative reverse-transcriptase-polymerase chain reaction technique. IL-10 signal strength was normalized to that of beta-actin in each sample. IL-10 mRNA signals were occasionally identified in normal epidermis but were uniformly enhanced 4 h after hapten application, and were maximal after 12 h. Contact allergens induced IL-10 mRNA signals whereas vehicles and irritants did not. Depletion of Langerhans cells, Thy-1+ dendritic epidermal cells, and T lymphocytes demonstrated that keratinocytes were the main source of IL-10 mRNA. IL-10 signals were also detected in mRNA derived from PAM 212 (spontaneously transformed keratinocyte) cells. IL-10 protein could be detected by immunoprecipitation, with an IL-10 mAB, of supernatants obtained 16 h after cultured epidermal cells were coupled with hapten. This study demonstrates that murine keratinocytes are capable of producing IL-10 mRNA and protein, and that signal strength of IL-10 mRNA is enhanced by hapten application.
Serum opsonins to serogroup B meningococci after disease and vaccination. (1991)

In this review the results of three previous studies are compared and discussed. Sera from 101 patients with meningococcal disease and from 113 volunteers immunized twice with vaccine preparations against serogroup B meningococci were examined for antimeningococcal opsonic activity using a chemiluminescence (CL) method. Twelve groups of vaccinees were immunized twice with one of four different doses of an outer membrane vesicle (OMV) preparation either alone or complexed to serogroup C polysaccharide and/or the adjuvant Al(OH)3. The OMV vaccine strain (44/76) was a patient isolate characterized as B:15:P1.16. The 89 surviving patients and 97/113 volunteers responded with significantly increased opsonic activity to the vaccine strain. Sera from all vaccinees with low preimmunization levels demonstrated a significant postimmunization increase in opsonic activity. The vaccine response was dose related, and the second injection induced a booster response in those who received preparations containing Al(OH)3. At 26 weeks a reduction in opsonic activity to preimmunization levels was noted in 19/97 previous responders. The reduction was less pronounced in those who were immunized with the higher doses. Using CL and flow cytometry we found vaccinee sera to show cross reacting opsonin responses to other serogroups and serotypes of meningococci except meningococci of serotype 2a and 2b. The increase in antimeningococcal opsonins after vaccination suggests that the serogroup B OMV vaccine may induce protection against clinical disease.
Biology and biochemistry of the chemokines: a family of chemotactic and inflammatory cytokines. (1992)

Studies conducted in many laboratories over the past several years have resulted in the identification and initial characterization of a large superfamily of structurally and functionally related inflammatory cytokines. This superfamily currently includes 14 distinct members: platelet factor 4, beta-thromboglobulin, neutrophil activating peptide-1/interleukin-8, gro, IP-10, mig, ENA-78, macrophage inflammatory proteins-1 alpha and -1 beta, monocyte chemoattractant protein-1/JE, RANTES, HC-14, C-10, and I-309. Although numerous biological activities have been assigned to these molecules, a common theme is their ability to stimulate the chemotactic migration of distinct sets of cells, including neutrophils, monocytes, lymphocytes, and fibroblasts. Accumulating evidence indicates that these molecules play important roles in mediating cell recruitment and activation necessary for inflammation and the repair of tissue damage.
Molecular Organization of the Alkali-insoluble Fraction ofAspergillus fumigatus Cell Wall (2000)

Physical and biological properties of the fungal cell wall are determined by the composition and arrangement of the structural polysaccharides. Cell wall polymers of fungi are classically divided into two groups depending on their solubility in hot alkali. We have analyzed the alkali-insoluble fraction of the Aspergillus fumigatus cell wall, which is the fraction believed to be responsible for fungal cell wall rigidity. Using enzymatic digestions with recombinant endo-beta-1,3-glucanase and chitinase, fractionation by gel filtration, affinity chromatography with immobilized lectins, and high performance liquid chromatography, several fractions that contained specific interpolysaccharide covalent linkages were isolated. Unique features of the A. fumigatus cell wall are (i) the absence of beta-1,6-glucan and (ii) the presence of a linear beta-1, 3/1,4-glucan, never previously described in fungi. Galactomannan, chitin, and beta-1,3-glucan were also found in the alkali-insoluble fraction. The beta-1,3-glucan is a branched polymer with 4% of beta-1,6 branch points. Chitin, galactomannan, and the linear beta-1, 3/1,4-glucan were covalently linked to the nonreducing end of beta-1, 3-glucan side chains. As in Saccharomyces cerevisiae, chitin was linked via a beta-1,4 linkage to beta-1,3-glucan. The data obtained suggested that the branching of beta-1,3-glucan is an early event in the construction of the cell wall, resulting in an increase of potential acceptor sites for chitin, galactomannan, and the linear beta-1,3/1,4-glucan.
Protein chemical shift analysis: a practical guide (1998)

Proper protein chemical shift analysis requires careful experimental measurements and the implementation of standardized referencing procedures. In this article we outline the steps necessary to ensure proper chemical shift referencing and the selection criteria for choosing appropriate "random coil" amino acid chemical shift values for predicting, comparing, and assigning 1 H, 13 C, and 15 N resonances in proteins. By making use of these standardized conditions we demonstrate how several recently developed methods, namely homologous assignment techniques and empirical chemical shift contour maps (or hypersurfaces), can significantly improve the accuracy of chemical shift prediction for 1 H, 13 C, and 15 N nuclei. In addition to illustrating the potential utility of chemical shift prediction, we also outline procedures for identifying secondary structure elements through heteronuclear chemical shift analysis and further demonstrate how empirical shift contour maps can actually be used to refine, and more importantly generate, reasonably good three-dimensional protein structures.Key words: NMR, chemical shift, prediction, structure, protein.
Indenoquinolines. I. Derivatives of 11H-Indeno[1,2-b]quinoline (1961)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIndenoquinolines. I. Derivatives of 11H-Indeno[1,2-b]quinolineNORMAN H. CROMWELL and RONALD A. MITSCHCite this: J. Org. Chem. 1961, 26, 10, 3812–3817Publication Date (Print):October 1, 1961Publication History Published online1 May 2002Published inissue 1 October 1961https://pubs.acs.org/doi/10.1021/jo01068a045https://doi.org/10.1021/jo01068a045research-articleACS PublicationsRequest reuse permissionsArticle Views246Altmetric-Citations18LEARN 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
Potential New Cardiovascular Risk Factors: Left Ventricular Hypertrophy, Homocysteine, Lipoprotein(a), Triglycerides, Oxidative Stress, and Fibrinogen (1999)

The 1996 Bethesda Conference acknowledged left ventricular hypertrophy, hyperhomocysteinemia, lipoprotein(a) excess, hypertriglyceridemia, oxidative stress, and hyperfibrinogenemia as possible new cardiac risk factors. This review summarizes the current literature that supports these conditions as cardiac risk factors. Left ventricular hypertrophy is an independent risk factor for vascular disease. Improvement or progression of left ventricular hypertrophy influences subsequent cardiovascular complications. Clinical trials are under way to assess the potential benefit of decreasing homocysteine levels. The role of lipoprotein(a) excess in vascular disease is controversial. The atherogenic potential of lipoprotein(a) seems to be neutralized by effective reduction of low-density lipoprotein cholesterol levels. Increasing evidence supports an independent role of hypertriglyceridemia in cardiovascular disease and a possible clinical benefit from decreasing triglyceride levels. Among antioxidant micronutrients, supplementation with vitamin E has been shown to be beneficial in primary and secondary prevention studies. Data supporting the use of other antioxidants are much weaker. Preliminary evidence suggests that reducing fibrinogen levels in patients with high baseline levels and coronary disease may be beneficial. Despite the potential relation between new risk factors and cardiovascular disease, routine clinical application of these conditions as cardiovascular risk factors would be premature. Evidence is needed that these conditions extend prognostic ability beyond conventional risk factors and that modification of these conditions can reduce the risk for cardiovascular events.
A reed‐solomon coded optically preamplified PPM system (1995)

Abstract A Reed‐Solomon coded optically preamplified pulse‐position modulation system is analyzed. Results are presented at a bit rate of 622 Mbit/s and a wavelength of 1.537 μm, comparing the system with an equivalent on‐off nonreturn‐to‐zero (OOK NRZ) system. The theoretical results demonstrate that the system offers a potential sensitivity of 7 photons/bit, which represents an improvement of 7.5 dB over the equivalent OOK system and is comparable with that of the best coherent systems reported to date. © 1995 John Wiley &amp; Sons, Inc.
Deletion screening of the Duchenne/Becker muscular dystrophy gene in Croatian population. (1997)

The dystrophin gene deletion in 53 Duchenne and 21 Becker muscular dystrophy (DMD/BMD) male patients was analyzed by DNA test using multiplex polymerize chain reaction (M-PCR) in Croatian population. The overall percentage of deletion cases observed was 50%; 61% (53/32) for DMD and 38% (21/8) for BMD. The number of deleted exons was variable, but generally DMD deletions involving single-exon 19, 44, 50, 51 and larger exon deletions 3-6, 4-12, 4-17, 8-13, 12-13, 12-19, 48-50, 50-51, 50-52, 51-52 were more frequent. Eight patients with BMD had deletions exon 45-47, 45-48, and exon 3. The results obtained in the present study showed location of breakpoints in the dystrophin gene, and pointed to variability of deletion patterns in Croatian population among different European populations.
Cleavage of single strand oligonucleotides and bacteriophage phi X174 DNA by Msp I endonuclease. (1980)

Type II restriction endonucleases cleave duplex DNA at nucleotide sequences displaying 2-fold symmetry. Our data show that Msp I cleaves single strand oligonucleotides, d(G-A-A-C-C-G-G-A-G-A) and d(T-C-T-C-C-G-G-T-T) at 4 degrees, 25 degrees, and 37 degrees C reaction temperatures. The rate of cleavage of d(G-A-A-C-C-G-G-A-G-A) is several-fold faster than that of d(T-C-T-C-C-G-G-T-T). Single strand phi X174 DNA is also, cleaved by Msp I endonuclease giving well defined fragments. 5'-Nucleotide analysis of the fragments generated from single strand and replicating form DNA suggest that cleavage occurs at the recognition sequence d(C-C-G-G). The data show that Msp I endonuclease cleaves single strand oligonucleotides and prefers a recognition sequence surrounded by purine nucleotides. A general model for endonuclease cleavage of single strand and duplex DNA is presented.
Oligonucleotides Linked to Reactive Groups (1989)

Coupling of reactive groups to the oligonucleotide moiety provides an additional dimension in the design of oligonucleotide derivatives as inhibitors of gene expression. Reactive oligonucleotide derivatives represent the affinity reagents capable of bringing about chemical modification of the target nucleic acid residues in the vicinity of the oligonucleotide binding area. In many cases reactive oligonucleotide derivatives are advantageous over the unreactive ones. A variety of the reactive groups available which can be coupled to oligonucleotides allows the accomplishment of different sequence-specific chemical modifications of nucleic acids, including cross-linking of oligonucleotides to the targets, sequence-specific cleavage of the polynucleotides and covalent coupling of special groups — e.g. reporter fluorescent groups.
Moving toward preventive therapy in acute lung injury* (2008)

Ohio State University—Pulmonary, Critical Care and Sleep Medicine, Columbus, OH (Ali) The author has not disclosed any potential conflicts of interest. For information regarding this article, E-mail: [email protected]
In Vitro Studies on the Cell-Mediated Immune Response to Human Brain Tumors. I. Requirement for Third-Party Stimulator Lymphocytes in the Induction of Cell-Mediated Cytotoxic Responses to Allogeneic Cultured Gliomas<xref ref-type="fn" rid="FN2">2</xref> (1982)

For study of those properties of human gliomas that might contribute to their ability to escape cell-mediated immune attack, cultured human glioma cells were examined for their ability to elicit allogeneic cytolytic lymphocyte responses in vitro. Of 9 glioma lines, 5 were unable to elicit allogeneic cytolytic lymphocyte responses in mixed lymphocyte--tumor cultures although the concentration of stimulating glioma cells was varied over a fortyfold range. However, lymphocytes specifically cytolytic for 4 of the nonstimulatory lines could be generated if irradiated, third-party stimulator lymphocytes were added to cultures containing responder lymphocytes and glioma cells. The specific cytolytic lymphocytes produced in these cultures were inactivated by treatment with the monoclonal anti-T-cell antibody OKT3 plus complement and were thus identified as T-cells. However, nonspecific, non-T-lytic effectors were also generated. The results of these experiments demonstrated that certain cultured gliomas possessed a defect in immunogenicity that can be overcome by "help" from an allogeneic mixed lymphocyte reaction. The possible nature of this help and the potential implications of these results for the immunotherapy of human gliomas are discussed.
Immunization with the RgpA-Kgp Proteinase-Adhesin Complexes ofPorphyromonas gingivalisProtects against Periodontal Bone Loss in the Rat Periodontitis Model (2002)

A major virulence factor of Porphyromonas gingivalis is the extracellular noncovalently associated complexes of Arg-X- and Lys-X-specific cysteine proteinases and adhesins designated the RgpA-Kgp complexes. In this study we investigated the ability of RgpA-Kgp as an immunogen to protect against P. gingivalis-induced periodontal bone loss in the rat. Specific-pathogen-free Sprague-Dawley rats were immunized with either formalin-killed whole P. gingivalis ATCC 33277 cells with incomplete Freund's adjuvant, RgpA-Kgp with incomplete Freund's adjuvant, or incomplete Freund's adjuvant alone. The animals were then challenged by oral inoculation with live P. gingivalis ATCC 33277 cells. Marked periodontal bone loss was observed in animals immunized with incomplete Freund's adjuvant alone; this bone loss was significantly (P < 0.05) greater than that detected in animals immunized with formalin-killed whole cells or RgpA-Kgp or in unchallenged animals. There was no significant difference in periodontal bone loss between animals immunized with formalin-killed whole cells and those immunized with RgpA-Kgp. The bone loss in these animals was also not significantly different from that in unchallenged animals. DNA probe analysis of subgingival plaque samples showed that 100% of the animals immunized with incomplete Freund's adjuvant alone and challenged with P. gingivalis ATCC 33277 were positive for the bacterium. However, P. gingivalis ATCC 33277 could not be detected in subgingival plaque samples from animals immunized with formalin-killed whole cells or with RgpA-Kgp. Immunization with formalin-killed whole cells or RgpA-Kgp induced a high-titer serum immunoglobulin G2a response. Western blot analysis of RgpA-Kgp using pooled protective antisera taken from rats immunized with RgpA-Kgp revealed immunodominant bands at 44, 39, and 27 kDa. In conclusion, immunization with RgpA-Kgp restricted colonization by P. gingivalis and periodontal bone loss in the rat.
Text enhancement in digital video using multiple frame integration (1999)

In this paper a multiple frame based technique to enhance text in digital video is presented. After extracting a reference text block, we use an image matching technique to find the corresponding text blocks in consecutive frames. We register these text blocks to subpixel levels by using image interpolation techniques to improve both correspondence and text resolution. The registered text blocks are averaged to obtain a new text block with a clean background and a higher resolution. Experiments conducted on several video sequences show that our enhancement scheme can improve the accuracy of commercial off-the-shelf OCR considerably.
Database update GeneCards Version 3: the human gene integrator (2013)

GeneCards (www.genecards.org) is a comprehensive, authoritative compendium of annotative information about human genes, widely used for nearly 15 years. Its gene-centric content is automatically mined and integrated from over 80 digital sources, resulting in a web-based deep-linked card for each of&amp;gt;73 000 human gene entries, encompassing the following categories: protein coding, pseudogene, RNA gene, genetic locus, cluster and uncategorized. We now introduce GeneCards Version 3, featuring a speedy and sophisticated search engine and a revamped, technologically enabling infrastructure, catering to the expanding needs of biomedical researchers. A key focus is on gene-set analyses, which leverage GeneCards’ unique wealth of combinatorial annotations. These include the GeneALaCart batch query facility, which tabulates user-selected annotations for multiple genes and GeneDecks, which identifies similar genes with shared annotations,