gebhart/patrepeval huggingface dataset:
DNA vaccines for cervical cancer. (2010)

Human papillomavirus (HPV), particularly type 16, has been associated with more than 99% of cervical cancers. There are two HPV oncogenic proteins, E6 and E7, which play a major role in the induction and maintenance of cellular transformation. Thus, immunotherapy targeting these proteins may be employed for the control of HPV-associated cervical lesions. Although the commercially available preventive HPV vaccines are highly efficient in preventing new HPV infection, they do not have therapeutic effects against established HPV infection or HPV-associated lesions. Since T cell-mediated immunity is important for treating established HPV infections and HPV-associated lesions, therapeutic HPV vaccine should aim at generating potent E6 and E7-specific T cell-mediated immune responses. DNA vaccines have now developed into a promising approach for antigen-specific T cell-mediated immunotherapy to combat infection and cancer. Because dendritic cells are the most potent professional antigen-presenting cells, and are highly effective in priming antigen-specific T cells, several DNA vaccines have employed innovative strategies to modify the properties of dendritic cells (DCs) for the enhancement of the DNA vaccine potency. These studies have revealed impressive pre-clinical data that has led to several ongoing HPV DNA vaccine clinical trials.
Epitope Tagging of Recombinant Proteins (1997)

Epitope tagging is a method of expressing proteins whereby an epitope for a specific monoclonal antibody is fused to a target protein using recombinant DNA techniques. The fusion gene is cloned into an appropriate expression vector for the experimental cell type and host cells are transfected. The fusion protein can then be detected and/or purified using a monoclonal antibody specific for the epitope tag. This unit presents protocols for detection and purification of proteins tagged with a particular epitope, the FLAG tag, although the same general approach can be applied to other epitope tags. The protocols in this unit employ the anti-FLAG M2 antibody to detect and purify FLAG-tagged proteins. The methods presented are immunoprecipitation of FLAG fusion proteins from cells using an anti-FLAG M2 affinity gel, detection of FLAG fusion proteins by western blotting, and purification of FLAG fusion proteins by anti-FLAG M2 affinity chromatography.
Storage monitoring systems for the year 2000 (1997)

In September 1993, President Clinton stated the US would ensure that its fissile material meet the highest standards of safety, security, and international accountability. Frequent human inspection of the material could be used to ensure these standards. However, it may be more effective and less expensive to replace these manual inspections with virtual inspections via remote monitoring technologies. To prepare for this future, Sandia National Laboratories has developed several monitoring systems, including the Modular Integrated Monitoring System (MIMS) and Project Straight-Line. The purpose of this paper is to describe a Sandia effort that merges remote monitoring technologies into a comprehensive storage monitoring system that will meet the near-term as well as the long-term requirements for these types of systems. Topics discussed include: motivations for storage monitoring systems to include remote monitoring; an overview of the needs and challenges of providing a storage monitoring system for the year 2000; an overview of how the MIMS and Straight-Line can be enhanced so that together they create an integrated and synergistic information system by the end of 1997; and suggested milestones for 1998 and 1999 to assure steady progress in preparing for the needs of 2000.
Coronary Stenting plus Platelet Glycoprotein IIb/IIIa Blockade Compared with Tissue Plasminogen Activator in Acute Myocardial Infarction (2000)

In patients with acute myocardial infarction, coronary stenting plus abciximab leads to a greater degree of myocardial salvage and a better clinical outcome than does fibrinolysis with a tissue plasminogen activator.
Thiostrepton binds to malarial plastid rRNA (1997)

Binding of the thiazolyl peptide antibiotic thiostrepton to the GTPase domain of 23S rRNA involves a few crucial nucleotides, notably A1067 (E. coli). Small RNA transcripts were prepared corresponding to the GTPase domain of the plastid 23S rRNA and the two forms of cytosolic 28S rRNAs found in the human malaria parasite Plasmodium falciparum, as well as the plastid form of rRNA of the AIDS-related pathogen Toxoplasma gondii. Binding affinities of the wild type and mutated RNA sequences were as predicted; the malarial plastid sequence had by far the highest affinity, whereas that from toxoplasma did not bind thiostrepton.
An unmodified heptadecapeptide pheromone induces competence for genetic transformation in Streptococcus pneumoniae. (1995)

Competence for genetic transformation in Streptococcus pneumoniae has been known for three decades to arise in growing cultures at a critical cell density, in response to a secreted protease-sensitive signal. We show that strain CP1200 produces a 17-residue peptide that induces cells of the species to develop competence. The sequence of the peptide was found to be H-Glu-Met-Arg-Leu-Ser-Lys-Phe-Phe-Arg-Asp-Phe-Ile-Leu-Gln-Arg- Lys-Lys-OH. A synthetic peptide of the same sequence was shown to be biologically active in small quantities and to extend the range of conditions suitable for development of competence. Cognate codons in the pneumococcal chromosome indicate that the peptide is made ribosomally. As the gene encodes a prepeptide containing the Gly-Gly consensus processing site found in peptide bacteriocins, the peptide is likely to be exported by a specialized ATP-binding cassette transport protein as is characteristic of these bacteriocins. The hypothesis is presented that this transport protein is encoded by comA, previously shown to be required for elaboration of the pneumococcal competence activator.
Blood, guts and chemical engineering (1989)

Abstract Basic chemical engineering sciences have been used to address selected medical problems. The natural anticoagulant, heparin, has been immobilized to a polyvinyl alcohol (PVA) coating on polyethylene or polyurethane, to prepare a blood compatible material. Modelling of the relationship between the rate of heparin leakage from the coating and the blood heparin concentration at the blood material interface supported the conclusion that the observed inhibition of clot formation induced by the material was due to the activity of the covalently immobilized heparin. The relationship between flow resistance and tube diameter was used to devise an ex vivo system for demonstrating this activity: 1 mm ID heparin‐PVA coated tubing was tested in a parallel flow circuit with a 3 mm ID silicone tubing so as to control the blood flow through the 1 mm test tubing. In another area of chemical engineering activity in biomedical sciences, live mammalian cells have been microencapsulated in a polymer membrane to prevent the host's antibodies, that are outside the capsule, from causing the immune destruction of the to‐be‐transplanted cells (e.g., pancreatic islets for the treatment of diabetes). These works illustrate the use of chemical engineering in nontraditional ways, consistent with what some consider the new “paradigm” for our profession.
Phenotypic characterization of CD4+ T cells that exhibit a transendothelial migratory capacity. (1995)

The phenotype of CD4+ T cells capable of transendothelial migration was determined using an in vitro model system, in which cells migrate through a monolayer of endothelial cells (EC) on collagen gels. A specific subset of resting CD4+ memory T cells was found to migrate. T cells within this subset can be defined by the bright expression of CD11a, CD26, CD44, and CD49d. Additionally, the migratory CD4+ T cell population is largely CD58bright, CD31-, CD62L-, and is also enriched in cells that brightly express CD49c, CD49e, and CD49f. Only a minority of the cells are activated, as indicated by expression of CD69. The EC were found to play a central role in facilitating migration of this subset because selective enrichment of CD11abright, CD26bright, CD44bright, CD4+ T cells was not observed when cells migrated in the absence of EC. Activation of the T cells induced a modest degree of migration of an additional subset of CD45RA+, CD31+ naive T cells. In contrast, TNF-alpha activation of the EC increased the transendothelial migration of an additional subset of activated memory T cells that expressed CD69 and CD62L. Neither activation of the T cells, stimulation of the EC, nor the presence of macrophage inflammatory protein-1 alpha (MIP-1 alpha) or RANTES, however, altered the phenotype of the majority of the migratory CD4+ T cell population, which is characteristic of a particular stage of memory cell differentiation. These results suggest that CD4+ T cells acquire the capacity for transendothelial migration at a specific phase of maturation that is only minimally altered by the activation of either the T cell or the EC, or by the presence of specific chemokines in the subendothelial matrix.
Chemical composition of chicken eggshell and shell membranes (2003)

This study was undertaken to determine the occurrence of uronic acid in chicken eggshell membranes and to compare chemical compositions among the inner and outer eggshell membranes and the organic matter of eggshell. We report here for the first time the occurrence of uronic acid in chicken eggshell membranes. Uronic acid concentrations were similar (P > 0.05) between the inner shell membrane and outer shell membrane but approximately fivefold higher (P < 0.05) in the organic matter of eggshell. Sialic acid concentrations were the highest (P < 0.05) in the organic matter of eggshell and higher (P < 0.05) in the inner than in the outer shell membrane. Nitrogen concentrations were the lowest (P < 0.05) in the organic matter of eggshell but relatively constant between the two shell membranes. Amino acid analysis showed that the contents of glycine and alanine were higher (P < 0.05) and those of proline and hydroxyproline were lower (P < 0.05) in the organic matter of eggshell compared to shell membranes.
New slot configurations for dual-band planar inverted-F antenna (2001)

This paper describes a novel planar dual-band inverted-F antenna (PIFA) for which the impedance bandwidth can be remarkably improved. The proposed PIFA uses a single feed only. Two top-plate geometries, an L-shaped and a novel U-shaped slot, are discussed. An example for both slot shapes is given for frequency bands of 2.4 and 5.2 GHz. Simulation based upon the method of moments is used to model the performance of the antennas. Comparisons with measured results on fabricated antenna structures are provided for simulation validation. © 2001 John Wiley & Sons, Inc. Microwave Opt Technol Lett 28: 293–298, 2001.
Exploratory Synthetic Studies Involving the Tricyclo[9.3.0.02,8]tetradecane Ring System Peculiar to the Cyathins (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTExploratory Synthetic Studies Involving the Tricyclo[9.3.0.02,8]tetradecane Ring System Peculiar to the CyathinsKarl R. Dahnke and Leo A. PaquetteCite this: J. Org. Chem. 1994, 59, 4, 885–899Publication Date (Print):February 1, 1994Publication History Published online1 May 2002Published inissue 1 February 1994https://pubs.acs.org/doi/10.1021/jo00083a034https://doi.org/10.1021/jo00083a034research-articleACS PublicationsRequest reuse permissionsArticle Views842Altmetric-Citations35LEARN 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 (1)»Supporting Information Supporting Information Get e-Alerts
Association and prognostic significance of BRCA1/2-mutation status with neoantigen load, number of tumor-infiltrating lymphocytes and expression of PD-1/PD-L1 in high grade serous ovarian cancer (2016)

Immune checkpoint inhibitors (e.g., anti-PD-1 and anti-PD-L1 antibodies) have demonstrated remarkable efficacy against hypermutated cancers such as melanomas and lung carcinomas. One explanation for this effect is that hypermutated lesions harbor more tumor-specific neoantigens that stimulate recruitment of an increased number of tumor-infiltrating lymphocytes (TILs), which is counterbalanced by overexpression of immune checkpoints such as PD-1 or PD-L1. Given that BRCA1/2-mutated high grade serous ovarian cancers (HGSOCs) exhibit a higher mutational load and a unique mutational signature with an elevated number of larger indels up to 50 bp, we hypothesized that they may also harbor more tumor-specific neoantigens, and, therefore, exhibit increased TILs and PD-1/PD-L1 expression. Here, we report significantly higher predicted neoantigens in BRCA1/2-mutated tumors compared to tumors without alterations in homologous recombination (HR) genes (HR-proficient tumors). Tumors with higher neoantigen load were associated with improved overall survival and higher expression of immune genes associated with tumor cytotoxicity such as genes of the TCR, the IFN-gamma and the TNFR pathways. Furthermore, immunohistochemistry studies demonstrated that BRCA1/2-mutated tumors exhibited significantly increased CD3+ and CD8+ TILs, as well as elevated expression of PD-1 and PD-L1 in tumor-associated immune cells compared to HR-proficient tumors. Survival analysis showed that both BRCA1/2-mutation status and number of TILs were independently associated with outcome. Of note, two distinct groups of HGSOCs, one with very poor prognosis (HR proficient with low number of TILs) and one with very good prognosis (BRCA1/2-mutated tumors with high number of TILs) were defined. These findings support a link between BRCA1/2-mutation status, immunogenicity and survival, and suggesting that BRCA1/2-mutated HGSOCs may be more sensitive to PD-1/PD-L1 inhibitors compared to HR-proficient HGSOCs.
A Glial Endogenous Cannabinoid System Is Upregulated in the Brains of Macaques with Simian Immunodeficiency Virus-Induced Encephalitis (2005)

Recent evidence supports the notion that the endocannabinoid system may play a crucial role in neuroinflammation. We explored the changes that some elements of this system exhibit in a macaque model of encephalitis induced by simian immunodeficiency virus. Our results show that profound alterations in the distribution of specific components of the endocannabinoid system occur as a consequence of the viral infection of the brain. Specifically, expression of cannabinoid receptors of the CB2 subtype was induced in the brains of infected animals, mainly in perivascular macrophages, microglial nodules, and T-lymphocytes, most likely of the CD8 subtype. In addition, the endogenous cannabinoid-degrading enzyme fatty acid amide hydrolase was overexpressed in perivascular astrocytes as well as in astrocytic processes reaching cellular infiltrates. Finally, the pattern of CB1 receptor expression was not modified in the brains of infected animals compared with that in control animals. These results resemble previous data obtained in Alzheimer's disease human tissue samples and suggest that the endocannabinoid system may participate in the development of human immunodeficiency virus-induced encephalitis, because activation of CB2 receptors expressed by immune cells is likely to reduce their antiviral response and thus could favor the CNS entry of infected monocytes.
RNA-dominant diseases (2006)

Several examples have come to light in which mutations in non-protein-coding regions give rise to a deleterious gain-of-function by non-coding RNA. Expression of the toxic RNA is associated with formation of nuclear inclusions and late-onset degenerative changes in brain, heart or skeletal muscle. In the best studied example, myotonic dystrophy, it appears that the main pathogenic effect of the toxic RNA is to sequester binding proteins and compromise the regulation of alternative splicing. This review describes some of the recent advances in understanding the pathophysiology of RNA-dominant diseases.
Inhibition of Sodium-Calcium Exchange by Ceramide and Sphingosine (2001)

Na(+)/Ca(2+) exchange activity in Chinese hamster ovary cells expressing the bovine cardiac Na(+)/Ca(2+) exchanger was inhibited by the short chain ceramide analogs N-acetylsphingosine and N-hexanoylsphingosine (5-15 micrometer). The sphingolipids reduced exchange-mediated Ba(2+) influx by 50-70% and also inhibited the Ca(2+) efflux mode of exchange activity. The biologically inactive ceramide analog N-acetylsphinganine had only modest effects on exchange activity. Cells expressing the Delta(241-680) and Delta(680-685) deletion mutants of the Na(+)/Ca(2+) exchanger were not inhibited by ceramide; these mutants show defects in both Na(+)-dependent and Ca(2+)-dependent regulatory behavior. Another mutant, which was defective only in Na(+)-dependent regulation, was as sensitive to ceramide inhibition as the wild-type exchanger. Inhibition of exchange activity by ceramide was time-dependent and was accelerated by depletion of internal Ca(2+) stores. Sphingosine (2.5 micrometer) also inhibited the Ca(2+) influx and efflux modes of exchange activity in cells expressing the wild-type exchanger; sphingosine did not affect Ba(2+) influx in the Delta(241-680) mutant. The effects of the exogenous sphingolipids were reproduced by blocking cellular ceramide utilization pathways, suggesting that exchange activity is inhibited by increased levels of endogenous ceramide and/or sphingosine. We propose that sphingolipids impair Ca(2+)-dependent activation of the exchanger and that in cardiac myocytes, this process serves as a feedback mechanism that links exchange activity to the diastolic concentration of cytosolic Ca(2+).
TGF-β prevents T follicular helper cell accumulation and B cell autoreactivity (2014)

T follicular helper (Tfh) cells contribute to the establishment of humoral immunity by controlling the delivery of helper signals to activated B cells; however, Tfh development must be restrained, as aberrant accumulation of these cells is associated with positive selection of self-reactive germinal center B cells and autoimmunity in both humans and mice. Here, we show that TGF-β signaling in T cells prevented Tfh cell accumulation, self-reactive B cell activation, and autoantibody production. Using mice with either T cell-specific loss or constitutive activation of TGF-β signaling, we demonstrated that TGF-β signaling is required for the thymic maturation of CD44⁺CD122⁺Ly49⁺CD8⁺ regulatory T cells (Tregs), which induce Tfh apoptosis and thus regulate this cell population. Moreover, peripheral Tfh cells escaping TGF-β control were resistant to apoptosis, exhibited high levels of the antiapoptotic protein BCL2, and remained refractory to regulation by CD8+ Tregs. The unrestrained accumulation of Tfh cells in the absence of TGF-β was dependent on T cell receptor engagement and required B cells. Together, these data indicate that TGF-β signaling restrains Tfh cell accumulation and B cell-associated autoimmunity and thereby controls self-tolerance.
Issues and Initiatives for Practical Deployment of Wireless Power Transfer Technologies in Japan (2013)

The Broadband Wireless Forum (BWF) was established in Japan under the guidance of the Ministry of Internal Affairs and Communications, Japan, to enhance future wireless technologies through collaboration involving industry, government, and academia. Wireless power transfer (WPT) is one of the key technologies expected to lead to the emergence of new business fields in the near future. In this context, the Wireless Power Transmission Working Group (WPT-WG) was formed in BWF to discuss problems concerning the commercialization of WPT technologies. In this paper, issues and initiatives of WPT-WG are presented.
Apolipoprotein B-48 Is the Product of a Messenger RNA with an Organ-Specific In-Frame Stop Codon (1987)

The primary structure of human apolipoprotein (apo) B-48 has been deduced and shown by a combination of DNA excess hybridization, sequencing of tryptic peptides, cloned complementary DNAs, and intestinal messenger RNAs (mRNAs) to be the product of an intestinal mRNA with an in-frame UAA stop codon resulting from a C to U change in the codon CAA encoding Gln2153 in apoB-100 mRNA. The carboxyl-terminal Ile2152 of apoB-48 purified from chylous ascites fluid has apparently been cleaved from the initial translation product, leaving Met2151 as the new carboxyl-terminus. These data indicate that approximately 85% of the intestinal mRNAs terminate within approximately 0.1 to 1.0 kilobase downstream from the stop codon. The other approximately 15% have lengths similar to hepatic apoB-100 mRNA even though they have the same in-frame stop codon. The organ-specific introduction of a stop codon to a mRNA appears unprecedented and might have implications for cryptic polyadenylation signal recognition and RNA processing.
Structure-from-Motion Revisited (2016)

Incremental Structure-from-Motion is a prevalent strategy for 3D reconstruction from unordered image collections. While incremental reconstruction systems have tremendously advanced in all regards, robustness, accuracy, completeness, and scalability remain the key problems towards building a truly general-purpose pipeline. We propose a new SfM technique that improves upon the state of the art to make a further step towards this ultimate goal. The full reconstruction pipeline is released to the public as an open-source implementation.
A New Synthesis of Pyrazino[2,3-c]isoquinolines (1990)

A convenient synthesis of 1-(p-chlorophenoxy )isoquinoline-3,4-diame is described. Condensation with ethyl pyruvate gave entry to the tricyclic title system, and some further nucleophilic displacement reactions of substituent groups are described. The direction of ring closure in the tricycle formation was proved by determining the crystal structure of one of the derivatives; rhombohedral crystals of (3b) belong to the space group R3 with a 21.822(5)?, a 116.81(2)° and Z 12. Full-matrix refinement using 3093 reflections converged at R 0.085.
New antibody drug treatments for lymphoma (2011)

Despite the large numbers of new anti-CD20 mAb currently undergoing clinical testing, improving on clinical efficacy of rituximab is a substantial challenge. Further improvements in outcome for patients will require rigorous testing in well designed clinical trials alongside the translation of new insights into mechanism of mAb action that lead to improvements in clinical efficacy.
Spectrum (2009)

On many-core chip designs, short, often-multicast, latency-critical messages, used extensively in high-level coherence and synchronization protocols, often become the bottleneck of parallel performance scaling. This paper presents Spectrum, a hybrid nanophotonic-electric on-chip network that optimizes both throughput and latency. Spectrum's novel planar nanophotonic subnetwork broadcasts latency-critical messages through a wavelength-division multiplexed (WDM) two-dimensional waveguide. Spectrum's throughput-optimized packet-switching electrical subnetwork handles high bandwidth traffic. Overall, Spectrum delivers an almost ideal CMOS-compatible interconnection network for many-core systems.