gebhart/patrepeval huggingface dataset:
Transgenes and knockout mutations in animal models of type 1 diabetes and multiple sclerosis (1999)

In this article, we will examine the roles of transgenic and knockout animals that aid us in understanding two autoimmune diseases-type 1 (insulin-dependent) diabetes and multiple sclerosis. The first sections will focus on studies in type 1 diabetes to show how genetically altered animals have given insight into the role of various immune cell types, autoantigens, co-stimulatory molecules, cytokines and, finally, the role of various effector pathways in the pathogenesis of diabetes. The second section concentrating on the animal model of multiple sclerosis, experimental autoimmune encephalomyelitis (EAE), will show how animals that express a T-cell receptor derived from a clone able to cause disease have given insight into the pathogenesis of EAE.
Unbiased amplification of a highly complex mixture of DNA fragments by ‘lone linker’-tagged PCR (1990)

Journal Article Unbiased amplification of a highly complex mixture of DNA fragments by ‘lone linker’-tagged PCR Get access M.S.H. Ko, M.S.H. Ko Furesawa MorphoGene Project, Research Development Corporation of Japan, 5-9-6 TohkohdaiTaukuba 300-26, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar S.B.H. Ko, S.B.H. Ko Furesawa MorphoGene Project, Research Development Corporation of Japan, 5-9-6 TohkohdaiTaukuba 300-26, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar N. Takahashi, N. Takahashi Furesawa MorphoGene Project, Research Development Corporation of Japan, 5-9-6 TohkohdaiTaukuba 300-26, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar K. Nishiguchi, K. Nishiguchi Furesawa MorphoGene Project, Research Development Corporation of Japan, 5-9-6 TohkohdaiTaukuba 300-26, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar K. Abe K. Abe Furesawa MorphoGene Project, Research Development Corporation of Japan, 5-9-6 TohkohdaiTaukuba 300-26, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 14, 25 July 1990, Page 4293, https://doi.org/10.1093/nar/18.14.4293 Published: 25 July 1990 Article history Received: 11 May 1990 Published: 25 July 1990
Passive Transfer of Sera with Antivirus Neutralizing Activity from Adult Channel Catfish Protects Juveniles from Channel Catfish Virus Disease (1987)

Juvenile channel catfish Ictalurus punctatus were found to be protected from experimental infections of channel catfish virus (CCV) after passive transfer of adult sera with anti-CCV neutralizing activity. Juveniles in control groups that received injections of normal serum or saline and were then challenged with CCV experienced average cumulative mortalities of 66 and 71%, respectively. In contrast, juveniles receiving serum with anti-CCV activity (neutralization index of 102.6) via intraperitoneal injections had an average cumulative mortality of 1%. Furthermore, fish in the control groups showed typical signs of channel catfish virus disease and contained virus concentrations of up to 107˙TCID50 (50% tissue culture infective dose endpoint) per gram of tissue. In comparison, no signs of disease were observed among fish receiving serum containing anti-CCV neutralizing activity. These studies demonstrated that serum with anti-CCV neutralizing activity (presumably due to anti-CCV antibody) obtained from adult channel catfish can protect juveniles from lethal challenges with CCV. However, the role of antivirus antibodies in recovery from primary infections and in virus expression during latent infections remains unknown.
Role of Protein Kinase C Signaling in Intestinal Ischemic Preconditioning (2003)

Ischemic preconditioning (IPC) is a phenomenon that a brief episode of ischemia to a tissue renders the tissue resistance from a subsequent prolonged ischemia. It is generally accepted that this protection is a receptor-mediated process, and is realized via signal transduction pathways. Protein kinase C (PKC), known to play key regulatory roles in cellular processes, has been proposed as a primary cellular mediator of preconditioning. However, the role of PKC in eliciting cardioprotection remains controversial. The evidences for the 'PKC hypothesis' of preconditioning in various tissue and organs are summarized. Especially in intestine, a brief ischemia induced a reversible epithelial injury to the jejunum that is associated with activation of several PKC isoforms. Injury induced by an additional period of ischemia is reduced by the prior IPC, and this effect is abolished by non-selective PKC inhibition but not by a selective inhibitor of cPKC/or PKC. This result suggest that activation of nPKC isoform (especially PKC) during and following ischemic insults may play an important role in protection against I/R injury in the intestine, and this mechanism is identical with previous study in heart tissue.
Source-Bias Dependent Charge Accumulation in P+-Poly Gate SOI Dynamic Random Access Memory Cell Transistors (1998)

In this paper, we report the dynamic data retention problems caused by the transient leakage current in a cell transistor during the bit-line pull down operation in p + -poly gate fully depleted silicon-on-insulator (FD-SOI) dynamic random access memories (DRAMs) due to the source-induced charge accumulation (SICA) effect in the silicon thin film. Due to the inherent floating body effect in the FD-SOI transistor, charge accumulation in the silicon thin film becomes inevitable when the gate-to-source voltage ( V GS ) is smaller than the flat-band voltage ( V FB ). In order to eliminate the transient leakage current problem in p + -poly gate FD-SOI cell transistor, the ground-precharged bit-line (GPB) sensing method is introduced.
beta-Lactamases of increasing clinical importance. (1999)

Resistance to b-lactam-containing antimicrobial agents continues to increase, frequently due to the presence of b-lactamases in Gram-negative bacteria. Over the past twenty-five years broad-spectrum enzymes such as TEM- and SHV-variants and the metallo-b-lactamases have become more prolific. As a result of the ability of plasmids to continue to acquire additional resistance determinants, many of the b-lactamase-producing Gram-negative pathogens have become multi-drug resistant. In combination with decreased permeability, the organisms can become virtually untreatable with current therapies. The major groups of b-lactamases that pose the most serious therapeutic problems include the extended-spectrum b-lactamases, the plasmid-mediated cephalosporinases, the inhibitor-resistant TEM- or SHV-derived b-lactamases and the carbapenem-hydrolyzing b-lactamases. Those enzymes that can be transferred on mobile elements are the most serious of the newer b-lactamases, and include enzymes in each of the four groups outlined above.
Protein Structure-Based Combinatorial Chemistry:  Discovery of Non-Peptide Binding Elements to Src SH3 Domain (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTProtein Structure-Based Combinatorial Chemistry: Discovery of Non-Peptide Binding Elements to Src SH3 DomainAndrew P. Combs, Tarun M. Kapoor, Sibo Feng, James K. Chen, Lygia F. Daudé-Snow, and Stuart L. SchreiberView Author Information Howard Hughes Medical Institute Department of Chemistry, Harvard University 12 Oxford Street, Cambridge, Massachusetts 02138 Cite this: J. Am. Chem. Soc. 1996, 118, 1, 287–288Publication Date (Web):January 10, 1996Publication History Received7 November 1995Published online10 January 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ja953750vhttps://doi.org/10.1021/ja953750vrapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views376Altmetric-Citations78LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information SUBJECTS:Chemical specificity,Electron correlation,Elements,Ligands,Monomers Get e-Alerts
The Reactions of Diborane with Hydrocarbons1 (1948)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Reactions of Diborane with Hydrocarbons1Dallas T. HurdCite this: J. Am. Chem. Soc. 1948, 70, 6, 2053–2055Publication Date (Print):June 1, 1948Publication History Published online1 May 2002Published inissue 1 June 1948https://doi.org/10.1021/ja01186a020RIGHTS & PERMISSIONSArticle Views804Altmetric-Citations68LEARN 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 InReddit PDF (432 KB) Get e-Alerts Get e-Alerts
Scavenger Receptor Class B, Type I, Mediates Selective Uptake of Low Density Lipoprotein Cholesteryl Ester (1999)

Scavenger receptor, class B, type I (SR-BI) is a cell-surface glycoprotein that mediates selective uptake of high density lipoprotein cholesteryl ester (CE) without the concomitant uptake and degradation of the particle. We have investigated the endocytic and selective uptake of low density lipoprotein (LDL)-CE by SR-BI using COS-7 cells transiently transfected with mouse SR-BI. Analysis of lipoprotein uptake data showed a concentration-dependent LDL-CE-selective uptake when doubly labeled LDL particles were incubated with SR-BI-expressing COS-7 cells. In contrast to vector-transfected cells, SR-BI-expressing COS-7 cells showed marked increases in LDL cell association and CE uptake by the selective uptake pathway, but only a modest increase in CE uptake by the endocytic pathway. SR-BI-mediated LDL-CE-selective uptake exceeded LDL endocytic uptake by 50-100-fold. SR-BI-mediated LDL-CE-selective uptake was not inhibited by the proteoglycan synthesis inhibitor, p-nitrophenyl-beta-D-xylopyranoside or by the sulfation inhibitor sodium chlorate, indicating that SR-BI-mediated LDL-CE uptake occurs independently of LDL interaction with cell-surface proteoglycan. Analyses with subclones of Y1 adrenocortical cells showed that LDL-CE-selective uptake was proportional to the level of SR-BI expression. Furthermore, antibody directed to the extracellular domain of SR-BI blocked LDL-CE-selective uptake in adrenocortical cells. Thus, in cells that normally express SR-BI and in transfected COS-7 cells SR-BI mediates the efficient uptake of LDL-CE via the selective uptake mechanism. These results suggest that SR-BI may influence the metabolism of apoB-containing lipoproteins in vivo by mediating LDL-CE uptake into SR-BI-expressing cells.
Evaluation of 111In-Labeled Cyclic RGD Peptides: Tetrameric not Tetravalent (2010)

This report presents the synthesis and evaluation of (111)In(DOTA-6G-RGD(4)) (DOTA = 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetracetic acid; 6G-RGD(4) = E{G(3)-E[G(3)-c(RGDfK)](2)}(2) and G(3) = Gly-Gly-Gly), (111)In(DOTA-RGD(4)) (RGD(4) = E{E[c(RGDfK)](2)}(2)) and (111)In(DOTA-3G-RGD(2)) (3G-RGD(2) = G(3)-E[G(3)-c(RGDfK)](2)) as new radiotracers for imaging integrin alpha(v)beta(3)-positive tumors. The IC(50) values of DOTA-6G-RGD(4), DOTA-RGD(4), and DOTA-3G-RGD(2) were determined to be 0.4 +/- 0.1, 1.4 +/- 0.1 and 1.1 +/- 0.1 nM against (125)I-c(RGDyK) bound to integrin alpha(v)beta(3)-positive U87MG human glioma cells. (111)In(DOTA-6G-RGD(4)), (111)In(DOTA-RGD(4)), and (111)In(DOTA-3G-RGD(2)) were prepared by reacting (111)InCl(3) with the respective DOTA conjugate in NH(4)OAc buffer (100 mM, pH = 5.5). Radiolabeling could be completed by heating the reaction mixture at 100 degrees C for 15-20 min. The specific activity was approximately 1850 MBq/micromol for (111)In(DOTA-3G-RGD(2)) and approximately 1480 MBq/micromol for (111)In(DOTA-6G-RGD(4)). The athymic nude mice bearing U87MG human glioma xenografts were used to evaluate tumor uptake and excretion kinetics of (111)In(DOTA-6G-RGD(4)), (111)In(DOTA-RGD(4)), and (111)In(DOTA-3G-RGD(2)). The results from both the integrin alpha(v)beta(3) binding assay and biodistribution studies suggest that the tetrameric cyclic RGD peptides, such as RGD(4) and 6G-RGD(4), are most likely bivalent in binding to the integrin alpha(v)beta(3). Both (111)In(DOTA-6G-RGD(4)) and (111)In(DOTA-RGD(4)) had significantly higher tumor uptake than (111)In(DOTA-3G-RGD(2)) at 24-72 h postinjection due to the extra RGD motifs in RGD(4) and 6G-RGD(4). (111)In(DOTA-3G-RGD(2)) had very little metabolism, while (111)In(DOTA-6G-RGD(4)) had significant metabolism during its excretion via both renal and hepatobiliary routes over the 2 h period, probably due to its much larger size. The combination of high tumor uptake with long tumor retention suggests that their corresponding (90)Y and (177)Lu analogues M(DOTA-6G-RGD(4)) (M = (90)Y and (177)Lu) might be useful as therapeutic radiotracers for treatment of integrin alpha(v)beta(3)-positive solid tumors.
Secondary Structure Prediction for Aligned RNA Sequences (2001)

SFI Working Papers contain accounts of scientific work of the author(s) and do not necessarily represent the views of the Santa Fe Institute. We accept papers intended for publication in peer-reviewed journals or proceedings volumes, but not papers that have already appeared in print. Except for papers by our external faculty, papers must be based on work done at SFI, inspired by an invited visit to or collaboration at SFI, or funded by an SFI grant. ©NOTICE: This working paper is included by permission of the contributing author(s) as a means to ensure timely distribution of the scholarly and technical work on a non-commercial basis. Copyright and all rights therein are maintained by the author(s). It is understood that all persons copying this information will adhere to the terms and constraints invoked by each author&amp;apos;s copyright. These works may be reposted only with the explicit permission of the copyright holder. www.santafe.edu
Role of N-Linked Glycans in the Functions of Hepatitis C Virus Envelope Proteins Incorporated into Infectious Virions (2010)

Hepatitis C virus (HCV) envelope glycoproteins are highly glycosylated, with generally 4 and 11 N-linked glycans on E1 and E2, respectively. Studies using mutated recombinant HCV envelope glycoproteins incorporated into retroviral pseudoparticles (HCVpp) suggest that some glycans play a role in protein folding, virus entry, and protection against neutralization. The development of a cell culture system producing infectious particles (HCVcc) in hepatoma cells provides an opportunity to characterize the role of these glycans in the context of authentic infectious virions. Here, we used HCVcc in which point mutations were engineered at N-linked glycosylation sites to determine the role of these glycans in the functions of HCV envelope proteins. The mutants were characterized for their effects on virus replication and envelope protein expression as well as on viral particle secretion, infectivity, and sensitivity to neutralizing antibodies. Our results indicate that several glycans play an important role in HCVcc assembly and/or infectivity. Furthermore, our data demonstrate that at least five glycans on E2 (denoted E2N1, E2N2, E2N4, E2N6, and E2N11) strongly reduce the sensitivity of HCVcc to antibody neutralization, with four of them surrounding the CD81 binding site. Altogether, these data indicate that the glycans associated with HCV envelope glycoproteins play roles at different steps of the viral life cycle. They also highlight differences in the effects of glycosylation mutations between the HCVpp and HCVcc systems. Furthermore, these carbohydrates form a "glycan shield" at the surface of the virion, which contributes to the evasion of HCV from the humoral immune response.
Photon-Counting Security Tagging and Verification Using Optically Encoded QR Codes (2014)

We propose an optical security method for object authentication using photon-counting encryption implemented with phase encoded QR codes. By combining the full phase double-random-phase encryption with photon-counting imaging method and applying an iterative Huffman coding technique, we are able to encrypt and compress an image containing primary information about the object. This data can then be stored inside of an optically phase encoded QR code for robust read out, decryption, and authentication. The optically encoded QR code is verified by examining the speckle signature of the optical masks using statistical analysis. Optical experimental results are presented to demonstrate the performance of the system. In addition, experiments with a commercial Smartphone to read the optically encoded QR code are presented. To the best of our knowledge, this is the first report on integrating photon-counting security with optically phase encoded QR codes.
CD4+CD25+ T Regulatory Cells in Transplantation Tolerance (2016)

In Brief In the 1970s, the capacity of T cells to inhibit immunity and those from transplant tolerant hosts to transfer alloantigen-specific suppression to lymphopenic recipients was described. CD4+ T suppressor cells that ex vivo reverted to effector cells were described in the 1980s. Their antigen-specific suppressor function could be preserved by stimulation by specific donor alloantigen and cytokines from activated lymphocytes. This led to the finding that alloantigen-specific T suppressor cells express IL-2 receptor (CD25) and that IL-2 in part promotes their survival. Whether these alloantigen-specific CD4+CD25+FOXP3+ regulatory T (Treg) cells are progeny of thymic-derived CD4+CD25+FOXP3+ Treg (tTreg) cells or are induced from peripheral effector CD4+CD25−FOXP3−T cells (iTreg) cells is still debated. In vitro studies of antigen specific Treg has been difficult as they die in the absence of cytokines produced by immune activated cells. The antigen-specific CD4+CD25+ T cells that control rejection in tolerant hosts differ from the naive tTreg. Thymic-derived Treg cells are not antigen-specific, and very high ratios are required to suppress rejection. Thymic-derived Treg cells can be expanded ex vivo and are currently being tested in trials to control allograft rejection and graft versus host disease. Thymic-derived Treg cells with specific receptors for alloantigen are activated by either IL-2 or IL-4 but rapidly become dependent on other cytokines, respectively, IFN-γ or IL-12 if activated by IL-2, or IL-5 if activated by IL-4. The Th1 and Th2 pathways for activation of tTreg produce more potent antigen-specific Treg that only suppress specific donor rejection. After 25 years, much remains unknown about antigen-specific CD4+CD25+FOXP3+ Treg-mediating transplant tolerance. A personal and extensive overview of CD4+CD25+ regulatory T cells in transplantation discussing key findings and future directions.
Bursectomy of chicken embryos at 60 hours of incubation leads to an oligoclonal B cell compartment and restricted Ig diversity. (1990)

Chickens that have been surgically bursectomized at 60 h of embryonic development usually generate Ig producing B cells; however, the bursectomized chickens are incapable of specific antibody responses, even after repeated immunization. In the present work, we analyzed the molecular basis of this immunodeficiency. In the bursectomized chickens, DNA sequencing revealed a repertoire of Ig L and H chains with a low number of different V-J and V-D-J joints, indicating an oligoclonal B cell compartment. In addition, the L and H chains belonging to each B cell clone had similar gene conversion events in the V region. In situ hybridization to Harderian gland tissue sections showed, that B cells of the bursectomized chickens were, however, capable of terminal plasma cell maturation. Thus, in chickens that were lacking the bursal microenvironment, 1) only a few B cell precursors differentiated into mature Ig-producing B cells, 2) low rate of gene conversion resulted in restricted Ig diversity. Regarding the chicken B cell differentiation, the present data support a model that the induction of B cell differentiation is a bursa-independent event, whereas the bursa of Fabricius has a crucial role in the amplification and diversification of the embryonic B cell repertoire.
Effects of docosahexaenoic acid on serum lipoproteins in patients with combined hyperlipidemia: a randomized, double-blind, placebo-controlled trial. (1997)

Dietary DHA, in the absence of EPA, can affect lipoprotein cholesterol and triglyceride levels in patients with combined hyperlipidemia. The desirable triglyceride and HDL-C changes were present at a dose which did not significantly increased non-HDL-C or LDL-C. These preliminary findings suggest that dietary supplementation with 1.25 g DHA/day, provided in a triglyceride form, may be an effective tool to aid in the management of hypertriglyceridemia.
Cell adhesion molecules in the development of inflammatory infiltrates in giant cell arteritis: Inflammation-induced angiogenesis as the preferential site of leukocyte-endothelial cell interactions (2000)

Inflammation-induced angiogenesis is the main site of leukocyte-endothelial cell interactions leading to the development of inflammatory infiltrates in GCA. The distribution of leukocyte-endothelial cell ligand pairs suggests a heterogeneity in leukocyte-endothelial cell interactions used by different functional cell subsets at distinct areas of the temporal artery.
An Economical and Convenient Synthesis of Vinyl Sulfones (2007)

A general process for the efficient synthesis of vinyl sultones has been developed using commercially available sulfinic acid sodium salts and dibromides. A variety of phenyl and methyl vinyl sulfones have been formed in good yields, in the absence of any catalyst.