gebhart/patrepeval huggingface dataset:
Antigen‐Specific, Major Histocompatibility Complex‐Restricted T Cell Receptors (1983)

In this paper we have summarized our work on the structure of the receptor for Ag/MHC on 3 T cell hybridomas. In each case, these receptors have been identified by their reaction with antibodies, thought to be directed against Ag/MHC receptors because of their clone-specificity, and their ability to interfere with Ag/MHC recognition by the relevant hybridoma. The antibodies precipitate approximately 85 kd molecular weight heterodimeric glycoproteins from these cells. These reduce to 2 chains of 40-43 kd, one of acidic and the other of basic pI. These bulk characteristics apply to receptors from Class II-restricted, as well as Class I-specific T cells. There is evidence of molecular weight heterogeneity for both alpha and beta-chains in the mouse, both having 40 and 43 kd forms. Isoelectric focussing patterns suggest that both chains vary in amino acid sequence between clones. Peptide maps show that the receptor varies in amino acid sequence between clones, but that some peptides appear common, i.e., the receptor seems to have both variable and constant amino acid sequences. It is even possible that allotypic differences between the peptide maps of BALB/c and C57BL/6-derived receptors have been identified, though more data will be needed to confirm this. Finally we have recently shown that reaction with an anti-idiotype predicts both the Ag and MHC specificity of the T cell hybridoma bearing it, suggesting that a single receptor, responsible for binding both Ag and MHC, is identified by the anti-idiotypic antibody. The similarities between these T cell-bourne molecules, and immunoglobulin are inescapable. Both are disulphide-linked glycoproteins made up of 2 chains, both of which may vary in amino acid sequence. Secreted immunoglobulin is, of course, polyvalent, being composed of two or more of each type of chain, this contributes to the efficiency with which the molecule can bind polyvalent antigen or build precipitable lattices. Similar constraints do not apply to T cell-bound receptors, which do not seem to have a secreted form.
Functional analysis of the human annexin A5 gene promoter: a downstream DNA element and an upstream long terminal repeat regulate transcription (2001)

Human annexin A5 is a ubiquitous protein implicated in diverse signal transduction processes associated with cell growth and differentiation, and its gene regulation is an important component of this function. Promoter transcriptional activity was determined for a wide 5′ portion of the human annexin A5 gene, from bp −1275 to +79 relative to the most 5′ of several discrete transcription start points. Transfection experiments carried out in HeLa cells identified the segment from bp −202 to +79 as the minimal promoter conferring optimal transcriptional activity. Two canonical Sp1 sites in the immediate 5′ flanking region of a CpG island were required for significant transcription. Strong repressive activity in the distal promoter region between bp −717 to −1153 was attributed to the presence of an endogenous retroviral long terminal repeat, homologous with long terminal repeat 47B. The downstream sequence from bp position +31 to +79 in untranslated exon 1 was also essential for transcription, as its deletion from any of the plasmid constructs abolished activity in transfection assays. Electrophoretic mobility-shift assays, Southwestern-blot analysis and affinity chromatography were used to identify a protein doublet of relative molecular mass 35kDa that bound an octanucleotide palindromic sequence in exon 1. The DNA cis-element resembled an E-box, but did not bind higher molecular mass transcription factors, such as upstream stimulatory factor or activator protein 4. The discovery of a downstream element crucial for annexin A5 gene transcription, and its interaction with a potentially novel transcription factor or complex, may provide a clue to understanding the initiation of transcription by TATA-less, multiple start site promoters.
Effect of Surface-Applied Sulfuric Acid on Growth and Nutrient Availability of Five Range Grasses in Calcareous Soils (1975)

In a greenhouse pot study, the application of concentrated sulfuric acid to two calcareous soil surfaces significantly increased growth of five range grasses: Lehmann lovegrass (Eragrostis lehmanniana Nees.), Wilman lovegrass (E. superba Peyr.), atherstone lovegrass (E. atherstonei Stapf.), weeping lovegrass (E. curvula (Schrad.) Nees.), and blue panicgrass (Panicum antidolale Retz.). These species varied in their response to soil applied phosphorus (P), iron (Fe), and sulfuric acid. The effectiveness of H2SO4 was attributed principally to increased solubility of these elements. Sulfuric acid, being produced in large quantities in the Southwest, may prove to be a suitable alternative to existing Fe and P fertilizers.
Ribonucleoprotein-masked nicks at 50-kbp intervals in the eukaryotic genomic DNA (2007)

By using a microscopic approach, field inversion single-cell gel electrophoresis, we show that preformed single-strand discontinuities are present in the chromatin of resting and proliferating mammalian and yeast cells. These single-strand breaks are primarily nicks positioned at approximately 50-kbp intervals throughout the entire genome that could be efficiently labeled in situ by DNA polymerase I holoenzyme but not by Klenow fragment and terminal transferase unless after ribonucleolytic treatments. The RNA molecules involved appear to comprise R-loops, recognized by the S9.6 RNA/DNA hybrid-specific antibody. By using the breakpoint cluster region of the Mixed Lineage Leukemia (MLL) gene as a model, we have found that the number of manifest nicks detected by FISH performed after field inversion single-cell gel electrophoresis depends on epigenetic context, but the difference between germ-line and translocated MLL alleles is abolished by protease treatment. Our data imply that the double-stranded genomic DNA is composed of contiguous rather than continuous single strands and reveal an aspect of higher-order chromatin organization with ribonucleoprotein-associated persistent nicks defining approximately 50-kbp domains.
Preformed Lymphocytotoxic Antibodies: the Effects of Class, Titer and Specificity on Liver Vs. Heart Allografts (1992)

The effect on liver and heart allograft survival (ACI rats to Lewis rats) was studied after three methods of recipient presensitization and after different intervals between sensitization and transplantation. With comparable lymphocytotoxic antibody titers, liver allografts always survived longer than heart grafts. The titer, class and specificity of the antibodies varied with the method of sensitization. Four skin grafts produced IgG and IgM lymphocytotoxic antibody titers of 1:2,000 to 4,000. The IgG fraction was shown to have hepatic vascular endothelial specificity by indirect immunofluorescence. These primed recipients hyperacutely rejected both heart and liver allografts, which showed vascular deposition of IgG antibodies. Survival of either kind of graft was inversely proportional to the lymphocytotoxic antibody titer and length of time after placement of the last skin graft. Presensitization with a single heterotopic heart graft produced an even higher mixed IgG and IgM lymphocytotoxic antibody titer of 1:8,000 but with less IgG vascular endothelial specificity. These animals also hyperacutely rejected heart or liver grafts with tissue deposition of IgG but less consistently and with a weaker correlation with lymphocytotoxic antibody titers and time after sensitization. Sensitization with two pretransplant blood transfusions produced the lowest titer (1:500 to 1,000) and the least IgG vascular endothelial specificity. Liver allograft survival was routinely enhanced in these animals, and little effect was seen on heart grafts. Collectively, the experiments showed that the liver is not only resistant to antibody-mediated rejection relative to the heart but is more easily enhanced.(ABSTRACT TRUNCATED AT 250 WORDS)
Low-Dose Aspirin for the Prevention of Atherothrombosis (2005)

This review considers the role of low-dose aspirin for the prevention of atherothrombosis, discussing the molecular mechanism of action of aspirin as well as clinical and epidemiologic studies of aspirin as an antiplatelet agent, with special emphasis on the benefits and risks in different patient populations.
Vegetation Recovery of Quarrying Sites in the Kitaikoma Area, Osaka (1986)

大規模な土砂採取のあと, 約10年前よりアカマツ・オオバヤシャブシ混植による緑化が行われた北生駒地域内15地点における毎木調査, 林床植生調査の結果, 植栽直後の乾燥によりヤシャブシが枯死したところではアカマツが生育するが, 両種が共存したところではヤシャブシによる被陰によりマツが枯死し, 混植の効果がないこと, 林床にはエノキ, クマノミズキなどが多く, かなり順調な植生回復が進行しつつあることなどが分った.
Predicting antigenic peptides suitable for the selection of phage antibodies (2004)

Selection from phage antibody libraries can be considered to be an in vitro immune system in which the antibody response is reduced to the bare minimum of antigen recognition. Using selections of antibodies on peptides from a phage antibody library, we investigated what constitutes peptide antigenicity in the context of the antibody-protein binding site. We selected polyclonal antibodies in a high throughput format against 44% of 90 overlapping peptides derived from three different proteins. Of these, 33% of peptides (epitopic peptides) were able to select antibodies that recognized the protein from which the peptides were derived. Although no algorithm was able to predict all epitopic peptides, solvent accessibility was the best predictor in this cell-free antibody selection context. We subsequently applied solvent accessibility to successfully predict epitopic peptides from p53 and Znf217, and showed that such peptide selected single-chain antibodies were able to recognize soluble p53 in ELISA and Znf217 in a western blot. This is likely to have considerable utility in functional genomics and proteomics where it should be possible to select antibodies against gene products on the basis of deduced amino acid sequence in a high throughput fashion.
T cell receptor alpha-chain gene rearrangements in B-precursor leukemia are in contrast to the findings in T cell acute lymphoblastic leukemia. Comparative study of T cell receptor gene rearrangement in childhood leukemia. (1987)

We have analyzed T cell receptor alpha-chain gene configuration using three genomic joining (J) region probes in 64 children with acute lymphoblastic leukemia (ALL). 11 out of 18 T-ALLs were T3 positive; alpha-chain gene rearrangements were demonstrated in only two of 18, indicating that the majority of T-ALLs would have rearrangements involving J alpha segments located upstream of these probes. In contrast, 15 out of 46 B-precursor ALLs showed rearrangements of the alpha-chain gene and J alpha segments located approximately 20-30 kb upstream of the constant region were involved in 13 of these patients. Nine of 15 B-precursor ALLs with rearranged alpha-chain genes had rearrangements of both gamma- and beta-chain genes, whereas the remaining six had no rearrangements of gamma- and beta-chain genes. These findings indicated that alpha-chain gene rearrangement is not specific for T lineage cells and gamma- and/or beta-chain gene rearrangement does not appear essential for alpha-chain gene rearrangement, at least in B-precursor leukemic cells.
Elevated chronic inflammatory factors and myeloid‐derived suppressor cells indicate poor prognosis in advanced melanoma patients (2014)

Chronic inflammation is considered to be one of the hallmarks for tumor initiation and progression. Moreover, a long-term production and accumulation of inflammatory factors lead to a local and systemic immunosuppression associated with cancer progression. However, the correlation between inflammatory mediators, immunosuppressive cells and the clinical outcome of malignant melanoma patients was poorly investigated. In this study, we performed a complex analysis of various inflammatory factors, myeloid-derived suppressor cells (MDSCs) and regulatory T cells (Tregs) in the peripheral blood of patients suffering from malignant melanoma of different stages. We demonstrated that levels of serum IL-1β, IFN-γ and CXCL10 were significantly increased in advanced melanoma patients. In addition, these factors were found to be associated with an increased frequency of MDSCs and Tregs as compared to age- and gender-matched healthy donors. Importantly, advanced melanoma patients with signs of progression displayed markedly elevated concentrations of IL-1β and CXCL10 as compared to patients with stable disease. Moreover, an enrichment of circulating monocytic (Mo)-MDSCs significantly correlated with a decreased progression free survival of these patients. Our data highlight a complex association between circulating inflammatory mediators, Mo-MDSCs and the clinical outcome as well as suggest that their levels in patients with advanced melanoma are of important prognostic value allowing the identification of those with high risk of disease progression.
Unprotected Peptides as Building Blocks for the Synthesis of Peptide Dendrimers with Oxime, Hydrazone, and Thiazolidine Linkages (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTUnprotected Peptides as Building Blocks for the Synthesis of Peptide Dendrimers with Oxime, Hydrazone, and Thiazolidine LinkagesJun Shao and James P. TamCite this: J. Am. Chem. Soc. 1995, 117, 14, 3893–3899Publication Date (Print):April 1, 1995Publication History Published online1 May 2002Published inissue 1 April 1995https://pubs.acs.org/doi/10.1021/ja00119a001https://doi.org/10.1021/ja00119a001research-articleACS PublicationsRequest reuse permissionsArticle Views2771Altmetric-Citations302LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information Get e-Alerts
Detection of mercury(ii) based on Hg2+–DNA complexes inducing the aggregation of gold nanoparticles (2008)

A DNA-Au NP probe for sensing Hg2+ using the formation of DNA-Hg2+ complexes through thymidine (T)-Hg2+ -T coordination to control the negative charge density of the DNA strands-thereby varying their structures-adsorbed onto Au NPs.
A multidrug efflux transporter inListeria monocytogenes (2000)

A chromosomal gene (mdrL) was found in Listeria monocytogenes L028, showing a high degree of similarity with multidrug efflux transporters of the major facilitator superfamily (family 2). An allele-substituted mutant of this gene failed to pump out ethidium bromide and presented lower minimal inhibitory concentrations of macrolides, cefotaxime and heavy metals. This is the first multidrug efflux pump described in Listeria.
Development of a Directly Compressible Poly(Ethylene Oxide) Matrix for the Sustained-Release of Dihydrocodeine Bitartrate (2003)

The purpose of this study was to design and evaluate a directly compressible hydrophilic poly(ethylene oxide) (PEO) matrix for the oral sustained delivery of dihydrocodeine bitartrate (DHCT). A direct compression method was used to prepare PEO matrices, and the amount of PEO in the matrices was varied to optimize in vitro DHCT release profiles. In vitro release studies indicated that the matrices containing 20%-70% w/w of PEO with molecular weight of 5.0 x 10(6) showed a similar release profile, as estimated with DT50%, to that exhibited by a marketed product, DHC Continus. In vivo bioavailability study revealed that the difference in the pharmacokinetic parameters such as AUC0-30 and Tmax of the selected sustained-release formulation containing 60% w/w of PEO 5.0 x 10(6) and DHC Continus was statistically insignificant (p > 0.05). Thus, it could be concluded that the extent of bioavailability of the sustained-release formulation developed here was similar to that of DHC Continus although Cmax values of these two preparations were significantly different (p < 0.05). From the data obtained in this research, hydrophilic PEO matrices were found to be a novel sustained-release carrier for the oral delivery of DHCT.
The plant transcriptome—from integrating observations to models (2013)

Transcriptomes as assessed by either microarrays or next-generation sequencing have produced a hitherto unprecedented data flood regarding transcript identity and levels in plant systems. Microarray data has been extensively used over the last 15 years or so and evaluation of the data thus produced has progressed well beyond early statistically quality evaluation and descriptive lists to a mature science whereby gene networks and cascades have been able to provide mechanistic insight. The development of sensitive quantitative PCR for lowly expressed genes such as transcription factors has additionally allowed another layer of complexity to be accessed and the modeling of transcription factor expression with that of target genes has met considerable success. Yet more recently, data emanating from RNAseq studies have greatly improved the coverage of transcript profiling. That said, this technology further compounded transcriptome analysis by making it possible to identify differentially spliced transcripts etc. In this research topic we would like to provide an “on the fly” portrait of the use of either microarray or RNAseq based datasets in contemporary Plant Systems Biology.
Lymphoid development in mice with a targeted deletion of the interleukin 2 receptor gamma chain. (1995)

The interleukin 2 receptor gamma chain (IL-2R gamma) is a component of the receptors for IL-2, IL-4, IL-7, and IL-15. Mutations in IL-2R gamma in man appear responsible for the X chromosome-linked immunodeficiency SCIDX1, characterized by a defect in T-cell and natural killer (NK)-cell differentiation with the presence of poorly functioning B cells. To explore at which level IL-2R gamma affects lymphoid development in vivo, we have analyzed mice derived from embryonic stem (ES) cells with mutant IL-2R gamma loci generated by Cre/loxP-mediated recombination. In the peripheral blood of chimeric animals, lymphoid cells derived from IL-2R gamma- ES cells were not detected, although control ES cells carrying an IL-2R gamma gene with embedded loxP sites gave rise to T-, B-, and NK-cell lineages. Germline IL-2R gamma-deficient male animals, however, developed some mature splenic B and T cells, although the absolute number of lymphocytes was almost 10-fold reduced. In contrast, there was a complete disappearance of NK cells (over 350-fold reduction). Development of gut-associated intraepithelial lymphocytes was also severely diminished, and Peyer's patches were not detected. In vitro mitogenic responses of thymocytes, IL-4-directed immunoglobulin class switch of splenocytes, and NK activity were defective. Thus, IL-2R gamma facilitates mainstream B- and T-cell generation and function and also appears to be essential for NK-cell development.
The Multifaceted Mechanisms of Estradiol and Estrogen Receptor Signaling (2001)

In recent years it has become apparent through the use of ER agonists and antagonists that the biological actions of estrogens are multifaceted. Estrogens and antiestrogens mediate their effects through diverse molecular mechanisms. Thus, SERMs can be viewed as a class of compounds that exhibit an expanse of estrogen actions and specificity that capitalize on the preexistence of multiple cellular pathways of ER action in different target tissues. It is anticipated that the continued use of in vitro and animal models will reveal additional mechanisms of ER signaling and tissue response and provide a more clear understanding of the spectrum of estrogen action, which will facilitate the development of novel pharmaceuticals for the treatment of estrogen-associated pathologies.
T suppressor lymphocytes inhibit NF-kappa B-mediated transcription of CD86 gene in APC. (1999)

CD8+CD28- human T suppressor cells (Ts) act on APC, inhibiting their ability to elicit Th activation and proliferation. This effect is due to inhibition of the CD40 pathway which normally leads to CD80 and CD86 up-regulation. To determine whether Ts inhibit expression of B7 molecules by blocking transcription, we cloned and characterized the CD86 promoter. Mutational analysis revealed that Ts inhibit transcription driven by the CD86 promoter. The NF-kappa B binding site, at -612 of the CD86 promoter, is essential for Th-induced transcription. In cultures containing Th and Ts, Ts inhibit Th-induced NF-kappa B activation in APC. Together, these findings indicate that Ts inhibition of NF-kappa B activation in APC is a means by which they regulate the activation and proliferation of Th.
A novel metastatic animal model reflecting the clinical appearance of human neuroblastoma: growth arrest of orthotopic tumors by natural, cytotoxic human immunoglobulin M antibodies. (2001)

Neuroblastoma (NB), the most common extracranial solid tumor in childhood is associated with poor prognosis in patients with advanced tumor stages. Natural human cytotoxic anti-NB IgM antibodies present in the serum of healthy humans are discussed as a potential novel immunotherapeutic regimen against human NB because these antibodies have been shown to affect growth arrest of solid s.c. xenografts of human NB in nude rats. Subcutaneously induced tumors, however, exhibit a different growth pattern compared with the typical growth pattern of NB tumors in humans. Therefore, we developed in this study a novel metastatic tumor model in nude rats that reflects the clinical appearance of human NB and used this model to study the therapeutic efficacy of human anti-NB IgM. Intra-aortal injection of human NB cells in nude rats resulted in the development of large invasive adrenal gland tumors and micrometastases in the liver and bones. Apparently, adrenal glands provide most favorable growth conditions for human NB cells, as documented by the preferential and rapid growth of NB cells in this location. We studied three different treatment protocols of natural human anti-NB IgM. Anti-NB IgM completely inhibited tumor formation and metastases when injected simultaneously with human LAN-1 NB cells (P < 0.05). When antibody treatment was started 6 days after tumor cell injection (i.e., micrometastatic stage), tumor growth was inhibited by 90% (P < 0.05). An anti-NB IgM therapy directed against established tumors (14 days after tumor cell injection) shrank adrenal gland tumors by 90% (P < 0.05). Analysis of the tumors revealed both complement activation and an induction of apoptosis as two independent mechanisms of antitumor function. This study strongly suggests human anti-NB IgM antibodies as new agents for the therapy of neuroblastoma.