gebhart/patrepeval huggingface dataset:
Nonclassical CD1d-restricted NK T cells that produce IL-13 characterize an atypical Th2 response in ulcerative colitis (2004)

While Crohn disease (CD) has been clearly identified as a Th1 inflammation, the immunopathogenesis of its counterpart inflammatory bowel disease, ulcerative colitis (UC), remains enigmatic. Here we show that lamina propria T (LPT) cells from UC patients produce significantly greater amounts of IL-13 (and IL-5) than control cells and little IFN-gamma, whereas comparable cells from CD patients produce large amounts of IFN-gamma and small amounts of IL-13. We then show that stimulation of UC LPT cells bearing an NK marker (CD161) with anti-CD2/anti-CD28 or with B cells expressing transfected CD1d induces substantial IL-13 production. While this provided firm evidence that the IL-13-producing cell is an NK T (NKT) cell, it became clear that this cell does not express invariant NKT cell receptors characteristic of most NKT cells since there was no increase in cells binding alpha-galactosylceramide-loaded tetramers, and alpha-galactosylceramide did not induce IL-13 secretion. Finally, we show that both human NKT cell lines as well as UC CD161(+) LPT cells are cytotoxic for HT-29 epithelial cells and that this cytotoxicity is augmented by IL-13. These studies show that UC is associated with an atypical Th2 response mediated by nonclassical NKT cells producing IL-13 and having cytotoxic potential for epithelial cells.
Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome (2003)

Functional analysis of a genome requires accurate gene structure information and a complete gene inventory. A dual experimental strategy was used to verify and correct the initial genome sequence annotation of the reference plant Arabidopsis. Sequencing full-length cDNAs and hybridizations using RNA populations from various tissues to a set of high-density oligonucleotide arrays spanning the entire genome allowed the accurate annotation of thousands of gene structures. We identified 5817 novel transcription units, including a substantial amount of antisense gene transcription, and 40 genes within the genetically defined centromeres. This approach resulted in completion of approximately 30% of the Arabidopsis ORFeome as a resource for global functional experimentation of the plant proteome.
A coarse frequency offset estimation in an OFDM system using the concept of the coherence phase bandwidth (2002)

A new coarse frequency offset estimation algorithm is proposed which performs robust operation in the presence of a symbol timing offset in an allowed range. The effect of a symbol timing offset on estimating a coarse frequency offset is analyzed and the coherence phase bandwidth according to the allowed symbol timing offset is introduced. In addition, a new technique for performing the coarse frequency estimation using the coherence phase bandwidth is described. Simulation results show that the proposed algorithm estimates a coarse frequency offset well under both AWGN and multipath channels even in the presence of the symbol timing offset within an allowed range.
Secretion of a single-gene-encoded immunoglobulin from myeloma cells. (1993)

We describe construction of a single gene encoding a single-chain immunoglobulin-like molecule. This single-gene approach circumvents inefficiencies inherent in delivering two genes into a mammalian cell and in the assembly of a functional immunoglobulin molecule. It would also facilitate ex vivo transfection of cells for gene-therapy protocols. SP2/0 murine myeloma cells transfected with the single gene SG delta CLCH1 expressed a single-chain protein, SC delta CLCH1, comprising approximately 60 kDa of the anti-carcinoma monoclonal antibody (mAb) CC49. The single-chain protein consisted of the heavy- and light-chain variable (VH and VL) domains of the mAb covalently joined through a short linker peptide, while the carboxyl end of the VL domain was linked to the amino terminus of the human gamma 1 Fc region through the hinge region. The single-chain protein assembled into a dimeric molecule, termed SCA delta CLCH1, of approximately 120 kDa and was secreted into the tissue culture fluid. SDS/PAGE analysis of the secreted immunoglobulin purified by protein G affinity chromatography confirmed the size of the molecule. The native mAb CC49 and SCA delta CLCH1 of CC49 showed similar binding to the tumor-associated glycoprotein TAG-72, and the chimeric mAb CC49 and SCA delta CLCH1 showed similar cytotoxic activity. This single-gene construct approach provides a way of generating an immunoglobulin-like molecule which retains the specificity, binding properties, and cytolytic activity of the chimeric mAb CC49. The immunoglobulin-like molecule SCA delta CLCH1 is potentially a therapeutic and diagnostic reagent against a range of human carcinomas.
DNA binding site of the growth factor-inducible protein Zif268. (1989)

Zif268, a zinc finger protein whose mRNA is rapidly activated in cells exposed to growth factors or other signaling agents, is thought to play a role in regulating the genetic program induced by extracellular ligands. We report that Zif268 has one of the characteristics of a transcriptional regulator, namely, sequence-specific binding to DNA. Zif268 synthesized in Escherichia coli bound to two sites upstream of the zif268 gene and to sites in the promoter regions of other genes. The nucleotide sequences responsible for binding were defined by DNase I footprinting, by methylation interference experiments, and by use of synthetic oligonucleotides. From these results we derived the following consensus sequence for a Zif268 high-affinity binding site: GCGTGGGGCG.
Development of Targeted Delivery Systems for Nucleic Acid Drugs (1997)

Our increased understanding of disease pathogenesis is the basis for developing novel nucleic acid drugs. The main challenge encountered in this development is how to maintain therapeutically meaningful concentrations of the drugs in the vicinity of their targets for the desired periods. The intrinsic difficulty arises from the fact that nucleic acid drugs are not readily transported across membranes. Hence, their delivery and transport characteristics at the whole body, organ and cellular levels need to be thoroughly examined. Liposomes and receptor-mediated polycation systems are promising carriers for their delivery in vivo. There are many barriers to be overcome for successful antisense and gene therapies. Along with other factors, disposition, stability against nucleases, binding to cell surface receptor and internalization, and intracellular trafficking affect the in vivo delivery and efficacy of nucleic acid drugs. This review article discusses the delivery and transport of these compounds.
Identification of T Cell Ligands in a Library of Peptides Covalently Attached to HLA-DR4 (2000)

While T cells have been clearly implicated in a number of disease processes including autoimmunity, graft rejection, and atypical immune responses, the precise Ags recognized by the pathogenic T cells have often been difficult to identify. This has particularly been true for MHC class II-restricted CD4+ T cells. Although such cells can be demonstrated to have undergone clonal expansion at sites of pathology, they are frequently difficult to establish as stable T cell clones. Furthermore, in general, larger peptides in higher concentrations are required to stimulate CD4+ T cells than CD8+ T cells, which makes some of the techniques developed to identify CD8+ T cell Ags impractical. To circumvent some of these problems, we developed a model system consisting of two parts. The first part involves the construction of an indicator T cell hybridoma expressing a chimeric TCR comprised of murine constant regions and human variable regions specific for influenza hemagglutinin 307-319 presented by DR4. The second part consists of a library of fibroblasts each expressing multiple peptides as amino terminal covalent extensions of the beta-chain of HLA-DR4 (DRA1*0101, DRB1*0401). Using this model system, we screened approximately 100, 000 peptides and identified three novel peptides stimulatory for the HA1.7 TCR. While there is some convergence at residues known to be important for T cell recognition, all three peptides differ markedly from each other and bear little resemblance to wild-type hemagglutinin 307-319.
Vasopressin-induced vasoconstriction: two concentration-dependent signaling pathways (2007)

Current scientific literature generally attributes the vasoconstrictor effects of [Arg(8)]vasopressin (AVP) to the activation of phospholipase C (PLC) and consequent release of Ca(2+) from the sarcoplasmic reticulum. However, half-maximal activation of PLC requires nanomolar concentrations of AVP, whereas vasoconstriction occurs when circulating concentrations of AVP are orders of magnitude lower. Using cultured vascular smooth muscle cells, we previously identified a novel Ca(2+) signaling pathway activated by 10-100 pM AVP. This pathway is distinguished from the PLC pathway by its dependence on protein kinase C (PKC) and L-type voltage-sensitive Ca(2+) channels (VSCC). In the present study, we used isolated, pressurized rat mesenteric arteries to examine the contributions of these different Ca(2+) signaling mechanisms to AVP-induced vasoconstriction. AVP (10(-14)-10(-6) M) induced a concentration-dependent constriction of arteries that was reversible with a V(1a) vasopressin receptor antagonist. Half-maximal vasoconstriction at 30 pM AVP was prevented by blockade of VSCC with verapamil (10 microM) or by PKC inhibition with calphostin-C (250 nM) or Ro-31-8220 (1 microM). In contrast, acute vasoconstriction induced by 10 nM AVP (maximal) was insensitive to blockade of VSCC or PKC inhibition. However, after 30 min, the remaining vasoconstriction induced by 10 nM AVP was partially dependent on PKC activation and almost fully dependent on VSCC. These results suggest that different Ca(2+) signaling mechanisms contribute to AVP-induced vasoconstriction over different ranges of AVP concentration. Vasoconstrictor actions of AVP, at concentrations of AVP found within the systemic circulation, utilize a Ca(2+) signaling pathway that is dependent on PKC activation and can be inhibited by Ca(2+) channel blockers.
Tissue culture‐based breast cancer biomarker discovery platform (2008)

Current cancer biomarkers suffer from low diagnostic sensitivity and specificity and have not yet made a major impact on reducing cancer burden. Proteomic methods based on mass spectrometry have matured significantly over the past few years and hold promise to deliver candidate markers for diagnosis, prognosis or monitoring therapeutic response. Because of the complex nature of biological fluids such as plasma, biomarker discovery efforts using proteomics have not as yet delivered any novel tumor markers. Recently, there has been a rise in the number of publications utilizing a cell culture-based model of cancer to identify novel candidate tumor markers. The secretome of cancer cell lines constitutes an important class of proteins that can act locally and systemically in the body. Secreted proteins, in addition to serving as serological markers, play a central role in physiology and pathophysiology. In this review, we focus on the proteomics of breast cancer and the different strategies to mine for biomarkers, with particular emphasis on a cell culture-based model developed in our laboratory.
The Wnt-5a–Derived Hexapeptide Foxy-5 Inhibits Breast Cancer Metastasis In vivo by Targeting Cell Motility (2008)

Abstract Purpose: An inherent problem in breast cancer treatment is that current therapeutic approaches fail to specifically target the dissemination of breast cancer cells from the primary tumor. Clinical findings show that the loss of Wnt-5a protein expression in the primary breast tumor predicts a faster tumor spread, and in vitro analyses reveal that it does so by inhibiting tumor cell migration. Therefore, we hypothesized that the reconstitution of Wnt-5a signaling could be a novel therapeutic strategy to inhibit breast cancer metastasis. Experimental Design: We used in vitro techniques to show that 4T1 mouse breast cancer cells responded to the reconstitution of Wnt-5a signaling using our novel Wnt-5a mimicking hexapeptide, Foxy-5, in the same way as human breast cancer cells. Therefore, we could subsequently study its effect in vivo on the metastatic spread of cancer following the inoculation of 4T1 cells into mice. Results: In vitro analyses revealed that both recombinant Wnt-5a and the Wnt-5a–derived Foxy-5 peptide impaired migration and invasion without affecting apoptosis or proliferation of 4T1 breast cancer cells. The in vivo experiments show that i.p. injections of Foxy-5 inhibited metastasis of inoculated 4T1 breast cancer cells from the mammary fat pad to the lungs and liver by 70% to 90%. Conclusions: These data provide proof of principle that the reconstitution of Wnt-5a signaling in breast cancer cells is a novel approach to impair breast tumor metastasis by targeting cell motility. In combination with existing therapies, this approach represents a potential novel therapeutic strategy for the treatment of breast cancer patients.
High-power K-band submicron insulating gate heterostructure field-effect transistors (2004)

In this paper, we report the high performance quarter micron gate Si/sub 3/N/sub 4//AlGaN/GaN metal-insulator-semiconductor heterostructure field effect transistors (MISHFET) with a 5 W/mm CW power at 26 GHz at drain bias of 35 V. The MISHFETs to have the same power gain and power added efficiency as the HFETs, in spite of lower transconductance. An improved RF linearity of MISHFETs is attributed to more linear transconductance-gate bias dependence.
Tissue Regeneration Based on Growth Factor Release (2003)

Tissue engineering is an emerging biomedical field intended to assist the regeneration of body tissue defects too large to self-repair as well as to substitute for the biological functions of damaged and injured organs by using cells with proliferative and differentiative potential. In addition to basic research on such cells, it is undoubtedly indispensable for successful tissue engineering to create an artificial environment enabling cells to induce tissue regeneration. Such an environment can be achieved by making use of a scaffold for cell proliferation and differentiation and for growth factors, as well as their combination. Growth factors are often required to promote tissue regeneration, as they can induce angiogenesis, which supplies oxygen and nutrients to cells transplanted for organ substitution to maintain their biological functions. However, the biological effects of growth factors cannot always be expected because of their poor in vivo stability, unless a drug delivery system is contrived. In this article, tissue regeneration based on the release of growth factors is reviewed to emphasize the significance of drug delivery systems in tissue engineering.
ChemInform Abstract: Synthesis of an N‐Alkyl Derivative of 2′‐Deoxyisoguanosine. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The biosynthesis of nascent membrane lipoteichoic acid of Streptococcus faecium (S. faecalis ATCC 9790) from phosphatidylkojibiosyl diacylglycerol and phosphatidylglycerol. (1980)

Phosphatidylkojibiosyl diacylglycerol functions as the acceptor of sn-glycerol 1-phosphate moieties from phosphatidylglycerol in the in vitro synthesis of the membrane lipoteichoic acid of Streptococcus faecium (S. faecalis ATCC 9790). The enzyme catalyzing this polymer-forming reaction is membrane-bound. The majority of the product is water-soluble, is excluded from Sepharose 6B, and, after longer incubations, changes to a form that co-precipitates with protein upon exposure to a denaturing agent. These properties are shared by the polyglycerol phosphate-containing membrane lipoteichoic acid isolated from whole cells of S. faecium. However, unlike the lipoteichoic acid generated in vivo, the glycerol phosphate polymer portion of the product synthesized in vitro is not substituted and, therefore, is considered a nascent lipoteichoic acid intermediate.
Angiogenesis in Oral Cancer (2001)

Head and neck squamous cell carcinoma (HNSCC) is an aggressive malignancy that develops after years of chronic exposure to alcohol and tobacco products. Exposure to these agents results in alterations of genes that are important in the regulation of various cellular functions. This loss of regulation allows the tumor cells to survive and grow in an unchecked manner by allowing the cells to perform functions that contribute to the growth of the tumor. Some of these important changes include the acquisition of immortality and the ability to invade tissue and/or metastasize to other sights, as well as acquiring the ability to induce angiogenesis. Angiogenesis, the growth of new blood vessels from pre-existing ones, is a complex phenomenon that is absolutely required for the continued growth and survival of solid neoplasms. Without new blood vessels to provide nutrients and remove waste, tumors would be unable to grow larger than 2-3 mm in diameter. Therefore, one could envision its potential role in both the treatment and prevention of malignancies such as HNSCC. The concept of chemoprevention is extremely important in HNSCC since patients often develop multiple independent lesions throughout the mucosa of the upper aerodigestive tract. Therefore, the comprehensive treatment of this disease must address not only the initial primary neoplasm, but also prevent the progression of the premalignant lesions lurking throughout the rest of the mucosal surfaces. This review will outline the basic changes that occur in tumor cells that result in the switch to angiogenic phenotype. In addition, it will discuss the present status of using antiangiogenic agents in the treatment of cancer. Finally, this paper will present a rationale for the use of multiple antiangiogenic agents as a means of developing new chemotherapeutic and chemopreventive protocols that may result in reduced patient toxicity while maintaining similar clinical efficacies.
Serum B12 Tryptase Level as a Marker of Allergic Airway Inflammation in Asthma (2002)

Tryptase is a specific marker of mast-cell activation and plays a part in the pathophysiology of various allergic diseases including asthma, but little is known of the spillover of this enzyme into the systemic circulation. Therefore, we measured serum levels of mast-cell-derived tryptase in 21 patients with mild to moderate asthma and 20 healthy, subjects, using a B12 monoclonal antibody-based immunofluoroassay that detects both monomers and tetramers of alpha- and beta-tryptases. There was a good correlation between serum and sputum tryptase levels, and, compared with healthy subjects (1.68 +/- 0.31 ng/ml), asthma patients had higher concentrations of serum tryptase (atopic asthma, 4.18 +/- 0.95 ng/ml, p = 0.022; nonatopic asthma, 3.93 +/- 0.82 ng/ml, p = 0.031). Although serum tryptase levels did not correlate with asthma symptom scores, peak expiratory flow, or forced expiratory volume in 1 s, they positively correlated with mast-cell and eosinophil counts (p = 0.041 and p = 0.025, respectively) and eosinophil cationic protein contents (p = 0.029) in induced sputum. These results suggest that serum tryptase detected with B12 antibody is a marker of allergic airway inflammation in asthma.
Asymmetric synthesis of anti-α-alkyl-β-amino acids (1994)

An investigation into the asymmetric induction accompanying alkylations of enolates derived from the highly diastereoselective conjugate addition of lithium (R)-N-benzyl-N-α-methylbenzylamide (R)-1 to crotonate and cinnamate esters has been performed. The access to different enolate geometries afforded by the conjugate addition process and subsequent enolate regeneration by deprotonation of the β-amino ester conjugate adducts enabled two disparate sets of selectivity data to be compiled. Although both approaches furnished predominantly anti-α-alkyl-β-amino esters, the two-step procedure proved to be considerably more selective. Several factors which play a major role in determining the alkylation selectivity are identified, including the cooperative influence of the α-methylbenzylamino stereocentre. Since debenzylation and hydrolysis of the alkylated products was straightforward, this methodology provides a direct route to anti-α-alkyl-β-amino acids in homochiral form.
Protein kinase C α and ε phosphorylation of troponin and myosin binding protein C reduce Ca2+ sensitivity in human myocardium (2009)

Previous studies indicated that the increase in protein kinase C (PKC)-mediated myofilament protein phosphorylation observed in failing myocardium might be detrimental for contractile function. This study was designed to reveal and compare the effects of PKCalpha- and PKCepsilon-mediated phosphorylation on myofilament function in human myocardium. Isometric force was measured at different [Ca2+] in single permeabilized cardiomyocytes from failing human left ventricular tissue. Activated PKCalpha and PKCepsilon equally reduced Ca2+ sensitivity in failing cardiomyocytes (DeltapCa50 = 0.08 +/- 0.01). Both PKC isoforms increased phosphorylation of troponin I- (cTnI) and myosin binding protein C (cMyBP-C) in failing cardiomyocytes. Subsequent incubation of failing cardiomyocytes with the catalytic subunit of protein kinase A (PKA) resulted in a further reduction in Ca2+ sensitivity, indicating that the effects of both PKC isoforms were not caused by cross-phosphorylation of PKA sites. Both isozymes showed no effects on maximal force and only PKCalpha resulted in a modest significant reduction in passive force. Effects of PKCalpha were only minor in donor cardiomyocytes, presumably because of already saturated cTnI and cMyBP-C phosphorylation levels. Donor tissue could therefore be used as a tool to reveal the functional effects of troponin T (cTnT) phosphorylation by PKCalpha. Massive dephosphorylation of cTnT with alkaline phosphatase increased Ca2+ sensitivity. Subsequently, PKCalpha treatment of donor cardiomyocytes reduced Ca2+ sensitivity (DeltapCa50 = 0.08 +/- 0.02) and solely increased phosphorylation of cTnT, but did not affect maximal and passive force. PKCalpha- and PKCepsilon-mediated phosphorylation of cMyBP-C and cTnI as well as cTnT decrease myofilament Ca2+ sensitivity and may thereby reduce contractility and enhance relaxation of human myocardium.