gebhart/patrepeval huggingface dataset:
Antigen-unspecific B Cells and Lymphoid Dendritic Cells Both Show Extensive Surface Expression of Processed Antigen–Major Histocompatibility Complex Class II Complexes after Soluble Protein Exposure In Vivo or In Vitro (1997)

Intravenous (i.v.) injection of high amounts of soluble proteins often results in the induction of antigen-specific tolerance or deviation to helper rather than inflammatory T cell immunity. It has been proposed that this outcome may be due to antigen presentation to T cells by a large cohort of poorly costimulatory or IL-12-deficient resting B cells lacking specific immunoglobulin receptors for the protein. However, previous studies using T cell activation in vitro to assess antigen display have failed to support this idea, showing evidence of specific peptide-major histocompatibility complex (MHC) class II ligand only on purified dendritic cells (DC) or antigen-specific B cells isolated from protein injected mice. Here we reexamine this question using a recently derived monoclonal antibody specific for the T cell receptor (TCR) ligand formed by the association of the 46-61 determinant of hen egg lysozyme (HEL) and the mouse MHC class II molecule I-Ak. In striking contrast to conclusions drawn from indirect T cell activation studies, this direct method of TCR ligand analysis shows that i.v. administration of HEL protein results in nearly all B cells in lymphoid tissues having substantial levels of HEL 46-61-Ak complexes on their surface. DC readily isolated from spleen also display this TCR ligand on their surface. Although the absolute number of displayed ligands is greater on such DC, the relative specific ligand expression compared to total MHC class II levels is similar or greater on B cells. These results demonstrate that in the absence of activating stimuli, both lymphoid DC and antigen-unspecific B cells present to a similar extent class II-associated peptides derived from soluble proteins in extracellular fluid. The numerical advantage of the TCR ligand-bearing B cells may permit them to interact first or more often with naive antigen-specific T cells, contributing to the induction of high-dose T cell tolerance or immune deviation.
Receptor Recognition Sites of Cytokines Are Organized as Exchangeable Modules (1999)

Interleukin-6 (IL-6) and ciliary neurotrophic factor (CNTF) are "4-helical bundle" cytokines of the IL-6 type family of neuropoietic and hematopoietic cytokines. IL-6 signals by induction of a gp130 homodimer (e.g. IL-6), whereas CNTF and leukemia inhibitory factor (LIF) signal via a heterodimer of gp130 and LIF receptor (LIFR). Despite binding to the same receptor component (gp130) and a similar protein structure, IL-6 and CNTF share only 6% sequence identity. Using molecular modeling we defined a putative LIFR binding epitope on CNTF that consists of three distinct regions (C-terminal A-helix/N-terminal AB loop, BC loop, C-terminal CD-loop/N-terminal D-helix). A corresponding gp130-binding site on IL-6 was exchanged with this epitope. The resulting IL-6/CNTF chimera lost the capacity to signal via gp130 on cells without LIFR, but acquired the ability to signal via the gp130/LIFR heterodimer and STAT3 on responsive cells. Besides identifying a specific LIFR binding epitope on CNTF, our results suggest that receptor recognition sites of cytokines are organized as modules that are exchangeable even between cytokines with limited sequence homology.
A Single Adenosine with a Neutral p K a in the Ribosomal Peptidyl Transferase Center (2000)

Biochemical and crystallographic evidence suggests that 23S ribosomal RNA (rRNA) is the catalyst of peptide bond formation. To explore the mechanism of this reaction, we screened for nucleotides in Escherichia coli 23S rRNA that may have a perturbed pKa (where Ka is the acid constant) based on the pH dependence of dimethylsulfate modification. A single universally conserved A (number 2451) within the central loop of domain V has a near neutral pKa of 7.6 +/- 0.2, which is about the same as that reported for the peptidyl transferase reaction. In vivo mutational analysis of this nucleotide indicates that it has an essential role in ribosomal function. These results are consistent with a mechanism wherein the nucleotide base of A2451 serves as a general acid base during peptide bond formation.
Identification of Nrf2-regulated genes induced by the chemopreventive agent sulforaphane by oligonucleotide microarray. (2002)

Electrophiles formed during metabolic activation of chemical carcinogens and reactive oxygen species generated from endogenous and exogenous sources play a significant role in carcinogenesis. Cancer chemoprevention by induction of phase 2 proteins to counteract the insults of these reactive intermediates has gained considerable attention. Nuclear factor E2 p45-related factor 2 (Nrf2), a bZIP transcription factor, plays a central role in the regulation (basal and or inducible expression) of phase 2 genes by binding to the "antioxidant response element" in their promoters. Identification of novel Nrf2-regulated genes is likely to provide insight into cellular defense systems against the toxicities of electrophiles and oxidants and may define effective targets for achieving cancer chemoprevention. Sulforaphane is a promising chemopreventive agent that exerts its effect by strong induction of phase 2 enzymes via activation of Nrf2. In the present study, a transcriptional profile of small intestine of wild-type (nrf2 +/+) and knock out (nrf2 -/-) mice treated with vehicle or sulforaphane (9 micromol/day for 1 week, p.o.) was generated using the Murine Genome U74Av2 oligonucleotide array (representing approximately 6000 well-characterized genes and nearly 6000 expressed sequence tags). Comparative analysis of gene expression changes between different treatment groups of wild-type and nrf2-deficient mice facilitated identification of numerous genes regulated by Nrf2 including previously reported Nrf2-regulated genes such as NAD(P)H:quinone reductase (NQO1), glutathione S-transferase (GST), gamma-glutamylcysteine synthetase (GCS), UDP-glucuronosyltransferases (UGT),epoxide hydrolase, as well as a number of new genes. Also identified were genes encoding for cellular NADPH regenerating enzymes (glucose 6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, and malic enzyme), various xenobiotic metabolizing enzymes, antioxidants (glutathione peroxidase, glutathione reductase, ferritin, and haptaglobin), and biosynthetic enzymes of the glutathione and glucuronidation conjugation pathways. The data were validated by Northern blot analysis and enzyme assays of selected genes. This investigation expands the horizon of Nrf2-regulated genes, highlights the cross-talk between various metabolic pathways, and divulges the pivotal role played by Nrf2 in regulating cellular defenses against carcinogens and other toxins.
HLA class I-restricted cytotoxic T lymphocytes specific for hepatitis C virus. Identification of multiple epitopes and characterization of patterns of cytokine release. (1995)

Cytotoxic T lymphocytes (CTL) are important to the control of viral replication and their presence may be important to disease outcome. An understanding of the spectrum of proteins recognized by hepatitis C virus (HCV)-specific CTL and the functional properties of these cells is an important step in understanding the disease process and the mechanisms of persistent infection, which occurs in the majority of HCV-infected individuals. In this report we identify HCV-specific CTL responses restricted by the HLA class I molecules A2, A3, A11, A23, B7, B8, and B53. The epitopes recognized by these intrahepatic CTL conform to published motifs for binding to HLA class I molecules, although in some cases we have identified CTL epitopes for which no published motif exists. The use of vectors expressing two different strains of HCV, HCV-1 and HCV-H, revealed both strain-specific and cross-reactive CTL. These HCV-specific CTL were shown to produce cytokines including IFN-gamma, TNF-alpha, GM-CSF, IL-8, and IL-10 in an antigen- and HLA class I-specific manner. These studies indicate that the CTL response to HCV is broadly directed and that as many as five different epitopes may be targeted in a single individual. The identification of minimal epitopes may facilitate peptide-specific immunization strategies. In addition, the release of proinflammatory cytokines by these cells may contribute to the pathogenesis of HCV-induced liver damage.
Detection of Massachusetts and Arkansas Serotypes of Infectious Bronchitis Virus in Broilers (2006)

The objective of this study was to compare the presence of the Arkansas (Ark) and Massachusetts (Mass) serotypes of infectious bronchitis virus (IBV) in the tracheas and cecal tonsils of commercial broilers after vaccination at 1 day of age by coarse spray. When given as a single serotype vaccine, the Mass strain was detected by reverse transcriptase-polymerase chain reaction (RT-PCR)-restriction fragment length polymorphism (RFLP) only in the tracheas, whereas the Ark strain was detected in both the tracheas and cecal tonsils. By in situ hybridization, the Mass and Ark nucleocapsid (Nc) genes were detected only at 7 days in the tracheas. When both strains were given in the mixed vaccine, the Mass strain was more consistently detected by RT-PCR-RFLP in the tracheas and cecal tonsils at early stages of infection (up to 14 days) and the Arkansas strain was more consistently detected at late stages of infection (21 and 28 days). By in situ hybridization, the IBV Nc gene was more consistently detected in the trachea at early stages of infection (7, 14, and 21 days) and in the cecal tonsils at late stages of infection (21, 28, and 35 days). In general, the Mass strain was more frequently recovered from the tracheal and cecal tonsil tissues at earlier stages of infection and the Ark strain was recovered at later stages of infection.
The Use of Nanoparticles for Gene Therapy in the Nervous System (2012)

Nanoparticles represent an alternative to viral vectors for genetic material transfer to the nervous system. However, to increase transfection efficiency in the central nervous system and to decrease toxicity, the design of nanoparticles needs to be improved to enhance blood-brain barrier crossing and endosomal escape. This paper reviews the strategies used to solve these difficulties and covers the use of various nanoparticles including natural inorganic particles, natural polymers, cationic lipids, polyethylenimine derivatives, dendrimers, and carbon-based nanoparticles. The effectiveness, both in vivo and in vitro, of each method to deliver genetic material to neural tissue is discussed.
Omeprazole Enhances the Efficacy of Pancreatin (Pancrease) in Cystic Fibrosis (1991)

We studied the effect of the addition of omeprazole (20 mg once a day) to treatment with pancreatin (Pancrease, Cilag, Herentals, Belgium), two or four capsules three times a day, on fecal fat excretion in a double-blind, crossover fashion in nine patients with cystic fibrosis having persistent steatorrhea while taking Pancrease, two capsules three times a day (mean fecal fat excretion, 22.3%; range, 12% to 44%). Neither doubling of the dose of Pancrease nor addition of omeprazole to the lower dose of Pancrease significantly reduced fecal fat excretion (mean, 19.6% [range, 10% to 34%]; mean, 16.4% [range, 6% to 32%], respectively). However, addition of omeprazole to the higher dose of Pancrease (four capsules three times a day) significantly reduced fecal fat excretion when compared with the two doses of Pancrease alone (mean, 10.7%; range, 4% to 25%; P less than 0.01). We conclude that adjunct therapy with omeprazole reduces fecal fat excretion in cystic fibrosis provided that a high dose of Pancrease is supplied.
Design and Fabrication of Large-Area, Redundant, Stretchable Interconnect Meshes Using Excimer Laser Photoablation and In Situ Masking (2009)

Stretchable interconnects play an important role towards the realization of the realm of systems that include large-area sensor skins and wearable electronics. These interconnects must be reliable and robust for viability, and must be flexible, stretchable, and conformable to nonplanar surfaces for diverse applicability. This research describes the design, modeling, fabrication, and testing of stretchable interconnects on polymer substrates using metal patterns both as functional interconnect layers and as <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in situ</i> masks for excimer laser photoablation. The fluences for photoablation of polymers are generally much lower than the threshold fluence for removal or damage of metals; thus, metal thin films that are designed as structural layers in the sensor skin can be used as <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in situ</i> masks for polymers if the proper fluence is used. Self-aligned single-layer and multilayer interconnects of various designs (rectilinear and “meandering”) have been fabricated, and certain “meandering” interconnect designs can be stretched up to 50% uniaxially while maintaining good electrical conductivity and structural integrity. Furthermore, redundant interconnect meshes have been modeled and fabricated that increase the viability of the interconnect mesh while stretching up to 30% uniaxially and a prototype redundant interconnect mesh has been fabricated using seamless-scanning large-area fabrication techniques.
Role of ω-3 long-chain polyunsaturated fatty acid in metabolic syndrome (2011)

This article reviews the long-term outcome data and guidelines up to date, and systemically reviews the effect of ω-3 long-chain polyunsaturated fatty acid consumption, the major effective component in deep-sea fish oil, on metabolic syndrome, including improvements in abdominal obesity, insulin resistance, dyslipidemia, and hypertension, etc. Its adverse effects are also commented.

Key words: 
Metabolic syndrome;  ω-3 long-chain polyunsaturated fatty acid;  Deep-sea fish oil;  Abdominal obesity;  Dyslipidemia
Viral envelope protein glycosylation is a molecular determinant of the neuroinvasiveness of the New York strain of West Nile virus (2004)

Two New York (NY) strains of the West Nile (WN) virus were plaque-purified and four variants that had different amino acid sequences at the N-linked glycosylation site in the envelope (E) protein sequence were isolated. The E protein was glycosylated in only two of these strain variants. To determine the relationship between E protein glycosylation and pathogenicity of the WN virus, 6-week-old mice were infected subcutaneously with these variants. Mice infected with viruses that carried the glycosylated E protein developed lethal infection, whereas mice infected with viruses that carried the non-glycosylated E protein showed low mortality. In contrast, intracerebral infection of mice with viruses carrying either the glycosylated or non-glycosylated forms of the E protein resulted in lethal infection. These results suggested that E protein glycosylation is a molecular determinant of neuroinvasiveness in the NY strains of WN virus.
Modified HPLC-Electrospray Ionization/Mass Spectrometry Method for HbA1c Based on IFCC Reference Measurement Procedure (2008)

This procedure for the determination of HbA(1c) improves the existing reference measurement procedure.
New mannotriosides and trimannosides as potential ligands for mannose-specific binding proteins (2002)

The α-D-mannopyranosyl and 3,6-di-O-(α-D-mannopyranosyl)-α-D-mannopyranosyl neoglycolipids 36 and the branched and cluster trimannosidic acids 38 and 41 have been made in connection with studies of liposomes as transporters of antigens to dendritic cells.Key words: mannotrioside, trimannoside, neoglycoconjugate, glycolipid, synthesis.
Progesterone Receptor Status Significantly Improves Outcome Prediction Over Estrogen Receptor Status Alone for Adjuvant Endocrine Therapy in Two Large Breast Cancer Databases (2003)

When accurately measured, PgR status is an independent predictive factor for benefit from adjuvant endocrine therapy. Therefore, PgR status should be taken into account when discussing RR reductions expected from endocrine treatment with individual patients.
Music and Autonomic Nervous System (Dys)Function (2010)

Despite a wealth of evidence for the involvement of the autonomic nervous system (ANS) in health and disease and the ability of music to affect ANS activity, few studies have systematically explored the therapeutic effects of music on ANS dysfunction. Furthermore, when ANS activity is quantified and analyzed, it is usually from a point of convenience rather than from an understanding of its physiological basis. After a review of the experimental and therapeutic literatures exploring music and the ANS, a "Neurovisceral Integration" perspective on the interplay between the central and autonomic nervous systems is introduced, and the associated implications for physiological, emotional, and cognitive health are explored. The construct of heart rate variability is discussed both as an example of this complex interplay and as a useful metric for exploring the sometimes subtle effect of music on autonomic response. Suggestions for future investigations using musical interventions are offered based on this integrative account.
Templated Self‐Assembly of Block Copolymers: Top‐Down Helps Bottom‐Up (2006)

Abstract One of the key challenges in nanotechnology is to control a self‐assembling system to create a specific structure. Self‐organizing block copolymers offer a rich variety of periodic nanoscale patterns, and researchers have succeeded in finding conditions that lead to very long range order of the domains. However, the array of microdomains typically still contains some uncontrolled defects and lacks global registration and orientation. Recent efforts in templated self‐assembly of block copolymers have demonstrated a promising route to control bottom‐up self‐organization processes through top‐down lithographic templates. The orientation and placement of block‐copolymer domains can be directed by topographically or chemically patterned templates. This templated self‐assembly method provides a path towards the rational design of hierarchical device structures with periodic features that cover several length scales.
An Essential Role of Domain D in the Hormone-Binding Activity of Human β1 Thyroid Hormone Nuclear Receptor (1991)

By analogy with steroid receptors, human placental thyroid hormone nuclear receptor (hTR beta 1) could be divided into four functional domains: A/B (Met1-Leu101), C (Cys102-Ala170), D (Thr171-Lys237), and E (Arg238-Asp456). The E domain was thought to bind thyroid hormone. To evaluate whether domain E alone is sufficient to bind T3 or requires the presence of other domains for functional T3-binding activity, a series of deletion mutants was constructed. The mutants were expressed in Escherichia coli, and the expressed proteins were purified. Analysis of the T3-binding affinity and analog specificity of the purified truncated hTR beta 1 indicated that domain E alone did not have T3-binding activity. Extension of the amino-terminal sequence of domain E to include part of domain D yielded a mutant (Lys201-Asp456) with a Ka for T3 of 0.5 +/- 0.2 x 10(9) M-1. Further extension to include the entire domain D (Met169-Asp456) yielded a mutant with T3-binding activity with a Ka of 0.8 +/- 0.1 x 10(9) M-1. Further extension of the amino-terminal sequence to include domain C increased the affinity for T3 by nearly 2-fold (Ka = 1.5 +/- 0.4 x 10(9) M-1). The Ka for the wild-type hTR beta 1 is 1.5 +/- 0.2 x 10(9) M-1. Furthermore, mutant (Met169-Asp456) binds to 3',5',3-triiodo-L-thyropropionic acid, D-T3, L-T4, and L-T3 with 307%, 37%, 7%, and 0.1%, respectively, of the activity of L-T3. This order of analog affinity is similar to that of the wild-type hTR beta 1.(ABSTRACT TRUNCATED AT 250 WORDS)
Mast cell tryptases and chymases in inflammation and host defense (2007)

Tryptases and chymases are the major proteins stored and secreted by mast cells. The types, amounts, and properties of these serine peptidases vary by mast cell subtype, tissue, and mammal of origin. Membrane-anchored gamma-tryptases are tryptic, prostasin-like, type I peptidases that remain membrane attached on release and act locally. Soluble tryptases, including their close relatives, mastins, form inhibitor-resistant oligomers that act more remotely. Befitting their greater destructive potential, chymases are quickly inhibited after release, although some gain protection by associating with proteoglycans. Most chymase-like enzymes, including mast cell cathepsin G, hydrolyze chymotryptic substrates, an uncommon capability in the proteome. Some rodent chymases, however, have mutations resulting in elastolytic activity. Secreted tryptases and chymases promote inflammation, matrix destruction, and tissue remodeling by several mechanisms, including destroying procoagulant, matrix, growth, and differentiation factors and activating proteinase-activated receptors, urokinase, metalloproteinases, and angiotensin. They also modulate immune responses by hydrolyzing chemokines and cytokines. At least one chymase protects mice from intestinal worms. Tryptases and chymases can also oppose inflammation by inactivating allergens and neuropeptides causing inflammation and bronchoconstriction. Thus, like mast cells themselves, mast cell serine peptidases play multiple roles in host defense, and any accounting of benefit versus harm is necessarily context specific.
Antidisialoganglioside ricin A-chain immunotoxins show potent antitumor effects in vitro and in a disseminated human neuroblastoma severe combined immunodeficiency mouse model. (1994)

Several monoclonal antibodies (mAbs) were screened on different neuroblastoma cell lines to evaluate ricin A-chain immunotoxins for possible use against human neuroblastoma. Four mAbs were identified that exhibited high antitumor activity against neuroblastoma cell lines as measured in an indirect cytotoxicity assay. These mAbs, including 14G2a (antidisialoganglioside), ch14.18 (a humanized switch variant), BW704 (antidisialoganglioside), and chCE7 (anti-glycoprotein of M(r) 190,000), were subsequently linked via the bivalent linker N-succinimidyloxycarbonyl-alpha-methyl-alpha-(2-piridyldithio++ +)toluene to deglycosylated ricin A chain. The most potent immunotoxin, 14G2a.dgA, inhibited the protein synthesis of neuroblastoma cell lines IMR5 and NMB by 50% at concentrations of 6 x 10(-12) M. To test the antitumor efficacy of these immunotoxins in vivo, we developed a disseminated human neuroblastoma model in severe combined immunodeficiency mice. Treatment of tumor-bearing mice with 14G2a.dgA 12 days after tumor challenge resulted in a significant prolongation of survival as compared with phosphate-buffered saline-treated controls (16.8 versus 6.5 weeks). We conclude that ricin A-chain immunotoxins might be of potential use in the treatment of human neuroblastoma.