gebhart/patrepeval huggingface dataset:
New Methods for Assessing T-Cell Responses (2000)

sensitive or provide more information than previously used assays. Importantly, some of these new techniques allow direct ex vivo analysis of T cells without in vitro amplification, thus providing a more accurate picture of the in vivo immune response. In this review, we describe some of the most widely used techniques for immune monitoring of specific T-cell responses. These various assays can be schematically divided into functional assays, which measure the secretion of a particular cytokine (ELISPOT and intracellular cytokines); assays which assess the specificity of the T cells irrespective of their functionality and which are based on structural features of the TCR (tetramers and immunoscope); and assays aimed at detecting T-cell precursors by amplifying cells that proliferate in response to antigenic stimulation. The sensitivity and immunological relevance of these various methods are discussed. Major findings and future applications in basic and clinical immunology are also presented.
Using Mass Spectrometry to Quantify Rituximab and Perform Individualized Immunoglobulin Phenotyping in ANCA-Associated Vasculitis (2016)

Therapeutic monoclonal immunoglobulins (mAbs) are used to treat patients with a wide range of disorders including autoimmune diseases. As pharmaceutical companies bring more fully humanized therapeutic mAb drugs to the healthcare market analytical platforms that perform therapeutic drug monitoring (TDM) without relying on mAb specific reagents will be needed. In this study we demonstrate that liquid-chromatography-mass spectrometry (LC-MS) can be used to perform TDM of mAbs in the same manner as smaller nonbiologic drugs. The assay uses commercially available reagents combined with heavy and light chain disulfide bond reduction followed by light chain analysis by microflow-LC-electrospray ionization-quadrupole-time-of-flight mass spectrometry (ESI-Q-TOF MS). Quantification is performed using the peak areas from multiply charged mAb light chain ions using an in-house developed software package developed for TDM of mAbs. The data presented here demonstrate the ability of an LC-MS assay to quantify a therapeutic mAb in a large cohort of patients in a clinical trial. The ability to quantify any mAb in serum via the reduced light chain without the need for reagents specific for each mAb demonstrates the unique capabilities of LC-MS. This fact, coupled with the ability to phenotype a patient's polyclonal repertoire in the same analysis further shows the potential of this approach to mAb analysis.
Role of the sympathetic nervous system and insulin in enhancing glucose uptake in peripheral tissues after intrahypothalamic injection of leptin in rats. (1999)

Our previous study demonstrated that microinjection of leptin into the ventromedial hypothalamus (VMH) dramatically increased glucose uptake in the heart, brown adipose tissue (BAT), and skeletal muscles, but not in white adipose tissue (WAT) in conscious unrestrained rats, as assessed in vivo by the 2-[3H]deoxyglucose method. Here we examined the role of the sympathetic nervous system and insulin in enhanced glucose uptake by tissues after hypothalamic leptin injection. Pretreatment with guanethidine significantly suppressed the increased glucose uptake by the tissues in response to leptin injected into the VMH, whereas bilateral adrenal demedullation had no significant effect. Treatment with propranolol but not phenoxybenzamine also decreased significantly enhanced glucose uptake by the tissues. We further examined the interaction of the effects of hypothalamic leptin and insulin administered peripherally by clamping the glucose concentrations at a constant level. When leptin was injected into the VMH and a maximal dose of insulin was administered intravenously, the rates of glucose uptake by the heart, BAT, and skeletal muscles, but not by WAT, markedly increased beyond the values reached by insulin stimulation alone. Surgical sympathetic denervation of BAT abolished the enhancement of glucose uptake in this tissue, decreasing to the level stimulated by insulin alone. These results appear to indicate that leptin in the hypothalamus enhances glucose uptake in certain peripheral tissues through mediation of a beta-adrenergic mechanism for the sympathetic nerves innervating the tissues and that central leptin and peripheral insulin have a synergistic role in augmenting tissue glucose uptake.
CLA-1 Is an 85-kD Plasma Membrane Glycoprotein That Acts as a High-Affinity Receptor for Both Native (HDL, LDL, and VLDL) and Modified (OxLDL and AcLDL) Lipoproteins (1997)

Lipoprotein metabolism is regulated by the functional interplay between lipoprotein components and the receptors and enzymes with which they interact. Recent evidence indicates that the structurally related glycoproteins CD36 and SR-BI act as cell surface receptors for some lipoproteins. Thus, CD36 has been reported to bind oxidized LDL (OxLDL) and acetylated LDL (AcLDL), while SR-BI also binds native LDL and HDL. The cDNA of human CLA-1 predicts a protein 509 amino acids long that displays a 30% and an 80% amino acid identity with CD36 and mouse or hamster SR-BI, respectively. In this report, we describe the structural characterization of CLA-1 as an 85-kD plasma membrane protein enriched in N-linked carbohydrates. The expression of CLA-1 on mammalian and insect cells has been used to demonstrate that CLA-1 is a high-affinity specific receptor for the lipoproteins HDL, LDL, VLDL, OxLDL, and AcLDL. Northern blot analysis of the tissue distribution of CLA-1 in humans indicated that its expression is mostly restricted to tissues performing very active cholesterol metabolism (liver and steroidogenic tissues). This finding, in the context of the capability of this receptor to bind to both native and modified lipoproteins, strongly suggests that the CLA-1 receptor contributes to lipid metabolism and atherogenesis.
Mutational Analyses of Packaging Signals in Influenza Virus PA, PB1, and PB2 Genomic RNA Segments (2007)

The influenza A virus genome consists of eight negative-sense RNA segments that must each be packaged to produce an infectious virion. We have previously mapped the minimal cis-acting regions necessary for efficient packaging of the PA, PB1, and PB2 segments, which encode the three protein subunits of the viral RNA polymerase. The packaging signals in each of these RNAs lie within two separate regions at the 3' and 5' termini, each encompassing the untranslated region and extending up to 80 bases into the adjacent coding sequence. In this study, we introduced scanning mutations across the coding regions in each of these RNA segments in order to finely define the packaging signals. We found that mutations producing the most severe defects were confined to a few discrete 5' sites in the PA or PB1 coding regions but extended across the entire (80-base) 5' coding region of PB2. In sequence comparisons among more than 580 influenza A strains from diverse hosts, these highly deleterious mutations were each found to affect one or more conserved bases, though they did not all lie within the most broadly conserved portions of the regions that we interrogated. We have introduced silent and conserved mutations to the critical packaging sites, which did not affect protein function but impaired viral replication at levels roughly similar to those of their defects in RNA packaging. Interestingly, certain mutations showed strong tendencies to revert to wild-type sequences, which implies that these putative packaging signals are critical for the influenza life cycle.
A Homolog of the armadillo Protein in Drosophila (Plakoglobin) Associated with E-Cadherin (1991)

Three cytoplasmic proteins, called catenins, bind to the cytoplasmic tail of the epithelial cell-cell adhesion molecule E-cadherin. The complementary DNA sequence was determined for the 92-kilodalton β catenin of Xenopus laevis . The sequence is homologous to mammalian plakoglobin, a protein of desmosomal and zonula adherens cell junctions, and to the plakoglobin homolog in Drosophila melanogaster , the product of the segment polarity gene armadillo . A monoclonal antibody to bovine plakoglobin recognizes the analogous β catenin in the Madin-Darby canine kidney (MDCK) cell line. Armadillo plakoglobin may link E-cadherin to the underlying actin cytoskeleton at cell-cell junctions; the E-cadherin-catenin protein complex may also participate in the transmission of developmental information.
Hydrogen as clean fuel via continuous fermentation by anaerobic photosynthetic bacteria, Rhodospirillum rubrum (2004)

Hydrogen has been considered a potential fuel for the future since it is carbon-free and oxidized to water as a combustion product. Bioconversion of synthesis gas to hydrogen was demonstrated in a continuous fermentation utilizing malate as a carbon source.Rhodospirillum rubrum, an anaerobic photosynthetic bacterium catalyzed water gas shift reaction which was used in this research. The synthesis gas (CO) was used as a source of energy along with tungsten light supplied for growth and bioconversion of the photosynthetic bacteria. The microbial process in fermentation media was carried out in continuous culture to observe the effect of light intensity, agitation and liquid dilution rate on hydrogen production. The maximum hydrogen yield at 500 rpm was 0.65 mmol H2/mmol CO. Desired media flow rate was preferable for high hydrogen production. At 0.65 ml/min media, hydrogen was produced at 7.2 mmol/h. This new approach, use of biocatalyst, can be considered as an alternative method to the conventional Fischer Tropsch synthetic reactions, which were able to convert synthesis gas into hydrogen. &nbsp; Key words:&nbsp;Hydrogen, syngas, continuous bioreactor,&nbsp;Rhodospirillum rubrum, light intensity, agitation rate and flow rate.
Preventive but Not Late Amiloride Therapy Reduces Morbidity and Mortality of Lung Disease in βENaC-overexpressing Mice (2008)

We conclude that preventive inhibition of increased airway Na(+) absorption provides an effective therapy for CF-like lung disease in vivo. These results suggest that amiloride therapy may be an effective preventive therapy for patients with CF if initiated early in life before the onset of lung disease.
Transposon-facilitated DNA sequencing. (1991)

We describe here a transposon-based DNA sequencing strategy that allows the introduction of sequencing priming sites throughout a target sequence by bacterial mating. A miniplasmid was designed to select against transposon insertions into the vector. Sites of transposon insertion are mapped by the polymerase chain reaction with bacterial overnight cultures providing the templates. A small set of plasmids with transposons spaced several hundred base pairs apart can then be sequenced. Sequencing primers corresponding to the transposon ends allow sequencing in both directions. Thus, the entire sequence of both strands can be easily determined.
Molecular Functions of Oxygen‐Evolving Complex Family Proteins in Photosynthetic Electron Flow (2010)

Oxygen-evolving complex (OEC) protein is the original name for membrane-peripheral subunits of photosystem (PS) II. Recently, multiple isoforms and homologs for OEC proteins have been identified in the chloroplast thylakoid lumen, indicating that functional diversification has occurred in the OEC family. Gene expression profiles suggest that the Arabidopsis OEC proteins are roughly categorized into three groups: the authentic OEC group, the stress-responsive group, and the group including proteins related to the chloroplast NAD(P)H dehydrogenase (NDH) complex involved in cyclic electron transport around PSI. Based on the above gene expression profiles, molecular functions of the OEC family proteins are discussed together with our current knowledge about their functions.
Multifunctional Composite Nanoparticles:  Magnetic, Luminescent, and Mesoporous (2006)

We demonstrate a strategy for the synthesis of multifunctional mesoporous silica nanoparticles. These uniform tumblerlike nanocomposites, which simultaneously possess magnetic, luminescent, and porous properties, have great potential in biomedical applications.
Therapeutic Interventions Following Mammalian Spinal Cord Injury (2001)

Every year in the United States spinal cord injuries (SCIs) occur in approximately 12 000 individuals, resulting in chronic, debilitating functional deficits in most of these patients. Owing to the extremely high costs associated with hospitalization, subsequent rehabilitation, and outpatient care, it is becoming evident that effective treatments for SCI could drastically reduce health care costs and, more importantly, improve the quality of life for thousands of individuals. In this review, we will briefly discuss the pathological events that contribute to the poor regenerative capacity of the injured spinal cord and describe experimental methods that are being used to both minimize tissue damage and promote the regrowth of injured spinal cord axons.
Serum and Dietary Magnesium and the Risk for Type 2 Diabetes Mellitus (1999)

Among white participants, low serum magnesium level is a strong, independent predictor of incident type 2 diabetes. That low dietary magnesium intake does not confer risk for type 2 diabetes implies that compartmentalization and renal handling of magnesium may be important in the relationship between low serum magnesium levels and the risk for type 2 diabetes.
Transplantation of human olfactory ensheathing cells elicits remyelination of demyelinated rat spinal cord (2000)

Human olfactory ensheathing cells (OECs) were prepared from adult human olfactory nerves, which were removed during surgery for frontal base tumors, and were transplanted into the demyelinated spinal cord of immunosuppressed adult rats. Extensive remyelination was observed in the lesion site: In situ hybridization using a human DNA probe (COT-1) indicated a similar number of COT-1-positive cells and OEC nuclei within the repaired lesion. The myelination was of a peripheral type with large nuclei and cytoplasmic regions surrounding the axons, characteristic of Schwann cell and OEC remyelination. These results provide evidence that adult human OECs are able to produce Schwann cell-like myelin sheaths around demyelinated axons in the adult mammalian CNS in vivo.
Baseband Signals and Power in Load-Modulated Digital Backscatter (2012)

Passive digital backscatter signals in systems like radio frequency identification (RFID) are usually received along with strong interference from a leaked carrier. The simplest way to quantify the “useful” communication signal is to separate it as an amplitude-shift keying (ASK) or biphase-shift keying (BPSK) component. These definitions give different power normalizations, posing some complexity in comparison of link quantities. This letter investigates their suitability in terms of basic signal theory and conservation of energy to clarify relationships between the baseband signals and “backscattered power.” Defining received backscatter as BPSK guarantees energy conservation for arbitrary tag modulation loads.
Control of cellular proliferation by the fibroblast and epidermal growth factors. (1978)

Recent studies on the effect of the fibroblast and epidermal growth factors (FGF and EGF, respectively) on the proliferation of ovarian cells and vascular endothelial cells are reviewed. During the ovarian cycle, luteal cells are derived from granulosa cells by a process of cytomorphosis. These two cell types thus allow a study of the changes that occur in growth control when one cell type is converted into another. Also described is the control of vascular endothelial cell proliferation by FGF (but not by EGF). We discuss the effects of FGF and EGF on cells derived from the embryonic ectoderm, mesoderm, and endoderm and examine the hypothesis that cellular specificity for various growth factors is conferred during embryo development. Finally, since antagonists of growth factors are probably as important as the mitogens in the overall control of cell proliferation, we review certain mechanisms and agents through which the mitogenic effect of FGF can be repressed, i.e., cell-cell interaction at confluence, trophic hormones, and a diffusible factor(s) from cartilage.
Neutralization of interleukin-1 beta activity in vivo with a monoclonal antibody alleviates collagen-induced arthritis in DBA/1 mice and prevents the associated acute-phase response. (1994)

Interleukin-1 (IL-1) has been implicated in the development and progression of a variety of acute and chronic inflammatory diseases. Due to its pro-inflammatory and tissue-degrading activities, IL-1 is regarded as a major mediator of chronic inflammatory joint diseases, including rheumatoid arthritis in man, adjuvant arthritis in rats and collagen-induced arthritis in mice. However, conclusive experimental evidence for the crucial role of IL-1 in the development of joint destruction has not been presented as yet. In the present study, we investigated the effect of a neutralizing monoclonal mouse antibody against mouse IL-1 beta (IgG1 isotype) on the development and progression of collagen-induced arthritis in DBA/1 mice. The antibody was injected intraperitoneally 3 times a week, either from day 3 or from day 21 after primary immunization, to day 60. In the positive control group an arthritis incidence of 80% was observed after 60 days. The injection of a control antibody of the same isotype did not influence the incidence of arthritis, whereas injection of anti-IL-1 beta from day 21 reduced the arthritis incidence to about 30%. Injection of anti-IL-1 beta starting at day 3 totally prevented both the development of arthritis and the associated increase of the acute phase protein serum amyloid P (SAP). Anti-collagen antibody titers, which increased significantly after immunization, were not influenced by the injection of anti-IL-1 beta antibodies, in spite of the suppressive effect on arthritis development.(ABSTRACT TRUNCATED AT 250 WORDS)
Effect of Impurities on the Matrix-Assisted Laser Desorption Mass Spectra of Single-Stranded Oligodeoxynucleotides (1996)

The effect of impurities on the analysis of single-stranded DNA oligomers by the technique of matrix-assisted laser desorption/ionization with time-of-flight mass spectrometry has been studied using the matrix 3-hydroxypicolinic acid and 355-nm pulsed light. By mixing the DNA oligomers with different concentrations of impurities and recording mass spectra, limits are set on the tolerable level of a given impurity in a sample. The tolerance limits for sodium chloride, potassium chloride, sodium acetate, sodium fluoride, sodium dodecyl sulfate (SDS), and manganese(II) chloride were found to be approximately 10(-2) M. It was found that magnesium salts degraded the mass spectrum at much lower levels of 10(-4) M. The organic compounds tris(hydroxymethyl)aminomethane (Tris), urea, dithiothreitol (DTT), glycerol, and ethylenediaminetetraacetic acid (EDTA), when present as its ammonium salt, were tolerable at concentrations into the range of 0.25-0.5 M, while the organic polyamine compound spermine substantially degraded the mass spectrum at concentrations above 10(-2) M. When comparing these results for DNA analysis with previously reported limits for protein analysis, large differences are seen for some of the impurities tested.
Amino acid preferences at protein binding sites (1994)

An analysis of the amino acid distribution at protein binding sites was carried out using 50 diverse macromolecules for which crystallographic data with a bound ligand are available. The purpose of this study is to determine whether differential trends in amino acid distributions exist at binding sites compared to other regions in the proteins. The results indicate that some residues, particularly Arg, His, Trp and Tyr are substantially more frequent at the binding sites, compared to the number of times these residues are present in proteins generally. These effects go beyond the differences seen comparing surface exposed residues to bulk protein. The resemblance in the residue utilization at the binding sites of unrelated proteins restricts the possible types of interactions with ligands, possibly accounting for the repetition of substructural motifs in chemicals with diverse pharmacological action. Further, the use of these diagnostic features may permit identification of ligand binding pockets in a protein structure deduced from sequence information or from data in the absence of a ligand. Some of these findings complement and extend previously described trends for antibody binding sites.
A stereochemical approach to pyranose ring flexibility: its implications for the conformation of dermatan sulfate. (1994)

Glycosaminoglycans, such as heparin, heparan sulfate, and dermatan sulfate, are characterized by a disaccharide repeating unit of a uronate and a hexosamine and are increasingly understood to be important physiologically as soluble components of the extracellular matrix. The secondary structure of this class of acidic polysaccharides is believed to play a key role in determining the wide range of biological specificities. Central to the structural diversity of the glycosaminoglycans is the experimentally documented conformational flexibility of the iduronate residue. Here, we outline an approach to explore the iduronate conformational flexibility by imposing stereochemical criteria of nonbonded contact distances. By performing a complete search of all possible torsions that define the iduronate ring geometry, we eliminate any prior bias with regard to minimum energy conformers. The approach led to alternative feasible conformers for the iduronate ring that are stereochemically satisfactory and are consistent with the available physico-chemical data.
Identification and characterization of the murine homologue of CD22, a B lymphocyte-restricted adhesion molecule (1992)

The human B lymphocyte-specific Ag, CD22, is a cell adhesion molecule expressed on the surface during a narrow window of B cell development, coincident with surface IgD. A ligand for CD22 has recently been identified on human T cells as the low molecular mass isoform of the leukocyte common Ag, CD45RO. CD22 has been reported to function in the regulation of both T and B cell activation in vitro. In this study, we report the isolation and expression of a molecular cDNA clone encoding the murine homologue of CD22, mCD22. Within their predicted protein sequences, murine and human sequences overall have 62% identity, which includes 18 of 20 extracellular cysteines and six of six cytoplasmic tyrosines. BHK cells transfected with mCD22 cDNA specifically adhere to resting and activated T lymphocytes and in addition bound activated, but not resting, B cells. Five Th clones were analyzed for their ability to adhere to mCD22; two Th0 clones and one Th1 clone bound CD22+ BHK transfectants, but not all T cell clones bound CD22+ cells: another Th1 clone and a Th2 clone did not. mCD22+ BHK transfectants were also specifically bound by the B cell-specific mAb, NIM-R6, demonstrating that this mAb is specific for murine CD22. Human cell lines expressing the counter-receptors for human CD22 were also examined for adhesion to the murine CD22 homologue; the epitope responsible for B cell adhesion to CD22 is conserved, whereas the T cell epitope binding to CD22 is not. The cDNA and mAb to murine CD22 will be useful for defining the in vivo function of CD22.