gebhart/patrepeval huggingface dataset:
Prediction of murine MHC class I epitopes in a major house dust mite allergen and induction of T1-type CD8+ T cell responses (1997)

The group I (Der p 1) allergen of Dermatophagoides pteronyssinus (house dust mite, HDM) contains several T helper (Th) epitopes recognized by C57BL/6 mice, with the peptide (111-139) containing a dominant MHC class II-restricted epitope (113-127). Since CD8+ T cells are thought to play a role in the regulation of allergic disease, we examined the Der p 1 sequence for potential MHC class I-binding motifs and observed that residues 111-119 (FGISNYCQI) contain motifs for H-2Db and Kb. Furthermore, immunization of C57BL/6 mice with unadjuvanted Ty virus-like particles (VLP) carrying Der p 1 (111-139), a method known to induce murine cytotoxic T lymphocyte (CTL) responses, primed Der p 1 (111-119)-specific Db-restricted CTL which produce high levels of IFN-gamma and low levels of IL-5 and IL-6 in vitro (T1-type CTL). VLP carrying the minimal epitope (FGISNYCQI) also induced a CTL response following immunization without adjuvant by various routes. Der p 1 (111-139)-VLP adjuvanted with alum did not prime CTL in C57BL/6 mice but were found to prime Th1-type CD4+ T cells that recognize the overlapping peptide (113-127) and native protein. The ability to successfully predict allergen-specific CD8+ T cell epitopes and prime CD8+ and/or CD4+ T cell responses provides an opportunity to dissect the relative roles of these T cells in the regulation of allergic responses and may offer therapeutic potential for reprogramming Th2-type allergic responses.
Infected Cell Protein (ICP)47 Enhances Herpes Simplex Virus Neurovirulence by Blocking the CD8+ T Cell Response (1998)

The herpes simplex virus (HSV) infected cell protein (ICP)47 blocks CD8+ T cell recognition of infected cells by inhibiting the transporter associated with antigen presentation (TAP). In vivo, HSV-1 replicates in two distinct tissues: in epithelial mucosa or epidermis, where the virus enters sensory neurons; and in the peripheral and central nervous system, where acute and subsequently latent infections occur. Here, we show that an HSV-1 ICP47- mutant is less neurovirulent than wild-type HSV-1 in mice, but replicates normally in epithelial tissues. The reduced neurovirulence of the ICP47- mutant was due to a protective CD8+ T cell response. When compared with wild-type virus, the ICP47- mutant expressed reduced neurovirulence in immunologically normal mice, and T cell-deficient nude mice after reconstitution with CD8+ T cells. However, the ICP47- mutant exhibited normal neurovirulence in mice that were acutely depleted of CD8+ T cells, and in nude mice that were not reconstituted, or were reconstituted with CD4+ T cells. In contrast, CD8+ T cell depletion did not increase the neurovirulence of an unrelated, attenuated HSV-1 glycoprotein (g)E- mutant. ICP47 is the first viral protein shown to influence neurovirulence by inhibiting CD8+ T cell protection.
Electrophoretic Growth of Lead Zirconate Titanate Nanorods (2001)

Nanorods of lead zirconate titanate (PZT)—a ferro- and piezoelectric material—up to 10 μm in length and 70 to 150 nm in diameter are produced by sol-gel electrophoresis of PZT in a track-etched polycarbonate membrane, which is used as a template. The Figure gives a close-up view of a PZT film with nanowires attached, as obtained after pyrolytic removal of the organic template.
A Potent and Highly Selective VPAC2 Agonist Enhances Glucose-Induced Insulin Release and Glucose Disposal (2002)

Pituitary adenylate cyclase-activating peptide (PACAP) and vasoactive intestinal peptide (VIP) activate two shared receptors, VPAC1 and VPAC2. Activation of VPAC1 has been implicated in elevating glucose output, whereas activation of VPAC2 may be involved in insulin secretion. A hypothesis that a VPAC2-selective agonist would enhance glucose disposal by stimulating insulin secretion without causing increased hepatic glucose production was tested using a novel selective agonist of VPAC2. This agonist, BAY 55-9837, was generated through site-directed mutagenesis based on sequence alignments of PACAP, VIP, and related analogs. The peptide bound to VPAC2 with a dissociation constant (K(d)) of 0.65 nmol/l and displayed >100-fold selectivity over VPAC1. BAY 55-9837 stimulated glucose-dependent insulin secretion in isolated rat and human pancreatic islets, increased insulin synthesis in purified rat islets, and caused a dose-dependent increase in plasma insulin levels in fasted rats, with a half-maximal stimulatory concentration of 3 pmol/kg. Continuous intravenous or subcutaneous infusion of the peptide reduced the glucose area under the curve following an intraperitoneal glucose tolerance test. The peptide had effects on intestinal water retention and mean arterial blood pressure in rats, but only at much higher doses. BAY 55-9837 may be a useful therapy for the treatment of type 2 diabetes.
Deacylation of A21978C, an acidic lipopeptide antibiotic complex, by Actinoplanes utahensis. (1988)

A21978C, produced by Streptomyces roseosporus NRRL 11379, is an acidic lipopeptide antibiotic complex that inhibits Gram-positive bacteria. Individual factors of the complex possess an identical peptide core or "nucleus", and are differentiated by the distinctive fatty acid acyl group attached to the N-terminus of the nucleus. Certain members of the family Actinoplanaceae deacylated A21978C to yield the unaltered nucleus, which was then reacylated to form new analogs. Actinoplanes utahensis NRRL 12052 was the most efficient of these cultures, producing up to 500 micrograms of nucleus per ml of culture broth per hour. Eacylation was also accomplished with semi-pure and tert-butoxycarbonyl (tert-BOC)-A21978C. In the latter, the ornithine amino group was blocked to prevent formation of diacyl analogs during reacylation. The acylase was an endoenzyme present in submerged cultures of A. utahensis from less than 18 to greater than 168 hours of incubation. Whole cells suspended in phosphate buffer or entrapped in polyacrylamide gel also deacylated A21978C efficiently.
Lipid rafts: bringing order to chaos (2003)

Lipid rafts are subdomains of the plasma membrane that contain high concentrations of cholesterol and glycosphingolipids. They exist as distinct liquid-ordered regions of the membrane that are resistant to extraction with nonionic detergents. Rafts appear to be small in size, but may constitute a relatively large fraction of the plasma membrane. While rafts have a distinctive protein and lipid composition, all rafts do not appear to be identical in terms of either the proteins or the lipids that they contain. A variety of proteins, especially those involved in cell signaling, have been shown to partition into lipid rafts. As a result, lipid rafts are thought to be involved in the regulation of signal transduction. Experimental evidence suggests that there are probably several different mechanisms through which rafts control cell signaling. For example, rafts may contain incomplete signaling pathways that are activated when a receptor or other required molecule is recruited into the raft. Rafts may also be important in limiting signaling, either by physical sequestration of signaling components to block nonspecific interactions, or by suppressing the intrinsic activity of signaling proteins present within rafts. This review provides an overview of the physical characteristics of lipid rafts and summarizes studies that have helped to elucidate the role of lipid rafts in signaling via receptor tyrosine kinases and G protein-coupled receptors.
Optical investigations of granular aerogel fills (1994)

The light scattering behaviour of granular silica aerogels is measured at a fixed wavelength of 633 nm. Two different correlation lengths ac,bulk and ac,sur, which characterize the bulk and surface scattering properties, are derived. A value of ac,bulk,=(45+or-5) nm is typical for the bulk scattering, whereas surface imperfections, such as dust grains and scratches as well as bubbles and streaks, cause a strongly forward-peaked scattering distribution with ac,sur=(600+or-50) nm. The spectral scattering coefficient in the visible region is also measured. By modelling the data, the contributions of large and small inhomogeneities to the scattering coefficient S can be separated. Typical values are Sbulk=(65+or-10) m-1 at a wavelength of 633 nm and Sbulk=(115+or-20) m-1 at 543 nm. For the large inhomogeneities a wavelength-independent scattering coefficient of Ssur=(100+or-30) m-1 is obtained. We have also measured the directional-hemispherical transmission tdh of a loose granular fill as a function of granule size. The influence of the aerogel nanostructure on tdh is determined from radiation transport calculations. Because of the forward-peaked scattering distribution of the large inhomogeneities, tdh is predominantly affected by the bulk.
Ag Nanocrystal Junctions as the Site for Surface-Enhanced Raman Scattering of Single Rhodamine 6G Molecules (2000)

Atomic force microscopy (AFM) measurements show that the Ag nanoparticles that yield surface-enhanced Raman scattering (SERS) of single molecules of Rhodamine (R6G) are all compact aggregates consisting of a minimum of two individual particles. Comparison of 514.5 and 632.8 nm excitation shows that the single molecule R6G signal is significantly higher when the excitation wavelength is resonant with the absorption band of R6G and suggests that the Raman excitation spectrum follows the absorption profile for R6G. We have also observed an interesting superlinear power dependence of the SERS signal. On average, by increasing the incident power by 2 orders of magnitude and decreasing the integration time by the same factor to maintain constant fluence, increases of 4 to 6 times were observed in the SERS intensity. We discuss these results in terms of model where the R6G molecule that yields single molecule SERS signals is located at the junction of two Ag nanoparticles. We have also modeled the system using molecular resonance Raman theory to provide further insight into the enhancement mechanism.
Electroosmotic pumping and electrophoretic separations for miniaturized chemical analysis systems (1994)

Electroosmotic pumping is highly efficient in capillaries of less than 100 mu m inner diameter bearing an immobilized surface charge. Electric fields in the kV cm-1 range allow for liquid motion of several mm s-1 in the case of an aqueous electrolyte. This pumping mechanism is used for miniaturized chemical analysis systems. Flow and mixing behaviour in branched channels are characterized. A capillary electrophoresis device allows for repetitive, electroosmotic injections of 100 pL samples, for efficiencies of up to 200000 theoretical plates in less than a minute, and for external laser induced fluorescence detection at any capillary length of choice between 5 and 50 mm.
Extracellular matrix of central nervous system white matter: Demonstration of an hyaluronate‐protein complex (1991)

Monoclonal antibodies were raised against human glial hyaluronate-binding protein (GHAP), a major CNS-specific glycoprotein known to bind hyaluronate in vitro. Frozen sections of dog and human spinal cord were digested with Streptomyces hyaluronidase in order to ascertain whether GHAP is bound to hyaluronate in vivo. Digestion with hyaluronidase, prior to staining of the sections by conventional indirect immunofluorescence, led to a drastic reduction in the intensity of the staining reaction. Chondroitinase ABC (protease-free) was also effective in bringing about the release of GHAP from tissue sections. This enzyme also degrades hyaluronate. The effects of the chondroitinase were completely reversed by the addition of 1 mM Zn2+, a known inhibitor of this enzyme. The intact protein was released into the soluble fraction of human brain homogenates by testicular hyaluronidase. An immunoreactive species of 70 kD was released into the soluble fraction of dog spinal cord homogenates by Streptomyces hyaluronidase. Dog GHAP was isolated from spinal cord by means of ion exchange and affinity chromatography. This protein bound efficiently to hyaluronate in vitro. Dog and human GHAP had identical isoelectric points and similar peptide maps but different molecular weights. Dog GHAP (70 kD) was larger than its human counterpart (60 kD). These findings imply that GHAP exists in association with hyaluronate in CNS white matter. Immunoelectron microscopy revealed that GHAP fills the space between myelin sheaths in dog spinal cord white matter. One is led to conclude therefore that an hyaluronate based extracellular matrix exists in CNS white matter.
Soybean oil extraction and separation using switchable or expanded solvents (2008)

The extraction of soy oil from soybean flakes in industry requires large amounts of hexane solvent and results in significant losses and energy consumption during the distillative removal of the solvent. Hexanes and related hydrocarbon extractants are also becoming an environmental and health concern. A new method for extraction of the oil is sought, that would require neither hexane nor distillative removal of solvent. This article presents a preliminary assessment of several new methods for soy oil extraction and subsequent solvent removal from the oil. The most promising are (a) extraction by an amidine switchable solvent that can then be removed from the soy oil by carbonated water and (b) extraction by a moderately hydrophilic solvent that can then be removed from the oil by water.
Metabolic Imaging of Head and Neck Cancer Organoids (2017)

Head and neck cancer patients suffer from toxicities, morbidities, and mortalities, and these ailments could be minimized through improved therapies. Drug discovery is a long, expensive, and complex process, so optimized assays can improve the success rate of drug candidates. This study applies optical imaging of cell metabolism to three-dimensional in vitro cultures of head and neck cancer grown from primary tumor tissue (organoids). This technique is advantageous because it measures cell metabolism using intrinsic fluorescence from NAD(P)H and FAD on a single cell level for a three-dimensional in vitro model. Head and neck cancer organoids are characterized alone and after treatment with standard therapies, including an antibody therapy, a chemotherapy, and combination therapy. Additionally, organoid cellular heterogeneity is analyzed quantitatively and qualitatively. Gold standard measures of treatment response, including cell proliferation, cell death, and in vivo tumor volume, validate therapeutic efficacy for each treatment group in a parallel study. Results indicate that optical metabolic imaging is sensitive to therapeutic response in organoids after 1 day of treatment (p<0.05) and resolves cell subpopulations with distinct metabolic phenotypes. Ultimately, this platform could provide a sensitive high-throughput assay to streamline the drug discovery process for head and neck cancer.
Myogenic factors that regulate expression of muscle-specific microRNAs (2006)

Since their discovery as key regulators of early animal development, microRNAs now are recognized as widespread regulators of gene expression. Despite their abundance, little is known regarding the regulation of microRNA biogenesis. We show that three highly conserved muscle-specific microRNAs, miR-1, miR-133 and miR-206, are robustly induced during the myoblast-myotube transition, both in primary human myoblasts and in the mouse mesenchymal C2C12 stem cell line. These microRNAs were not induced during osteogenic conversion of C2C12 cells. Moreover, both loci encoding miR-1, miR-1-1, and miR-1-2, and two of the three encoding miR-133, miR-133a-1 and miR-133a-2, are strongly induced during myogenesis. Some of the induced microRNAs are in intergenic regions, whereas two are transcribed in the opposite direction to the nonmuscle-specific gene in which they are embedded. By using CHIP analysis, we demonstrate that the myogenic factors Myogenin and MyoD bind to regions upstream of these microRNAs and, therefore, are likely to regulate their expression. Because miR-1 and miR-206 are predicted to repress similar mRNA targets, our work suggests that induction of these microRNAs is important in regulating the expression of muscle-specific proteins.
A Multistep, ATP-dependent Pathway for Assembly of Human Immunodeficiency Virus Capsids in a Cell-free System (1997)

To understand the mechanism by which human immunodeficiency virus type 1 (HIV) capsids are formed, we have reconstituted the assembly of immature HIV capsids de novo in a cell-free system. Capsid authenticity is established by multiple biochemical and morphologic criteria. Known features of the assembly process are closely reproduced, indicating the fidelity of the cell-free reaction. Assembly is separated into co- and posttranslational phases, and three independent posttranslational requirements are demonstrated: (a) ATP, (b) a detergent-sensitive host factor, and (c) a detergent-insensitive host subcellular fraction that can be depleted and reconstituted. Assembly appears to proceed by way of multiple intermediates whose conversion to completed capsids can be blocked by either ATP depletion or treatment with nondenaturing detergent. Specific subsets of these intermediates accumulate upon expression of various assembly-defective Gag mutants in the cell-free system, suggesting that each mutant is blocked at a particular step in assembly. Furthermore, the accumulation of complexes of similar sizes in cells expressing the corresponding mutants suggests that comparable intermediates may exist in vivo. From these data, we propose a multi-step pathway for the biogenesis of HIV capsids, in which the assembly process can be disrupted at a number of discrete points.
DNA sequences of three beta-1,4-endoglucanase genes from Thermomonospora fusca (1991)

The DNA sequences of the Thermomonospora fusca genes encoding cellulases E2 and E5 and the N-terminal end of E4 were determined. Each sequence contains an identical 14-bp inverted repeat upstream of the initiation codon. There were no significant homologies between the coding regions of the three genes. The E2 gene is 73% identical to the celA gene from Microbispora bispora, but this was the only homology found with other cellulase genes. E2 belongs to a family of cellulases that includes celA from M. bispora, cenA from Cellulomonas fimi, casA from an alkalophilic Streptomyces strain, and cellobiohydrolase II from Trichoderma reesei. E4 shows 44% identity to an avocado cellulase, while E5 belongs to the Bacillus cellulase family. There were strong similarities between the amino acid sequences of the E2 and E5 cellulose binding domains, and these regions also showed homology with C. fimi and Pseudomonas fluorescens cellulose binding domains.
Up-regulation and Activation of Proteinase-Activated Receptor 2 in Early and Delayed Radiation Injury in the Rat Intestine: Influence of Biological Activators of Proteinase-Activated Receptor 2 (2003)

Proteinase-activated receptor 2 (Par2, F2rl1, also designated PAR-2 or PAR2) is prominently expressed in the intestine and has been suggested as a mediator of inflammatory, mitogenic and fibrogenic responses to injury. Mast cell proteinases and pancreatic trypsin, both of which have been shown to affect the intestinal radiation response, are the major biological activators of Par2. Conventional Sprague-Dawley rats, mast cell-deficient rats, and rats in which pancreatic exocrine secretion was blocked pharmacologically by octreotide underwent localized irradiation of a 4-cm loop of small bowel. Radiation injury was assessed 2 weeks after irradiation (early, inflammatory phase) and 26 weeks after irradiation (chronic, fibrotic phase). Par2 expression and activation were assessed by in situ hybridization and immunohistochemistry, using antibodies that distinguished between total (preactivated and activated) Par2 and preactivated Par2. Compared to unirradiated intestine, irradiated intestine exhibited increased Par2 expression, particularly in areas of myofibroblast proliferation and collagen accumulation, after both single-dose and fractionated irradiation. The majority of Par2 expressed in fibrotic areas was activated. Postirradiation Par2 overexpression was greatly attenuated in both mast cell-deficient and octreotide-treated rats. The severity of acute mucosal injury did not affect postirradiation Par2 expression. Mast cells and pancreatic proteinases may exert their fibro-proliferative effects partly through activation of Par2. Par2 may be a potential target for modulating the intestinal radiation response, particularly delayed intestinal wall fibrosis.
Observations and modeling of biomass and soil organic matter dynamics for the grassland biome worldwide (1993)

Century is a model of terrestrial biogeochemistry based on relationships between climate, human management (fire, grazing), soil properties, plant productivity, and decomposition. The grassland version of the Century model was tested using observed data from 11 temperate and tropical grasslands around the world. The results show that soil C and N levels can be simulated to within ±25% of the observed values (100 and 75% of the time, respectively) for a diverse set of soils. Peak live biomass and plant production can be simulated within ± 25% of the observed values (57 and 60% of the time, respectively) for burned, fertilized, and irrigated grassland sites where precipitation ranged from 22 to over 150 cm. Live biomass can be generally predicted to within ±50% of the observed values (57% of the time). The model underestimated the live biomass in extremely high plant production years at two of the Russian sites. A comparison of Century model results with statistical models showed that the Century model had slightly higher r 2 values than the statistical models. Data and calibrated model results from this study are useful for analysis and description of grassland carbon dynamics, and as a reference point for testing more physiologically based models prediction's of net primary production and biomass. Results indicate that prediction of plant and soil organic matter (C and N) dynamics requires knowledge of climate, soil texture, and N inputs.