gebhart/patrepeval huggingface dataset:
Evolutionary Origins and Ecological Consequences of Endophyte Symbiosis with Grasses (2002)

Over the past 20 yr much has been learned about a unique symbiotic interaction between fungal endophytes and grasses. The fungi (Clavicipitaceae, Ascomycota) grow intercellularly and systemically in aboveground plant parts. Vertically transmitted asexual endophytes forming asymptomatic infections of cool-season grasses have been repeatedly derived from sexual species that abort host inflorescences. The phylogenetic distribution of seed-transmitted endophytes is strongly suggestive of cocladogenesis with their hosts. Molecular evidence indicates that many seed-transmitted endophytes are interspecific hybrids. Superinfection may result in hyphal fusion and parasexual recombination. Most endophytes produce one or more alkaloid classes that likely play some role in defending the host plant against pests. Hybridization may have led to the proliferation of alkaloid-production genes among asexual endophytes, favoring hybrids. The ergot alkaloid ergovaline, lolitrems, and lolines are produced by only a single sexual species, Epichloë festucae, but they are common in seed-transmitted endophytes, suggesting that E. festucae contributed genes for their synthesis. Asexual hybrids may also be favored by the counteracting of the accumulation of deleterious mutations (Muller's rachet). Endophyte infection can provide other benefits, such as enhanced drought tolerance, photosynthetic rate, and growth. Estimates of infection frequency have revealed variable levels of infection with especially high prevalence in the subfamily Pooideae. Longitudinal studies suggest that the prevalence of seed-transmitted endophytes can increase rapidly over time. In field experiments, infected tall fescue suppressed other grasses and forbs relative to uninfected fescue and supported lower consumer populations. Unlike other widespread plant/microbial symbioses based on the acquisition of mineral resources, grass/endophyte associations are based primarily on protection of the host from biotic and abiotic stresses.
Structure of influenza hemagglutinin in complex with an inhibitor of membrane fusion (2008)

The influenza surface glycoprotein hemagglutinin (HA) is a potential target for antiviral drugs because of its key roles in the initial stages of infection: receptor binding and the fusion of virus and cell membranes. The structure of HA in complex with a known inhibitor of membrane fusion and virus infectivity, tert-butyl hydroquinone (TBHQ), shows that the inhibitor binds in a hydrophobic pocket formed at an interface between HA monomers. Occupation of this site by TBHQ stabilizes the neutral pH structure through intersubunit and intrasubunit interactions that presumably inhibit the conformational rearrangements required for membrane fusion. The nature of the binding site suggests routes for the chemical modification of TBHQ that could lead to the development of more potent inhibitors of membrane fusion and potential anti-influenza drugs.
Herpes Simplex Virus Type 1 Glycoprotein gC Mediates Immune Evasion In Vivo (1998)

Many microorganisms encode proteins that interact with molecules involved in host immunity; however, few of these molecules have been proven to promote immune evasion in vivo. Herpes simplex virus type 1 (HSV-1) glycoprotein C (gC) binds complement component C3 and inhibits complement-mediated virus neutralization and lysis of infected cells in vitro. To investigate the importance of the interaction between gC and C3 in vivo, we studied the virulence of a gC-null strain in complement-intact and C3-deficient animals. Using a vaginal infection model in complement-intact guinea pigs, we showed that gC-null virus grows to lower titers and produces less severe vaginitis than wild-type or gC rescued virus, indicating a role for gC in virulence. To determine the importance of complement, studies were performed with C3-deficient guinea pigs; the results demonstrated significant increases in vaginal titers of gC-null virus, while wild-type and gC rescued viruses showed nonsignificant changes in titers. Similar findings were observed for mice where gC null virus produced significantly less disease than gC rescued virus at the skin inoculation site. Proof that C3 is important was provided by studies of C3 knockout mice, where disease scores of gC-null virus were significantly higher than in complement-intact mice. The results indicate that gC-null virus is approximately 100-fold (2 log10) less virulent that wild-type virus in animals and that gC-C3 interactions are involved in pathogenesis.
Analysis of adeno-associated virus (AAV) wild-type and mutant Rep proteins for their abilities to negatively regulate AAV p5 and p19 mRNA levels (1994)

The rep gene of adeno-associated virus type 2 (AAV) encodes four overlapping Rep proteins that are involved in gene regulation and replication of the virus. We studied here the regulation of mRNA transcribed from the AAV p5 and p19 promoters, using transient expression in human 293 cells followed by Northern (RNA) blot analysis of the mRNA. The p5 transcript encodes the larger Rep proteins, Rep78 and Rep68, while the p19 transcript encodes the smaller proteins, Rep52 and Rep40. A plasmid (pNTC3) containing the entire AAV genome with an amber mutation in the rep gene accumulated higher levels of p5 and p19 mRNA than a plasmid containing the wild-type AAV genome. Addition of increasing amounts of the wild-type rep gene in trans from a heterologous promoter inhibited p5 and p19 mRNA accumulation from pNTC3, indicating that the levels of both transcripts were decreased by the Rep proteins. Cotransfections with plasmids producing individual wild-type Rep proteins in trans showed that p5 and p19 mRNA accumulation was inhibited 5- to 10-fold by Rep78 and Rep68 and 2- to 3-fold by Rep52 and Rep40. Analysis of carboxyl-terminal truncation mutants of Rep78 showed that the ability of Rep78 to decrease p5 and p19 mRNA levels was lost when 159 or more amino acids were deleted. Rep78 and Rep68 mutants deleted for the methionine at residue 225 showed decreased abilities to down-regulate both p5 and p19 transcript levels, while mutants containing a substitution of glycine for the methionine resembled the wild-type Rep78. A Rep78 protein with a mutation in the putative nucleoside triphosphate binding site inhibited expression from p5 but not from p19, suggesting that the regulation of p5 transcript levels by Rep78 and Rep68 differs from that of p19. A deletion analysis of AAV cis sequences revealed that an intact terminal repeat was not required for negative regulation of p5 and p19 transcript levels and that the regulation of p19 mRNA levels by Rep78 did not require the presence of the p5 promoter.
MP1: A MEK Binding Partner That Enhances Enzymatic Activation of the MAP Kinase Cascade (1998)

Signal transduction is controlled both by regulation of enzyme activation and by organization of enzymatic complexes with nonenzymatic adapters, scaffolds, and anchor proteins. The extracellular signal-regulated kinase (ERK) cascade is one of several evolutionarily conserved mitogen-activated protein (MAP) kinase cascades important in the regulation of growth, apoptosis, and differentiation. A two-hybrid screen was conducted to identify nonenzymatic components of this signaling cascade that might be important in regulating its activity. A protein called MP1 (MEK Partner 1) was identified that bound specifically to MEK1 and ERK1 and facilitated their activation. When overexpressed in cultured cells, MP1 enhanced activation of ERK1 and activation of a reporter driven by the transcription factor Elk-1. Expression of MP1 in cells increased binding of ERK1 to MEK1. MP1 apparently functions as an adapter to enhance the efficiency of the MAP kinase cascade.
Prevention of tumor metastasis formation by anti-variant CD44. (1993)

A splice variant of CD44 (CD44v) originally discovered on metastases of a rat pancreatic adenocarcinoma (BSp73ASML) has been shown by transfection to confer metastatic behavior to nonmetastatic tumor cells (Günthert U., M. Hofmann, W. Rudy, S. Reber, M. Zöller, I. Haussmann, S. Matzku, A. Wenzel, H. Ponta, and P. Herrlich. 1991. Cell. 65:13). A monoclonal antibody (mAb), 1.1ASML, to the metastasis-specific domain of the CD44v molecule retards growth of lymph node and lung metastases of the metastatic tumor line BSp73ASML, and can efficiently prevent formation of metastases by the transfected line. The antibody is only effective when given before lymph node colonization. Anti-CD44v does not downregulate the expression of CD44v, and prevention of metastatic growth by anti-CD44v is not due to activation of any kind of immune defense. We suggest that the mAb interferes with proliferation of metastasizing tumor cells in the draining lymph node, most probably by blocking a ligand interaction. The interference with metastatic spread will greatly facilitate the exploration of the function of CD44v and, in particular, may also open new strategies for the therapy of human metastases.
Processing, shedding, and endocytosis of membrane type 1‐matrix metalloproteinase (MT1‐MMP) (2004)

Matrix metalloproteinases (MMPs) are multidomain zinc-dependent proteolytic enzymes that play pivotal roles in many normal and pathological processes. Some members of the MMP family are anchored to the plasma membrane via specialized domains and thus are perfectly suited for pericellular proteolysis. Membrane-anchoring also confers the membrane type-MMPs (MT-MMPs) a unique and complex array of regulatory processes that endow cells with the ability to control MT-MMP-dependent proteolytic activity independently of the levels of endogenous protease inhibitors. Emerging evidence indicates that mechanisms as diverse as autocatalytic processing, ectodomain shedding, homodimerization and internalization can all contribute to the modulation of MT-MMP activity on the cell surface. How these distinct processes interact to attain the optimal level of enzyme activity in a particular setting and the molecular signals that trigger them constitute a new paradigm in MMP regulation. This review will discuss the recent findings concerning these diverse regulatory mechanisms in the context of MT1-MMP (MMP-14).
Test structures for ISFET chemical sensors (2003)

Simple test structures and measurements were studied for determining their usefulness for the online monitoring of the aging effects on pH ion sensitive field effect transistor (ISFET) chemical sensors used in automatic systems. Devices consisted of long drain and field transistors and metallic meanders. Current and capacitance measurements were carried out with standard instruments. Results showed that not all the test structures and their related parameters were equally sensitive, and in some cases tests at a high temperature were necessary to accelerate the desired effects. The metallic meander structure proved to be quite sensitive to epoxy-coating degradation. For dielectric passivating layers, the parasitic transistors also showed sensitivity, especially when electrolyte was heated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Reversed-Phase High-Performance Liquid Chromatographic Prefractionation of Immunodepleted Human Serum Proteins to Enhance Mass Spectrometry Identification of Lower-Abundant Proteins (2005)

Serum analysis represents an extreme challenge due to the dynamic range of the proteins of interest, and the high structural complexity of the constituent proteins. In serum, the quantities of proteins and peptides of interest range from those considered "high abundance", present at 2-70% by mass of total protein, to those considered "low abundance", present at 10(-12) M or less. This range of analytical target molecules is outside the realm of available technologies for proteomic analysis. Therefore, in this study, we have developed a workflow toward addressing the complexity of these samples through the application of multidimensional separation techniques. The use of reversed-phase methods for the separation and fractionation of protein samples has been investigated, with the goal of developing an optimized serum separation for application to proteomic analysis. Samples of human serum were depleted of the six most abundant proteins, using an immunoaffinity LC method, then were separated under a variety of reversed-phase (RP) conditions using a macroporous silica C18 surface modified column material. To compare the qualities of the RP separations of this complex protein sample, absorbance chromatograms were compared, and fractions were collected for off-line SDS-PAGE and 2D-LC-MS/MS analysis. The column fractions were further investigated by determination of protein identities using either whole selected fractions, or gel bands excised from SDS-PAGE gels of the fractions. In either case samples underwent tryptic fragmentation and peptide analysis using MALDI-MS or LC-MS/MS. The preferred conditions for RP protein separation exhibited reproducibly high resolution and high protein recoveries (>98%, as determined by protein assay). Using the preferred conditions also permitted high column mass load, with up to 500 microg of protein well tolerated using a 4.6 mm ID x 50 mm column, or up to 1.5 mg on a 9.4 mm ID x 50 mm column. Elevated column temperature (80 degrees C) was observed to be a critical operational parameter, with poorer results observed at lower temperatures. The combination of sample simplification by immunoaffinity depletion combined with a robust and high recovery RP-HPLC fractionation yields samples permitting higher quality protein identifications by coupled LC-MS methods.
Food Security and Hunger Policy for the 1990s (1990)

Attempts to develop effective solutions to problems of hunger involve an understanding of its causes. Food security can and must be improved and hunger relieved and prevented.
Microscale Inorganic Light-Emitting Diodes on Flexible and Stretchable Substrates (2012)

Recent work involving microscale inorganic light-emitting diodes on flexible and stretchable substrates is reviewed. Techniques for materials growth, device fabrication, and assembly are summarized, along with highlights of optical, electrical, and mechanical properties that can be achieved. Some examples of emerging applications in biomedical devices illustrate the value of these methods in areas where conventional approaches are unsuitable.
Medication-related osteonecrosis of the jaw: Clinical and practical guidelines (2016)

Medication-related osteonecrosis of the jaw (MRONJ) is a severe adverse drug reaction, consisting of progressive bone destruction in the maxillofacial region of patients. ONJ can be caused by two pharmacological agents: Antiresorptive (including bisphosphonates (BPs) and receptor activator of nuclear factor kappa-B ligand inhibitors) and antiangiogenic. MRONJ pathophysiology is not completely elucidated. There are several suggested hypothesis that could explain its unique localization to the jaws: Inflammation or infection, microtrauma, altered bone remodeling or over suppression of bone resorption, angiogenesis inhibition, soft tissue BPs toxicity, peculiar biofilm of the oral cavity, terminal vascularization of the mandible, suppression of immunity, or Vitamin D deficiency. Dental screening and adequate treatment are fundamental to reduce the risk of osteonecrosis in patients under antiresorptive or antiangiogenic therapy, or before initiating the administration. The treatment of MRONJ is generally difficult and the optimal therapy strategy is still to be established. For this reason, prevention is even more important. It is suggested that a multidisciplinary team approach including a dentist, an oncologist, and a maxillofacial surgeon to evaluate and decide the best therapy for the patient. The choice between a conservative treatment and surgery is not easy, and it should be made on a case by case basis. However, the initial approach should be as conservative as possible. The most important goals of treatment for patients with established MRONJ are primarily the control of infection, bone necrosis progression, and pain. The aim of this paper is to represent the current knowledge about MRONJ, its preventive measures and management strategies.
In situ product recovery of n‐butanol using polymeric resins (2008)

Polymeric resins with high n-butanol adsorption affinities were identified from a candidate pool of commercially available materials representing a wide array of physical and chemical properties. Resin hydrophobicity, which was dictated by the chemical structure of its constituent monomer units, most greatly influenced the resin-aqueous equilibrium partitioning of n-butanol whereas ionic functionalization appeared to have no effect. In general, those materials derived from poly(styrene-co-divinylbenzene) possessed the greatest n-butanol affinity, while the adsorption potential of these resins was limited by their specific surface area. Resins were tested for their ability to serve as effective in situ product recovery (ISPR) devices in the n-butanol fermentation by Clostridium acetobutylicum ATCC 824. In small-scale batch fermentations, the addition of 0.05 kg/L Dowex Optipore SD-2 facilitated achievement of effective n-butanol titers as high as 2.22% (w/v), well above the inhibitory threshold of C. acetobutylicum ATCC 824, and nearly twice that of traditional, single-phase fermentations. Retrieval of n-butanol from resins via thermal treatment was demonstrated with high efficiency and predicted to be economically favorable. Due to its modular nature, the proposed ISPR design exhibits strong potential for compatibility with future n-butanol fermentation efforts.
Interleukin-1β in Coronary Arteries of Patients With Ischemic Heart Disease (1996)

Interleukin-1 beta (IL-1 beta) is known to have a number of effects on the different cell types present within coronary arteries. In this study we identified the location and phenotype of cells containing IL-1 beta in human coronary artery specimens from patients suffering from either coronary atherosclerosis or cardiomyopathy and correlated the presence of IL-1 beta with disease severity. Luminal endothelial cells, adventitial vessel wall cells, and macrophages were double labeled immunohistochemically for IL-1 beta protein and a cell type-specific monoclonal antibody for either endothelial cells or macrophages. In situ hybridization was performed to locate the presence of IL-1 beta mRNA within the coronary artery wall. In this study IL-1 beta protein was found to be increased in the adventitial vessel walls of atherosclerotic coronary arteries compared with coronary arteries from nonischemic cardiomyopathic hearts. This increase was directly proportional to the severity of coronary atherosclerosis. IL-1 beta protein was also detected in luminal endothelium and macrophages of atherosclerotic coronary arteries and coronary arteries from nonischemic cardiomyopathic hearts. IL-1 beta mRNA was found in luminal endothelial cells, adventitial vessel endothelial cells, and macrophages. We conclude that IL-1 beta is produced by endothelial cells and macrophages in coronary arteries from ischemic hearts and to a lesser extent from nonischemic cardiomyopathic hearts.
Sub-micron absolute distance measurements in sub-millisecond times with dual free-running femtosecond Er fiber-lasers (2011)

We demonstrate a simplified dual-comb LIDAR setup for precision absolute ranging that can achieve a ranging precision of 2 μm in 140 μs acquisition time. With averaging, the precision drops below 1 μm at 0.8 ms and below 200 nm at 20 ms. The system can measure the distance to multiple targets with negligible dead zones and a ranging ambiguity of 1 meter. The system is much simpler than a previous coherent dual-comb LIDAR because the two combs are replaced by free-running, saturable-absorber-based femtosecond Er fiber lasers, rather than tightly phase-locked combs, with the entire time base provided by a single 10-digit frequency counter. Despite the simpler design, the system provides a factor of three improved performance over the previous coherent dual comb LIDAR system.
[Sodium and calcium channels of the somatic membrane of neuroblastoma cells during artificially induced differentiation]. (1986)

Sodium and calcium channels passing inward currents were studied by intracellular dialysis technique and voltage clamp in the somatic membrane of neuroblastoma cells during their morphological differentiation induced by increasing pH of the culture medium up to 8.0-8.2. Kinetic and voltage-dependent properties of sodium and calcium channels of differentiated cells and cells grown in the suspension culture were identical. Densities of sodium currents in the somatic membrane of neuroblastoma cells grown in suspension culture were about 7.3 +/- 0.8 microA/microF and from 37 +/- 5.2 microA/microF to 54.7 +/- 3.6 microA/microF of differentiated cells at different terms of cultivation. Densities of calcium currents in the membrane of cells grown in suspension were about 1.4 +/- 0.2 microA/microF, while in differentiated cells they ranged from 1.1 +/- 0.2 to 2.8 +/- 0.4 microA/microF at different terms of cultivation. Induction or reduction of differentiation by varying pH of the culture medium produced reciprocal changes in densities of sodium and calcium channels.
Translocation of a Thioether-Bridged Azurin Peptide Fragment via the Sec Pathway in Lactococcus lactis (2009)

This study demonstrates for the first time that a thioether-containing peptide, an azurin fragment, can be translocated via the Sec pathway. This methyl-lanthionine was introduced by the nisin modification enzymes. The Sec pathway can therefore be a successful alternative for those cyclized peptides that are inefficiently transported via NisT.
Primary Structure of a Base Non-Specific Ribonuclease from Rhizopus niveus (1988)

The primary structure of a base non-specific ribonuclease from Rhizopus niveus (RNase Rh) was determined by nucleotide sequence analysis of the DNA fragment encoding RNase Rh gene including signal peptide sequence, and amino acid sequence analysis of the peptide obtained from RNase Rh and RNase Rh' (a protease-modified RNase Rh created during the course of purification). The sequence determined was: MKAVLALATLIGSTLASSCSSTA LSCSNSANSDTCCSPEYGLVVLNMQWAPGYGPANAFTLHGLWPDKCSGAYAPSGGCDSN RASSSIASVIKSKDSSLYNSMLTYWPSNQGNNNVFWSHEWSKHGTCVSTYDPDCYDNYE EGEDIVDYFQKAMDLRSQYNVYKAFSSNGITPGGTYTATEMQSAIESYFGAKAKIDCSSG TLSDVALYFYVRGRDTYVITDALSTGSCSGDVEYPTK (the sequence of signal peptide is underlined). The sequence indicates that the homology with the sequence of RNase T2 from A. oryzae with the same base specificity is about 42% and that the sequences around the two histidine residues which are supposed to be involved in the active site are fairly conserved.